Archive for the ‘Educational’ Category

Treating cancer as a chronic disease

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Posted 31 Mar 2012 — by James Street
Category Educational, General Cancer Research, Stem Cell Research, Understanding Cancer

March 30th, 2012 in Cancer
Treating cancer as a chronic disease

 

Professor Karl Skorecki

New research from the Technion-Israel Institute of Technology Rappaport Faculty of Medicine and Research Institute and the Rambam Medical Center may lead to the development of new methods for controlling the growth of cancer, and perhaps lead to treatments that will transform cancer from a lethal disease to a chronic, manageable one, similar to AIDS.

By placing cancer in and near a growth developed from a population of human , scientists have demonstrated that the cancer cells grow and proliferate more robustly when exposed to than they do in a typical petri dish or mouse model. The cancer cell population is also more diverse than had previously been understood.  The research was published in the current advanced online issue of the journal Stem Cells. Maty Tzukerman, Rambam senior research scientist and the project leader and senior co-author on the report, says that this model will facilitate targeted drug discovery aimed at blocking the cancer cell self-renewal process.

Previous studies have determined that some tumor cells appear to be differentiated, while others retain the self-renewal property that makes cancer so deadly. According to Technion Professor Karl Skorecki, director of Medical Research and Development at Rambam Health Care Campus and senior co-author on the report, this new research attempts to understand how cancer grows, and to find ways to halt the runaway replication.

In order to mimic the environment as closely as possible, the research team developed a teratoma – a tumor made of a heterogenous mix of cells and tissues – by enabling the differentiation of human embryonic stem cells into a variety of normally occuring human cell lines on a carrier mouse. The human cellular teratoma constitutes a new platform of healthy human cells for monitoring the behavior and proliferation of human cancer cells.

For this study, the team took cells from one woman’s ovarian clear cell carcinoma and injected them either into or alongside the human stem cell-derived environment. “We noticed very early on, rather strikingly, that the human cancer cells grow more robustly when they are in the teratoma environment compared to any other means in which we grew them, such as in a mouse muscle or under the skin of a mouse,” says Skorecki.

The scientists were able to tease out six different kinds of self-renewing cells, based on behavior – how quickly they grow, how aggressive they are, how they differentiate – and on their molecular profile. This was a previously unknown finding, that one tumor might have such a diversity of cells with crucial fundamental growth properties. Tzukerman explains that the growth of the cancer cell subpopulations can now be explained by their proximity to the human cell environment.

The researchers cloned and expanded the six distinct cell populations and injected them into the human stem cell teratomas. One key observation is that some cells, which were not self-replicating in any other model, became self-replicating when exposed to the human cells.

Skorecki said that while he wasn’t surprised that the human environment affected the growth, he was in fact surprised by the magnitude of the effect: “We’ve known for years now that cancers are complex organs, but I didn’t think the power of the human stem cell environment would be so robust, that it would make such a big difference in how the cells were grown.”

The researchers point out that they do not yet know the cues that particularly enhance the cancer’s proliferation, and the team is now working on isolating the factors from human cells that promote such plasticity and self-renewing properties. The scientists explain that this may eventually allow physicians to manage cancer as a chronic disease: instead of one therapy against the entire tumor, researchers may develop a method to tease out the variety of self-renewing cell lines of a particular tumor and determine what allows each to thrive, then attack that mechanism.

Skorecki and Tzukerman say that an important next step in this line of cancer research will be to identify and develop ways of blocking the factor or factors that promote this essential self-renewing property of cancer, thus relegating many forms of to controllable, chronic diseases.

This research was supported with grants from the Daniel M. Soref Charitable Trust, the Skirball Foundation, the Richard D. Satell Foundation, the Sohnis and Forman families, and the Science Foundation.

Provided by American Technion Society

Lessons from the Past and Charting the Future of Marine Natural Products Drug Discovery and Chemical Biology

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Posted 15 Mar 2012 — by James Street
Category Cancer Journals, Educational, Trabectedin, Understanding Cancer, Yondelis
Chemistry & Biology

Volume 19, Issue 1, 27 January 2012, Pages 85–98

Cover image
Review

  • William H. Gerwick1, Corresponding author contact information, E-mail the corresponding author,
  • Bradley S. Moore1, Corresponding author contact information, E-mail the corresponding author
  • 1 Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA 92037, USA
  • Available online 26 January 2012.

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Marine life forms are an important source of structurally diverse and biologically active secondary metabolites, several of which have inspired the development of new classes of therapeutic agents. These success stories have had to overcome difficulties inherent to natural products-derived drugs, such as adequate sourcing of the agent and issues related to structural complexity. Nevertheless, several marine-derived agents are now approved, most as “first-in-class” drugs, with five of seven appearing in the past few years. Additionally, there is a rich pipeline of clinical and preclinical marine compounds to suggest their continued application in human medicine. Understanding of how these agents are biosynthetically assembled has accelerated in recent years, especially through interdisciplinary approaches, and innovative manipulations and re-engineering of some of these gene clusters are yielding novel agents of enhanced pharmaceutical properties compared with the natural product.


Figures and tables from this article:

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Figure 1. Examples of Marine Natural Products with Characterized Biosynthetic Pathways(A) Laboratory cultured and (B) environmental uncultured marine microbes whose biosynthetic pathways have been established by a variety of omic approaches (includes ecteinascidin-743 shown in Figure 4).

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Figure 2. Pie Charts Illustrating the Collected Sources and Predicted Biosynthetic Sources of Marine Derived or Inspired Drugs and Clinical Trial Agents(A) Pie chart illustrating the original collected sources of marine natural product derived or inspired agents currently as approved drugs or in clinical trials (20 total).(B) Pie chart of the marine-derived drugs and clinical trial agents divided by their subsequently shown or predicted source organisms (20 total). Cyanobacteria are differentiated from other bacteria in this chart because of their distinctive and characteristic physiological and metabolic capabilities.

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Figure 3. Pie Chart Illustrating the Collected Sources of Marine Natural Products Used as Research BiochemicalsProducts that are available commercially for their useful pharmacological properties in biomedical research (121 total).

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Figure 4. Chemical Structures of the Approved Drugs Deriving from or Inspired by a Marine Natural Product and Other Marine Metabolites Discussed in the TextOne-letter amino acid codes are used for depicting the structure of ziconotide.

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Figure 5. Assembly Line Biosynthesis of Salinosporamide and Library Development of Structure Analogs via Mutasynthesis and Other Genetic Engineering ApproachesDomain abbreviations for the SalA and SalB multifunctional proteins are as follows: ACP, acyl carrier protein; KS, ketosynthase; AT, acyltransferase; C, condensation; A, adenylation; PCP, peptidyl carrier protein.

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Figure 6. Parallel Strategy Employed by Grindberg et al. (2011) to Rapidly Access the Biosynthetic Gene Cluster for Apratoxin A, a Promising Anticancer Lead Compound from the Marine Cyanobacterium Moorea bouilloniiOn the top arm, single cells are obtained by microdissection from nonaxenic cultures of cyanobacteria, and DNA is extracted and amplified by Multiple Displacement Amplification (MDA) for partial genome sequencing. The sequences of recognizable gene motifs associated with natural product pathways are then used to construct PCR probes to screen a fosmid library that is produced in the normal fashion (lower arm). Fosmids probing positively by this process can be further characterized for desired gene motifs, and then sequenced. The melding of these approaches can accelerate the process of biosynthetic gene cluster discovery and description, such as is illustrated here for apratoxin A, especially in cases of nonaxenic cultures or environmental samples.

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Table 1. Six Marine Natural Products and Fourteen Marine Natural Products Inspired Compounds that Are FDA-Approved Agents or in Clinical Trial with Details of Their Collected Source, Predicted Biosynthetic Source, Molecular Target, and Disease Treated

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Additional perspectives on approved FDA drugs and clinical trial agents that were derived or inspired by marine natural products can be found in Mayer et al. (2010) and Newman and Cragg (2010).

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Is there more than one road to melanoma?

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Posted 20 Nov 2011 — by James Street
Category Carcinogens, Educational, Melanoma, Prevention, Vitamin D
Context Sunlight is the main environmental cause of most cutaneous melanomas. Exposure to intense bursts of ultraviolet radiation, especially in childhood, starts the transformation of benign melanocytes into a malignant phenotype. Paradoxically, outdoor workers have a decreased risk of melanoma compared with indoor workers, suggesting that chronic sunlight exposure can have a protective effect. Further, some melanomas form on sun-exposed regions; others do not. Although some melanomas arise from pre-existing melanocytic naevi (mo …

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Molecular alterations as target for therapy in metastatic osteosarcoma: a review of literature

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Posted 30 Oct 2011 — by James Street
Category Educational, Metastases, Osteosarcoma, Understanding Cancer
Clinical & Experimental Metastasis
Official Journal of the Metastasis Research Society
© The Author(s) 2011
10.1007/s10585-011-9384-x

Review

Molecular alterations as target for therapy in metastatic osteosarcoma: a review of literature

J. PosthumaDeBoer1, M. A. Witlox2, G. J. L. Kaspers3 and B. J. van Royen1, 4 Contact Information

(1) Department of Orthopaedic Surgery, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
(2) Department of Orthopaedic Surgery, Westfries Gasthuis, Hoorn, The Netherlands
(3) Paediatric Oncology/Haematology, VU University Medical Center, Amsterdam, The Netherlands
(4) VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands

Contact Information B. J. van Royen
Email: bj.vanroyen@vumc.nl

Received: 15 July 2010  Accepted: 18 March 2011  Published online: 2 April 2011

Abstract

Treating metastatic osteosarcoma (OS) remains a challenge in oncology. Current treatment strategies target the primary tumour rather than metastases and have a limited efficacy in the treatment of metastatic disease. Metastatic cells have specific features that render them less sensitive to therapy and targeting these features might enhance the efficacy of current treatment. A detailed study of the biological characteristics and behaviour of metastatic OS cells may provide a rational basis for innovative treatment strategies. The aim of this review is to give an overview of the biological changes in metastatic OS cells and the preclinical and clinical efforts targeting the different steps in OS metastases and how these contribute to designing a metastasis directed treatment for OS.

Keywords  Drug resistance – Metastasis – Osteosarcoma – Therapy

Abbreviations  Bcl-2

B cell lymphoma 2 associated oncogene

- Bcl-XL

Bcl2-like 1

- CXCR4

Chemokine (C-X-C-motif) receptor 4

- CXCL

Chemokine (C-X-C-motif) ligand

- ECM

Extracellular matrix

- EGFR

Epidermal growth factor receptor

- ERK

Extracellular signal regulated kinase

- FAK

Focal adhesion kinase

- GH

Growth hormone

- HLA

Human leukocyte antigen

- IGF-1R

Insulin-like growth factor 1 receptor

- IFN-α

Interferon-alpha

- IL

Interleukin

- JAK

Janus kinase

- mAB

Monoclonal antibody

- MAP(K)

Mitogen-activated protein (kinase)

- MMP

Matrix metalloproteinase

- MTP-PE

Muramyl tripeptide phosphatidyl ethanolamine

- mTOR

Mammalian target of rapamycin

- NF-κB

Nuclear factor-kappa B

- NK cells

Natural killer cells

- PI3K

Phosphatidylinositol 3-kinase

- PDGF-R

Platelet-derived growht factor receptor

- OS

Osteosarcoma

- SARC

Sarcoma Alliance for Research through Collaboration

- STAT

Signal transducer and activator of transcription

- TGF-β

Transforming growth factor-beta

- VEGF

Vascular endothelial growth factor

- WIF-1

Wnt inhibitory factor 1


Introduction

Osteosarcoma (OS) is the most common primary malignant bone tumour in children and adolescents. The estimated incidence rate worldwide is 4/million/year, with a peak incidence at the age of 15–19 years [1]. In OS there is a high tendency to metastatic spread. Approximately 20% of patients present with lung metastases at initial diagnosis and, additionally, in 40% of patients metastases occur at a later stage. Eighty percent of all metastases arise in the lungs, most commonly in the periphery of the lungs, and exhibit resistance to conventional chemotherapy [27]. The 5-year survival rate for OS patients with metastases is 20% compared to 65% for patients with localised disease and most deaths associated with OS are the result of metastatic disease [5, 811].

For patients with pulmonary metastasis, especially those who have metastasis at initial diagnosis, the combination of radical metastasectomy and chemotherapy offers the best outcome and even potential cure. Nevertheless, recurrent development of pulmonary metastases after initial radical metastasectomy is reported to be high and repeated metastasectomies are sometimes performed. As metastasectomy does yield an improved survival in most patients it should therefore always be performed when feasible [2, 4, 1214].

In order to improve survival, the ultimate questions to be answered are: Why does OS metastasize, particularly to the lungs? And, more importantly: Why does therapy fail in metastatic disease? In this regard, we hypothesise that drug resistance is a key issue in the failure to control metastatic disease. It has been shown that OS lung metastases display a biological behaviour different from the primary tumours [2, 1427]. Metastases are comprised of cell clones that differ from primary tumours with respect to ploidy, enzyme profile, karyotype and chemosensitivity [2, 2832]. Therapeutic regimens that target primary tumours are therefore unlikely to be successful in the treatment of metastatic disease.

Metastasis is considered to be the final though most critical step in tumorigenesis of malignant tumours [33]. The metastatic cancer cells subsequently complete the following steps: Invasion through the extracellular host matrix and entrance into the circulation (I), survival in the circulation (II) and evasion of the host immune system (III), arrest and extravasation at a target organ site (IV), adherence and survival in the target organ microenvironment (V, VI) and finally formation of neovasculature to allow growth at the target organ site (VII) [14, 3336]. Each step is of equal importance and must be fully completed by the tumour cell to achieve successful metastasis. The altered biological behaviour in metastatic cells is the result of specific molecular changes. We will discuss each of these specific steps with special attention to the molecules involved in OS metastasis (Table 1) and implications for therapy. Over the last decade, much research has been performed to try to unravel the biology of OS metastasis and many (pre)clinical studies have attempted to discover new treatment options for metastatic OS. For example, gene expression profiling of metastatic cells using a cDNA microarray approach has identified genes responsible for metastasis [27, 3739]. Also, expression levels of specific proteins in OS lung metastases have been analysed. In these studies, expression levels of proteins involved in metastases link the molecular aberrancies to clinical outcome in terms of survival rates. These alterations may also provide novel drug targets [21, 23, 25, 36, 4042]. Table 2 summarises (pre)clinical studies for treating OS metastases.

Table 1 Steps of metastasis in OS and molecular alterations that contribute to each process
Steps of metastasis Molecular involvement References
I Migration and invasion MMPs [10, 14, 16, 18, 19, 27, 34, 35, 4446]
m-Calpain [35, 43]
Wnt [9, 35, 46, 47]
Src [35, 44]
Notch [41, 4850]
II (a) Anoikis resistance PI3K/Akt [9, 14, 16, 51]
Src/PI3k/Akt [9, 14, 16, 44]
Src/Ras/MAPK [18, 35]
NF-κB [27]
Wnt/β-catenin [14]
BcL family [9, 35, 51]
(b) Apoptosis resistance Src [9, 16, 18, 35, 44]
NF-κB [27, 44, 51, 67]
Wnt/β-catenin [14, 17, 19, 46, 47, 53, 54]
Fas/FasL [5, 23, 28, 36, 55, 56]
III Evasion of immune system HLA-1 [14, 60]
IL-10 [14]
Fas [62]
IV Arrest and extravasation CXCR4-CXCL12 [9, 10, 14, 15, 22, 42, 69]
CXCR3-CXCL9-11 [10]
CXCR4/MMPs [9, 10, 15]
CXCR3-4/Erk/NF-κB [10, 67]
V Adherence Ezrin/MAPK/Akt [14, 21, 25, 35]
Ezrin/β4-Integrin/PI3K [70]
CD44/Akt/mTOR [14, 19, 21]
VI Dormancy Integrin-α5β1 [73, 74]
Integrin-α5β1/Erk/p38 [14, 35]
Bcl-XL [14, 35]
IGF/PI3K [75]
ECM [73, 74]
VII Angiogenesis and proliferation EGFR. PDGFR, VEGF, IGFR, TGF-β [9, 14, 35, 40, 68, 77, 78, 81]
MMPs [9, 44, 78]
VEGF/Erk/NF-κB [35, 68]
VEGF/PI3K [35, 40]
EGFR/Src/Ras/MAPK/STAT3 [9, 18]
Src [14, 35, 44]
Integrin/PI3K/Erk1-2 [9, 35, 67, 75]
Wnt/β-catenin/CyclinD-Survivin [46, 52]

Table 2 Preclinical and clinical studies targeting specific molecules in OS metastasis
Steps of metastasis Target Drug References
Preclinical
I Migration and Invasion Notch [41, 50]
II (a) Anoikis resistance
(b) Apoptosis resistance Preclinical
Wnt [46, 52]
Src [18]
Clincial
Src
Dasatinib [60]
www.clinicaltrials.gov/NCT00752206
III Evasion of immune system Preclinical
Fas
IL12 [36, 56, 62]
IL18 [63]
Gemcitabine [55]
Clinical
Fas
Liposomal MTP-PE [64]
IFN-α [61, 66]
IV Arrest and extravasation Preclinical
CXCR4 [22]
CXCR3 [10]
V Adherence Preclinical
Ezrin [21, 25, 45, 70]
VI Dormancy
VII Proliferation and angiogenesis Preclinical
Endostatin [83]
IGF-1R [79, 84]
Clinical
IGF-1R
OncoLar [78]
R1507 www.clinicaltrials.gov/NCT00642941
SCH717454 www.clinicaltrials.gov/NCT00617890

The aim of this review is to give an overview of the biology of metastatic OS cells and of (pre)clinical efforts targeting the different steps in OS metastases and how these may contribute to designing a metastasis directed treatment for OS.


OS metastasis

(I) Migration and invasion

Migration of cells away from the primary tumour and invasion through the extracellular matrix (ECM) towards the bloodstream is considered the first step contributing to metastasis. In OS, it has been described that MetalloProteinases (MMPs) 2 and 9 and m-Calpain play a role in degradation of the ECM [10, 14, 16, 18, 19, 27, 34, 35, 4346]. Also, the Wnt/β-catenin pathway and Src-kinase are implicated as inducers of migration [9, 35, 46, 47]. In OS, Notch is a relatively recently identified pathway and has been identified as a promoter of invasion in OS. In highly metastatic OS cell lines there is an upregulation of the Notch1 and Notch2 receptor, as well as the Notch induced gene Hes1. In patient samples, expression of the Hes1 gene inversely correlated with survival [41, 4850].

(Pre)clinical studies: Notch

In a preclinical setting, downregulation of the Notch signalling pathway has been shown to impair the invasiveness of cell lines, but has no effect on cell proliferation or in vitro tumorigenesis. Notch-inhibited cell lines had less potential to form lung metastases in an orthotopic mouse model when compared to untreated cell lines. The exact mechanism through which inhibition of the Notch pathway and its target gene Hes1 leads to reduced invasion still remains unknown [41, 50].

(IIa) Survival in the bloodstream

Dissemination of cancer cells through the body requires the cells to survive in the circulation. Non-malignant cells, as well as non-metastatic tumour cells, become apoptotic after loss of cell–cell adhesions or interaction with the ECM in their original tissue. This specific mode of apoptosis is called anoikis. One reason for this type of apoptosis to occur is that Integrin signalling ceases to exist in solitary cells. Under adherent conditions, survival is often mediated through Integrin signalling pathways in which Focal adhesion kinase (FAK) is a central player. FAK activates the important PI3K/Akt survival pathway. Metastatic tumour cells evade anoikis by intrinsically activated survival pathways via for example PI3K or Akt signalling, independent of extrinsic Integrin and FAK signalling [9, 14, 16, 51]. Src kinase can also activate the PI3K/Akt and the Ras/MAPK survival pathways independent of FAK signalling and thus stimulate ainoikis resistance [9, 14, 16, 18, 35, 44, 51]. Other survival mechanisms are also of importance in the evasion of ainoikis, such as activation the nuclear factor-kappa B (NF-κB) pathway [27, 51] and Wnt-mediated upregulation of the β-catenin activity. High levels of β-catenin expression have been shown to be associated with a metastatic phenotype in OS [14, 19, 20, 46]. Finally, overexpression of anti-apoptotic genes such as Bcl-2, Bcl-XL or FAK is exploited by solitary metastatic cells to obtain a survival benefit [9, 35, 51].

(IIb) Apoptosis resistance

The survival of tumour cells through all stages of metastasis (not only in the bloodstream) is paramount to successful metastasis. Mechanisms involved in apoptosis resistance throughout metastasis include activation of the Src and NF-κB pathways and the overexpression of anti-apoptotic genes [9, 44, 46, 51, 52]. Wnt-signalling is also involved in resistance to apoptosis throughout other steps of metastasis and is considered to be important for tumour progression in general. Upon binding of Wnt to one of its receptors, β-catenin degradation in the cytoplasm is prevented. After β-catenin is stabilised it translocates to the nucleus where it co-regulates oncogene transcription and cell cycle progression and hence promotes survival and proliferation [14, 17, 46, 47, 53, 54].

In established metastases, the tumour cells are confronted with receptor-mediated cell death. Binding of Fas on the surface of metastatic cells to its Fas-ligand (FasL) expressed constitutively on lung tissue, activates the Fas-apoptosis pathway and leads to cell death. Cross-linkage of Fas with FasL on one cell results in apoptosis as well [36, 55]. Resistance to death-receptor-induced apoptosis is commonly seen and is highly important for the successful maintenance of metastases. The Fas/Fas-ligand pathway is a death receptor pathway that is often down-regulated in metastatic cell populations, rather than in primary tumours [23, 28, 36]. The Fas pathway is also of influence on chemotherapy-induced apoptosis and thus on its therapeutic efficacy [56]. Much (pre) clinical research has been performed concerning this pathway in metastatic OS and promising results have been obtained. These results are discussed following the section on immune evasion, since the Fas pathway plays a role in that as well.

Thus, apoptosis resistance is very much exploited by the metastatic cell and this feature is likely to contribute to resistance to therapy in metastatic OS [51, 52]. The failure to induce apoptosis upon treatment is thought to be the result of a misbalance between pro- and anti-apoptotic signalling. Restoration of this balance, thereby creating an environment in favour of pro-apoptotic signalling could theoretically enhance treatment with cytotoxic agents [9, 35, 45, 51, 5658].

(Pre)clinical studies: Wnt and Src

The Wnt-pathway is a putative therapeutic target because a majority of OS samples show aberrant activation of this pathway, leading to the transcription of oncogenes and cell cycle progression. This in turn leads to proliferation and enhanced survival [46, 53, 59]. When targeting the Wnt-pathway, activating mutations in downstream molecules for example β-catenin can be of negative influence as it may bypass Wnt inhibition and preserve the invasive phenotype of the metastatic cell [19]. A preclinical study by Leow et al. [52] has shown that inhibition of the Wnt/β-catenin pathway resulted in lower levels of nuclear β-catenin, resulting in a decreased expression of β-catenin target genes. This led to an inhibition of migratory potential through downregulation of MMP-9, and a decrease in expression of Cyclin-D, c-myc and Survivin. The latter was responsible for an anti-proliferative effect and an increase in cell death. These results were recently confirmed by Rubin et al. [46], who showed that re-expression of Wnt inhibitory factor 1 (WIF-1), a secreted Wnt-antagonist, inhibited Wnt signalling and reduced tumour growth and metastasis in OS mouse models. These results show a possible therapeutic benefit of Wnt-pathway disruption in the treatment of metastatic OS.

Src-kinase is a kinase that is involved in almost all steps of cancer metastasis, namely in proliferation, adhesion, migration, survival and angiogenesis [44]. Based on its multi-step involvement in metastasis, it could be an interesting therapeutic target in OS metastasis. Pre-clinical work shows that Src inhibition with Dasatinib effectively inhibits Src phosphorylation in primary tumours; however, it did not impair the development of pulmonary metastases. Histopathological analysis of both OS primary tumours and lung nodules showed minimal Src-kinase phosphorylation after treatment with Dasatinib. However, Src-kinase phosphorylation was low in untreated lung metastasis as well. This suggests that Dasatinib was effective in inhibiting Src-pathway activation in OS cells, but it is not clear what the phosphorylation status is during the stages of OS metastasis and how this influences the process [18]. The use of Dasatinib in patients with advanced (osteo)sarcomas was examined recently by the SARC (Sarcoma Alliance for Research through Collaboration) in a phase II clinical trial. Disappointingly, preliminary results show no treatment effect of Dasatinib as a single agent in patients with overt lung metastases [60]. The same group is looking into the effectiveness of Src inhibition with a more specific Src-kinase inhibitor (Saracatinib) to obtain progression free survival among patients with resectable OS lung metastases (clinicaltrials.gov/NCT00752206).

(III) Evasion of the immune system

Another important precondition for the survival of metastatic cells is the evasion of the host immune surveillance throughout all the steps of metastasis. Tumour cells, either circulating or at the site of metastases, can modulate the immune system of the host in order to achieve a survival advantage. Down-regulation of cell surface receptor HLA class 1 is one of such mechanisms. This impairs the recognition of tumour cells by the host cytotoxic T-lymphocytes. Tumour cells can also induce the production of immunosuppressive molecules such as IL-10 [14, 61]. Modulation of the immune system such that it recognizes and destroys (circulating) tumour cells would be a successful anti-metastatic treatment. Interferons are cytokines that can affect the recognition of tumour cells by the immune system by influencing the (re)expression of HLA molecules on the cell surface. Interferons also exert an anti-proliferative effect on OS cells through pathways that are yet unknown [61]. The balance between the intrinsic downregulation of HLA molecules of the tumour cells and the effect of Interferon stimulation will eventually determine whether the circulating tumour cell is cleared by the immune system or not.

Fas also plays a role in immune evasion. Fas expression leads to recognition by, and activation of cytotoxic natural killer (NK) cells and promotes elimination from the circulation by the host immune system. Successful down-regulation of the Fas molecule on the cell surface or corruption of downstream elements in the Fas pathway provides metastatic tumour cells with a survival advantage in the circulation and leads to an increase in metastatic potential. Patient samples from pulmonary OS metastases have been shown to be Fas-negative [40, 62]. Indeed, absence of Fas expression correlates with disease progression and poor survival outcome [23, 36, 55, 62].

(Pre)clinical studies: Fas

As the Fas receptor pathway is so important in the survival of metastatic cells, it is an attractive therapeutic target. Restoration of the Fas death pathway has been tried with success in preclinical models. Interleukin-12 (cytokine) therapy can achieve a dose-dependent upregulation of Fas on the surface of OS cells as well as a stimulation of cytotoxic T-cells and NK-cells. This renders the metastatic cells more sensitive to Fas-induced cell death in the microenvironment of the lung and enhances clearage of the cells from the circulation by the host immune system [36]. A drawback is the potent immunostimulatory effect of Interleukin-12 that can induce severe adverse effects after systemic administration in patients [56, 62].

In an in vivo experiment, intranasal administration of IL-12 resulted in Fas overexpression on OS lung metastases, leading to a decrease in tumour burden. Combination therapy with Ifosfamide, which induces the expression of FasL on the tumours, could further augment anti-tumour effect [28, 56].

IL-18 was reported to have similar effects on the activation of T-cells and NK-cells, as well as induction of the expression of FasL on already Fas expressing tumours. This compound did not, however, exert an anti-tumour effect in mice bearing OS lung metastases [63].

Gemcitabine is an agent that upregulates Fas-expression when administered as an aerosol therapy in mice bearing OS lung metastases. Gemcitabine aerosol therapy has been shown to effectively reduce size and number of pulmonary metastases [5, 55].

Liposomal MTP-PE (muramyl tripeptide phosphatidyl ethanolamine) is a promising agent for clinical use as it can induce endogenous IL-12 production and thus provide an up-regulation of Fas on OS cells but without the systemic toxicity encountered when exogenous IL-12 is administered to patients [28]. MTP-PE is a synthetic analogue of a component of bacterial cell walls. As an immunomodulatory agent it can also stimulate monocytes and macrophages to exert anti-tumour activity. The Children’s Oncology Group performed a prospective randomised phase III clinical trial with this compound in patients with high-grade conventional OS with metastases at diagnosis. Treatment with liposomal MTP-PE improved overall survival, irrespective of the chemotherapy regimen. These data are promising and suggest that there is a critical role for the Fas death pathway in chemotherapy response which can be exploited in clinical practice to enhance the efficacy of chemotherapy in OS [40, 64, 65].

(Pre)clinical studies: Immune modulation

Modulation of the immune system to exert anti-tumour activity by the addition of interferon-α (IFN-α) as a maintenance treatment after standard chemotherapeutic treatment is currently under investigation in the EURAMOS-1 trial, which is an initiative of the European and American Osteosarcoma Study Group [66]. IFN-α is immunomodulatory and able to stimulate a host-anti-tumour immune reaction and induce anti-proliferative signalling via the JAK/STAT1 pathway [58]. Accrual of patients for this worldwide trial is due to be completed in July 2011 [61, 66].

(IV) Arrest and extravasation

The mechanism of arrest of metastatic tumour cells at the distant organ sites remains controversial. One hypothesis is that metastatic cells are larger than ordinary cells in the circulation and that they become trapped in the microcirculation of a capillary bed. When trapped they form micro-embolisms and start interaction with the local environment. It is striking, however, that different tumour types have an organ specific preference for metastasis. The metastatic behaviour of OS is very distinct as over 80% of all metastases arise in the lungs and other organs usually remain unaffected. This suggests that the circulating tumour cell specifically ‘homes’ to distinct molecules that are expressed on the endothelium of the organ of preference. Although it might be trapped in different capillary beds throughout the body, it will interact with the surface molecules on the endothelium of the organ of interest rather than with endothelium at other sites [35]. There is evidence of endothelium-specific tropism in OS [10, 14, 15, 22, 42, 67]. The processes of exit of the circulation and invasion at the distant organ site are mediated by chemokines and proteinases. Proteinases are responsible for extravasation whereas chemokines determine the site at which circulating tumour cells adhere [9, 15]. Chemokines were initially thought to regulate leukocyte trafficking and homing, but recently they are also known as important components in the regulation of site-specific metastasis as they bind to G-protein coupled receptors on the plasma membrane of specific cells, in the case of OS to receptors in the lung [14, 42, 6769]. CXCR-4, a commonly expressed chemokine in OS, is involved in site-specific metastasis. Its sole ligand is CXCL12 which is expressed abundantly in the lung. Binding of CXCR-4 to CXCL12 allows adherence and extravasation of OS cells in the lung [9, 10, 14, 15, 22, 42, 69]. Laverdiere et al. [42] found that CXCR-4 expression levels in patient samples inversely correlated to event-free and overall survival. There was a positive correlation between CXCR-4 expression in primary tumours and the presence of metastases at initial diagnosis. Interestingly, expression levels of CXCR-4 were similar in primary tumours and lung metastases. This suggests that CXCR-4 expression is not regulated during metastasis, but is simply present. It could be of predictive value for the formation of metastasis.

CXCR-3, another chemokine, is expressed by OS as well as other malignancies. Its ligands are CXCL9, -10 and -11, all of which are expressed by lung, and this molecule is thought to co-operate with CXCR-4. Apart from mediating adherence, the interactions of CXCR-3 and -4 with their respective ligands also trigger pathways involved in other necessary events in metastasis, namely in invasion, survival and proliferation in the secondary tissue [10, 22, 67].

For example, hypoxia upregulates CXCR-3 and -4 expression, which in turn induce the expression of MMP-2 and -9 on the cell surface and modulate the microenvironment into an inflammation-like condition, abundant with growth factors and stimulation of angiogenesis. Furthermore, binding of CXCR-4 to CXCL12 can activate the NF-κB survival pathway via ERK (Extracellular-signal-Regulating-Kinase)-signalling and stimulate proliferation through MAPK signalling. Thus, apart from facilitating seeding at the distant organs site, chemokines play a very important role in the modulation of the microenvironment into a place permissive for the tumour cells to proliferate [9, 10, 15, 67].

(Pre)clinical studies: Chemokines

CXCR-4 is the most important chemokine-player in OS. Kim et al. [22] have demonstrated a reduction in metastatic tumour burden in an orthotopic mouse model in which cells were treated with a CXCR-4 inhibitor prior to injection of tumour cells into the mice. However, reduction of metastatic tumour burden without pre-treatment could not been shown consistently. The authors argue that the critical event, namely binding of CXCR-4 to CXCL12 with consecutive activation of signalling pathways, granting survival and proliferation, occurs too early in the establishment of metastases for inhibitory therapy of CXCR-4 to be beneficial for the patient with already existing metastasis. To what extent CXCR-4 inhibition could be beneficial in a preventive setting requires additional studies.

CXCR-3 inhibition was tested in an animal model for human OS lung metastases and showed a significant decrease in the development and progression of pulmonary lesions compared to the non-treated group [10].

(V) Adherence

Establishment at a distant organ requires the metastatic cell to connect to its new environment and re-establish cell–cell adhesions. Ezrin is a membrane-cytoskeleton linker protein that plays an important role in cell–microenvironment interaction. It is thought to facilitate anchorage of OS cells to lung tissue, as well as to enhance survival mechanisms in the new environment through Integrin mediated activation of Akt and MAPK survival pathways [14, 21, 25, 35]. The exact mechanism through which Ezrin mediates metastasis is not entirely clear, however, recently Wan et al. [70] discovered that β4-Integrin is an important mediator. β4-Integrin can bind Ezrin and Ezrin is required for the maintenance of this protein. β4-Integrin can activate the PI3K pathway and thus stimulate survival and proliferation in the newly arrived cells in the lung. β4-Integrin is found to be highly expressed in OS tumour samples from both primary and metastatic lesions. Furthermore, it was shown that β4-Integrin knockdown inhibits the formation of OS lung metastasis in vivo, and leads to prolonged survival.

High expression of Ezrin correlated with a higher risk of metastatic relapse and poor survival in OS patients [21, 25]. Furthermore, it was found to be 3-fold overexpressed in lung metastases in a murine model for OS lung metastases [38]. CD44 is another surface molecule that can form a complex with Ezrin and correlates with metastasis and poor prognosis. Apart from influence on the cytoskeleton and cell shape, CD44 controls proliferation, growth arrest and survival via the Akt/mTOR pathway [14, 19, 21].

(Pre)clinical studies: Ezrin

Suppression of Ezrin with a full-length anti-Ezrin construct did not inhibit primary tumour growth in a mouse model of OS, but it effectively inhibited the formation of metastases. It was speculated that metastatic OS cells express phosphorylated Ezrin only early after arrival in the lung, and this causes limited efficacy of suppression of Ezrin in readily established metastases, since its essential function in metastasis, namely connecting with the target organ site had already been fulfille [21]. Recently however, Ren et al. [25] suggested that Ezrin phosphorylation is not only present in the early stage of metastasis, but also late in tumour progression, at the leading edge of large metastasic lesions. This finding was verified on sections of patient OS metastases.

Pignochino et al. [45] reported that Sorafenib inhibited invasion via reduction in MMP-2 production and inhibited survival via downregulation of Ezrin-activated MAPK/Akt signalling. Furthermore, Sorafenib could also induce apoptosis in OS cells through downregulation of members of the anti-apoptotic Bcl-2 family. Wan et al. [70] showed that inhibition of Ezrin-related β4-Integrin can reduce metastasis in a mouse model. Taken together, targeting Ezrin seems promising in the management of OS lung metastases.

(VI) Dormancy

Dormancy refers to a prolonged period of survival of single cells or small micrometastases. OS patients can progress with metastases after a disease free interval of many years [71, 72]. This is likely explained by the presence of micrometastases in a dormant state, which at some point are triggered develop into gross metastases.

Little is known concerning the biological processes regulating dormancy in OS. The anti-apoptotic gene Bcl-XL is thought to be involved in the survival of dormant cells, as well as α5β1-Integrin mediated activation of NF-κB. Furthermore the dormant state is thought to be regulated by the ratio between the ERK and p38-MAPK proteins, also steered by Integrin-α5β1 signalling [14, 35, 73, 74].

The mechanisms by which dormant tumour cells are at one point triggered to start proliferating are yet unaccounted for, however, the microenvironment is thought to play a regulatory role. Tumour outgrowth is dependent on vascularisation, and it has been suggested that endothelial cells in the microenvironment can both activate dormant tumour cells through cell-to-cell signalling and induce angiogenesis for nutrition [74]. The ECM is also thought to be involved in activation of dormant cells, as it serves as a source of growth and survival signals. It has been postulated that micrometastases that fail to properly connect to the ECM remain in the dormant state because they remain deprived of growth- and angiogenic signalling and go into quiescence as a means to survive. Anchorage to the ECM would stimulate cells to convert to a proliferative state via β1-Integrin signalling [73]. The microenvironment can be regulated by the tumour cells themselves, but also by host stromal cells. Leucocytes and macrophages can modulate the ECM to either form a pro- or anti-angiogenic microenvironment. Apart from this, other mediating factors can also be influenced by stromal cells. For example, Wnt can be secreted from macrophages, and cytokines secreted by stromal cells can upregulate the intracellular Wnt/β-catenin signalling pathway and hence induce survival and proliferation in a late stage in the process of metastasis [9, 35, 54, 73]. Also, bone marrow derived progenitor cells (creating a ‘pre-metastatic niche’) can modulate the microenvironment and thus influence whether solitary cells or micrometastases remain dormant or are allowed to progress [68, 73]. In an effort to elucidate the cellular mechanisms that establish the switch of dormant to rapidly growing cells, Almog et al. [75] designed an in vivo model for dormancy of various cancers, including OS, and performed gene-expression analysis of cells in the dormant state versus cells in a proliferative state. They found that during dormancy, there is an upregulation of anti-angiogenic proteins. In this pre-angiogenic situation, the tumour cells would lack the nutrition and oxygen needed to proliferate. The cells that had switched to the proliferative phenotype had elevated RNA levels of common cancer pathways such as PI3K- and IGF-pathways. They also found that Endocan was upregulated in rapidly proliferating cells, a protein that is also expressed on tumour endothelial cells. This might indicate that endothelial changes support the switch of cells from dormancy into the proliferative state.

Dormancy could have a role in therapy resistance in OS metastases, however, whether this applies to OS and to what extent remains unknown. In general, dormancy can bring about drug resistance because non-proliferating cells are not so susceptible to conventional treatment. Most treatment modalities induce DNA damage which is usually more lethal to rapidly proliferating cells [14, 73, 76]. To intervene in this step of metastasis seems difficult. Angiogenesis seems to be an important factor. Elucidation of mechanisms that steer the switch from dormant to proliferative state may give some options. If it would be possible to keep the cells locked in the dormant state, it may grant the patient stable metastatic disease with prolonged survival.

(VII) Angiogenesis and proliferation

Tumour growth and progression is often restricted by vascularisation and thus nutrition. Hypoxia leads to the upregulation of growth factor receptors, angiogenic cytokines and proteolytic enzymes, among which EGFR, PDGF-R, VEGF, IGF-1R, TGF-β, IL-8 and MMPs, all of these providing neo-angiogenesis and allowing proliferation. These molecules can be overexpressed by the tumour cell population itself, but can also be provided by host endothelial (progenitor) cells during neo-angiogenesis [9, 14, 35, 40, 44, 68, 77]. Apart from induction of neo-angiogenesis, VEGF also provides the tumour cells with a survival benefit via activation of ERK-1/2/NF-κB and PI3K pathways [35].

Players involved in provision of vasculature and nourishment are often encountered in other processes within OS metastasis as well. For example, Src-kinase activity is regulated through various growth factor receptors, such as EGFR and Integrin receptors. Src activation leads to Ras/MAPK signalling and activation of the transcription factor STAT3, allowing cell cycle progression and production of angiogenic factors such as fibroblast growth factor, VEGF and IL-8. Src phosphorylation by EGFR especially is considered to stimulate the onset of hyper-proliferation of tumour cells and induction of vascular permeability and neovascularisation [18, 44].

Proliferation of OS cells at a distant organ site is often mediated by Receptor-Tyrosine-Kinase or Integrin induced activation of PI3K and ERK1/2 pathways [9, 35, 67]. Alterations in cell cycle regulation can also promote proliferation by facilitating progression through the cell cycle checkpoints and speeding up the cycle. For example, the Wnt/β-catenin pathway is of influence on both G1/S and G2/M progression via activation of Cyclin-D by c-myc and activation of Survivin respectively [46, 52].

The Insulin-Like-Growth-Factor 1 (IGF-1) Receptor axis is also implicated in the development of OS. It is striking that most OS arise during or shortly after puberty. The influence of GH and IGF-1 on bone growth steer the longitudinal growth during the adolescent growth spurt and contribute to approximately 50% of bone cell proliferation. As there is a peak incidence of OS during the adolescent growth spurt, it is conceivable that there could be GH/IGF-1 axis involvement in tumour development. IGF-1R signalling can activate the PI3K/Akt/mTOR pathway and stimulate survival and proliferation in tumour cells [40, 7779].

(Pre)clinical studies: Angiogenesis

As OS is a highly vascularised tumour, a rationale exists to use this feature as a therapeutic target. High serum-VEGF levels correlate with metastatic relapse, tumour progression, poor response to chemotherapy and a decrease in survival [40, 77, 80]. Endostatin is an endogenous angiogenesis inhibitor, produced by tumours itself, involved in repression of neo-angiogenesis and is commonly expressed in human OS samples. It can also induce apoptosis in endothelial cells. Given its important role in angiogenesis, it was hypothesised that Endostatin could impair OS tumour growth and metastasis [18, 77, 81, 82]. However, in a murine model of OS lung metastasis, Endostatin failed to induce tumour shrinkage in the lungs, although, it did retard growth of lung nodules. Treatment with this drug will not cure OS patients, but it may result in stable metastatic disease with prolonged survival [83].

(Pre)clinical studies: Proliferation

Pharmacologic inhibition of the GH/IGF-1 axis and thus IGF-1R pathways has been explored. However, whereas there is evidence that IGF-1R signalling is important to primary OS growth, the extent to which IGF-1R (inhibition) could regulate OS metastases is not clear. In 2002, Mansky et al. [78] performed a phase I study in OS patients with metastatic and/or recurrent disease testing the clinical efficacy of the Somatostatin analog OncoLar. OncoLar was shown to significantly reduce circulating IGF-1 in patients. However, all patients enrolled showed disease progression.

More recently, fully humanised monoclonal antibodies (mABs) directed against the IGF-1R were tested in preclinical and clinical setting. In vivo IGF-1R inhibition with monoclonal antibodies induced growth retardation in subcutaneous models of OS [79, 84]. Whether this growth delay will also be shown in OS metastasis is unknown. The SARC-011 clinical trial is evaluating the treatment effect of R1507, a mAB targeting the IGF-1R in patients with recurrent sarcomas, including OS (clinicaltrials.gov/NCT00642941). In another clinical trial the efficacy of SCH717454, also targeting the IGF-1R, is evaluated in relapsed OS patients. In this trial, both inoperable patients and patients in whom metastasectomy is feasible are included. The latter group will be treated pre- and post-metastasectomy and might, apart from tumour response rate, give information about progression-free survival (clinicaltrials.gov/NCT00617890).


Conclusion

In conclusion, this review summarises potential molecular alterations that contribute to metastasis in OS and gives an overview of (pre)clinical efforts to develop new therapeutic targets for the treatment of metastatic OS. In spite of these efforts, OS metastasis is not yet well understood and there has been little evolvement in the treatment of this disease over the last decade. We hypothesise that certain molecular alterations seen in metastatic cells can also contribute to resistance to chemotherapy, and targeting these features might enhance the efficacy of current treatments. Further unravelling the biology of OS metastasis will hopefully provide new insights to be used as a rational basis for innovative metastasis directed treatments for OS.

Acknowledgements

We would like to acknowledge prof. E.S. Kleinerman (M.D. Anderson Cancer Center, Houston, TX, USA) for her input and guidance in the preparation of this manuscript. JP is supported by the Individualised Musculoskeletal Regeneration and Reconstruction Network (Danish Research Council) Aarhus, Denmark and by VONK: VUmc Onderzoek naar Kinderkanker (Stichting Research Fonds Kindergeneeskunde VUmc) Amsterdam, the Netherlands.
Open Access

This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.

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Vast hidden network regulates gene expression in cancer

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Posted 15 Oct 2011 — by James Street
Category Educational, genetic research, MicroRNA, mPR network, RNAi, Understanding Cancer

Contact: Karin Eskenazi
ket2116@columbia.edu
212-342-0508
Columbia University Medical Center

Study illuminates the ‘dark matter’ of the genome

New York, NY (October 14, 2011) — Researchers at Columbia University Medical Center (CUMC) and two other institutions have uncovered a vast new gene regulatory network in mammalian cells that could explain genetic variability in cancer and other diseases. The studies appear in today’s online edition of Cell.

“The discovery of this regulatory network fills in a missing piece in the puzzle of cell regulation and allows us to identify genes never before associated with a particular type of tumor or disease,” said Andrea Califano, PhD, professor of systems biology, director of the Columbia Initiative in Systems Biology, and senior author of the CUMC research team.

For decades, scientists have thought that the primary role of messenger RNA (mRNA) is to shuttle information from the DNA to the ribosomes, the sites of protein synthesis. However, these new studies suggest that the mRNA of one gene can control, and be controlled by, the mRNA of other genes via a large pool of microRNA molecules, with dozens to hundreds of genes working together in complex self-regulating sub-networks.

The findings have the potential to broaden investigations into how tumors develop and grow, who is at risk for cancer, and how to identify and inactivate key molecules that encourage the growth and spread of cancer.

For example, in the case of the phosphatase and tensin homolog gene (PTEN), a major tumor suppressor, deletions of its mRNA network regulators in patients appear to be as damaging as mutations of the gene itself in several types of cancer, the studies show.

The newly identified regulatory network (called the mPR network by the CUMC investigators) allows mRNAs to communicate through small bits of RNA called microRNAs. Researchers first realized about a decade ago that microRNAs, by binding to complementary genetic sequences on mRNAs, can prevent those mRNAs from making proteins. Turning this concept on end, the new studies reveal that mRNAs actually use microRNAs to influence the expression of other genes.

When two genes share a set of microRNA regulators, changes in expression of one gene affects the other. If, for instance, one of those genes is highly expressed, the increase in its mRNA molecules will “sponge up” more of the available microRNAs. As a result, fewer microRNA molecules will be available to bind and repress the other gene’s mRNAs, leading to a corresponding increase in expression. Although such an effect had been previously elucidated, the range and relevance of this kind of interaction had not been characterized.

“It turns out that this type of microRNA-mediated regulation is commonplace in the cell, and thousands of genes are regulating one another through hundreds of thousands of microRNA-mediated interactions,” says Pavel Sumazin, PhD, research scientist in systems biology and a first author of the CUMC paper. “This is similar in size and effect to other regulatory networks, such as transcriptional regulatory networks, where target genes are regulated by transcription factors.”

In the CUMC study, Dr. Sumazin and his colleagues analyzed glioblastoma mRNA and microRNA expression data from the Cancer Genome Atlas, a public database, uncovering a regulatory layer comprising more than 248,000 microRNA-mediated interactions.

Looking specifically at the tumor suppressor gene PTEN, the researchers found that it is part of a sub-network of more than 500 genes. Of these genes, 13 are frequently deleted in glioblastoma and seem to work together through microRNAs to stop PTEN activity — achieving the same result as if the tumors had inactivating mutations or deletions of PTEN itself.

The finding explains, at least in part, why all patients with glioblastoma do not share the same genetic profile. In about 80 percent of patients, their tumors have a deletion of PTEN. In most of the remaining 20 percent, PTEN is intact, but the gene is not expressed — an observation that had confounded researchers. “This suggested that there must be some other mechanism by which PTEN can be completely suppressed,” said Dr. Sumazin. “Now we know that there are at least 13 other genes — none of which had ever been implicated in cancer — that can ‘gang up’ on PTEN to suppress its activity, with different combination of deletions in different patients.”

“This network helps explain the so-called dark matter of the genome,” added Dr. Califano. “For years, scientists have been cataloguing all the genes involved in particular diseases. But if you add up all the genetic and epigenetic alterations that have been identified, even with high-resolution studies, there are still many cases where you cannot explain why a person has the disease. Now we have a new tool for explaining these genetic variations, for gaining a better understanding of the disease and, ultimately, for finding new treatments.”

In another study published in Cell, Pier Paolo Pandolfi, MD, PhD, director of the Cancer Genetics Program at Beth Israel Deaconess Medical Center, and his colleagues linked about 150 new genes to PTEN in human prostate and colon cancer cell lines. In a second paper, the Pandolfi group showed that mutations in the PTEN-RNA network speeded up the growth of cancer in a mouse model of melanoma. The final related study in Cell, led by Irene Bozzoni at the Sapienza University of Rome, extends functional evidence of the new RNA network phenomenon to the normal differentiation of human muscle cells and to the large realm of human non-coding RNAs.

###

Dr. Sumazin’s paper is titled, “An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma.” The paper’s other co-first authors include postdoctoral fellow Xuerui Yang and graduate student Hua-Sheng Chiu. Other co-authors include Wei-Jen Chung, Archana Iyer, David Llobet-Navas, Presha Rajbhandari, Mukesh Bansal, Paolo Guarnieri, and Jose Silva, all at CUMC.

This research was supported by the National Institutes of Health.

The authors declare no financial or other conflicts of interest.

 

Columbia University Medical Center provides international leadership in basic, pre-clinical and clinical research, in medical and health sciences education, and in patient care. The medical center trains future leaders and includes the dedicated work of many physicians, scientists, public health professionals, dentists, and nurses at the College of Physicians and Surgeons, the Mailman School of Public Health, the College of Dental Medicine, the School of Nursing, the biomedical departments of the Graduate School of Arts and Sciences, and allied research centers and institutions. Established in 1767, Columbia’s College of Physicians and Surgeons was the first institution in the country to grant the M.D. degree and is among the most selective medical schools in the country. Columbia University Medical Center is home to the largest medical research enterprise in New York City and State and one of the largest in the United States.

EMCC Speakers Look Forward To Widespread Personalized Patient Care

By Anna Azvolinsky, PhD | September 28, 2011

 

The European Multidisciplinary Cancer Congress (EMCC), took place September 23–27 in Stockholm, brought together the European oncology community in a joint effort between the European Society for Medical Oncology (ESMO), the European Cancer Organisation (ECCO), and the European Society for Therapeutic Radiology and Oncology (ESTRO).

The multidisciplinary nature of the meeting is highlighted by the tagline of the congress—“Integrating basic and translational science, surgery, radiotherapy, medical oncology and care”—and, indeed, the meeting has emphasized the integration of these components and their important roles in driving cancer research toward providing better patient treatment and care. As clinical practice is becoming increasingly interdisciplinary with patients being treated in multidisciplinary teams, a multifaceted meeting such as this one is important for the continued dialogue, education, and communication among cancer clinicians and researchers.

The EMCC had 285 sessions and over 2,000 presentations from 707 experts in the field, with over 16,000 attendees from around the world.

A call to drive better personalized care deliverables for patients

The opening session of the EMCC emphasized that the field of oncology should continue to strive torward streamlined and personalized patient care. José Baselga, MD, PhD, the associate director and chair in hematology/oncology at the Massachusetts General Hospital Cancer Center gave a presentation, “New World of Cancer: Personalized Medicine for All Patients” that urged the cancer community to see molecular targeting of cancer as a new era. Dr. Baselga pointed out that he believes that classic approaches to cancer therapy such as radiation therapy and chemotherapy have achieved a plateau in terms of patient response. In this “classic therapy” era, only an empirical approach to clinical trial design was possible, where patient populations were unselected and large-scale trials were necessary in order to see any treatment benefit. These types of trials led to a high failure rate and minimal benefits. “The system can no longer tolerate an incremental benefit,” he stated as he transitioned to a discussion of what he calls the “new era of molecular targeting of cancer.”

As researchers and clinicians are beginning to understand the wiring of cancer and the underlying molecular causes, Baselga stated, “we are getting into an era of the right drug for the right tumor.” He went on to highlight that identifying the right molecular targets can result in the creation of specific molecules that act on these targets, and said, “chemistry is on our side, to design new treatments.” Dr. Baselga cited early success stories of targeted therapies that have resulted in dramatic patient benefits, including gefitinib (Iressa) and erlotinib (Tarceva), two selective inhibitors of EGFR for lung cancer, crizotinib (Xalkori) for lung cancer patients, which inhibits ALK in patients that harbor the EML4-ALK fusion; and vemurafenib (Zelboraf), the BRAF inhibitor that has recently been approved for metastatic melanoma.

“We will have an incremental number of genetic mutations identified in tumors and we will have an increased number of therapies to treat these tumors,” Baselga said, highlighting his optimism in the collaboration of bench-scientists and clinicians to develop new treatments, in conjunction with the increasing understanding of cancer mutations from patient tumor data.

“We have to realize that this is a watershed moment in cancer history. We have to make sure we match each drug with each individual tumor and we have to change the way we test these new drugs,” said Dr. Baselga.

Looking forward, Dr. Baselga spoke about the need for better, streamlined, and throughput methods to test these new agents for efficacy in a rational way that will provide meaningful data. After isolating compounds that have the potential to be efficacious, the ability to identify patients that will benefit is crucial. Baselga stated, “We have to embark on a comprehensive genetic characterization of tumors: chrosomomsal alterations, epigenetics, mutations, and proteomics.”

While the challenging tasks of platform and clinical validation, archiving quality specimens, improving turnaround time and informatics approaches, and looking for novel mutations is daunting, it is “far less than treating patients with expensive drugs that may not work unless they are targeted for the patient.” In this sense, the field has progressed significantly over the last decade, with the mutational landscapes for lung and breast cancers providing a categorization of subclassifications of these disease that facilitate tailored therapy treatments.

Baselga pointed out that one highly important point that, thus far, has not been widespread due to high cost and the inability to obtain appropriate patient sampling, is the serial monitoring of tumors during therapy. Looking at the genetic makeup of a tumor prior to and post-treatment will greatly facilitate the knowledge about how tumor genetic factors influence treatment response and resistance. Baselga cited the new research on circulating tumor cells (CTCs), and said that by applying novel therapies earlier in disease “you can identify very early on when a patient responds, which can help clinicians modulate therapy.”

He highlighted a particular example of the use of technology to predict response that was subsequently presented at EMCC (Gamez et al. “FDG-PET/CT for Early Prediction of Response to Neoadjuvant Lapatinib, Trastuzumab, and Their Combination in HER2-positive Breast Cancer Patients: the Neo-ALTTO Study Results, abstract #5013).

Dr. Baselga ended by listing his vision of novel clinical trial design in the new molecular era: 1) smaller smarter clinical trials without the need for 1000+ , expensive trials, 2) the importance of combination treatments 3) applying novel targeted agents earlier in the course of disease, and 4) the study of resistance to therapies. “Over the course of the next ten years,” he said, “we need good biomarker programs and facilities, the sharing of data, attracting the best pool of physician scientists into our culture of teamwork, and we need creativity and willingness in our clinical trial design.”

A pragmatic assessment of today’s personalized molecular medicine

Following Dr. Baselga’s talk, Gordon B. Mills, MD, PhD and chairman of the department of systems biology at the M.D. Anderson Cancer Center addressed what the cancer community needs to be doing to deliver personalized medicine outside of the research environment. “We have to determine to work with medicine and industry in a better manner. Drugs coming out of the pipeline must be linked to the right patient,” he stated.

Professor Mills defined personalized medicine as “the right treatment for the right person at the right and first time,” in contrast to the current practice of “trial and error.” He asked the audience to think about whether they are educating patients and physicians enough and whether they are overpromising on what the current treatments and care can deliver.

In the view of Professor Mills, there are still only subpopulations of patients that experience the biomarker benefit, calling the current phase “stratified and precision medicine.” He stated that he agreed with Dr. Baselga that breast cancer is leading the way in this. “Breast cancer is now a series of different diseases, at least eight of them. But the problem is that some of these subpopulations are too small to have clinical trials that will show good enough data. Rather than distinct diseases, currently, there are still only subpopulations,” he asserted.

Emphasizing that despite the latest positive results with targeted agents, “every single patient on [vemurafenib] has recurred.” His goal was for the oncology community to aim for higher achievements.

Finally, Professor Mills outlined the current landscape of challenges he sees that need to be overcome. In terms of patients, these include the need to identify a patient’s genetic makeup to determine whether a treatment will succeed, the need to assess individualized dosing and toxicity limits, and the issue of intra-tumoral heterogeneity and the evolution of the tumor from primary to recurrent stages of cancer.

As far as technology challenges, filtering passenger vs driver mutations is necessary, and Mills also cited the need to find actionable aberrations, as there are still a limited number of drugs for all of the mutations identified in tumors. He highlighted the fact that most tumor suppressors are still recalcitrant to treatments and that the cost of treatments is continually on the rise.

The issue of the accrual of large amounts of sequencing information is such that database storage costs outweigh the costs of generating sequencing data, and said that this is something that needs to be addressed. “The $1000 genome is now the $100,000 analysis cost,” he said. Lastly, he pointed to the expanded number of parties that are involved in treatment development and implementation. He stated that the ethics of telling patients about germ-line mutations that are discovered during genomic sequencing needs to be discussed thoroughly, and mentioned the need for participation by the U.S. Food and Drug Administration in the education of patients and physicians and the issue of reimbursement for testing and sequencing.

The communication, education, and open dialogue about these issues going forward among the global oncology community and other key stakeholders, as well as about novel treatment paradigms and progress, will be highly important for oncologists to be fully entrenched in this promising molecular therapy era.

The Empowered Patient

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The Empowered Patient

by Elizabeth S. Cohen
paperback, 240 pp.

Item Catalog Number: 33825

How to get the right diagnosis, buy the cheapest drugs, beat your insurance company and get the best medical care, every time.

Navigating the labyrinth of the medical establishment can be extraordinarily difficult, especially in the current climate of health care uncertainty. Fortunately, CNN Senior Correspondent Elizabeth Cohen has written The Empowered Patient (Ballantine Books, 2010), a book that is a virtual GPS to help guide you through the byzantine maze.

Her goal is simple: to help you get the best care humanly possible should you unfortunately fall ill. In order to jar you into taking action and, as the book’s title says, become an Empowered Patient, she first lays out some startling facts.

Fact 1: Medical errors kill more people each year than AIDS, breast cancer, or car accidents

Fact 2: 99,000 Americans die each year from infections they acquire in the hospital

Fact 3: As many as 98,000 Americans die from medical mistakes in the hospital.

With chapter headers like “How to be a “Bad Patient,” “How to Avoid a Misdiagnosis,” “Don’t Fall for Medical Marketing,” and “Don’t Let a Hospital Kill You,” Cohen stakes out her claim early on that from the moment you enter the medical world, your head needs to be on a swivel. The surest way to do that is to stay constantly informed about what is happening around you. Simply accepting what a doctor is telling you is unacceptable.

The beauty of Cohen’s book is that she writes from experience in dealing with hospitals and from the perspective of being an expert. Yes, the facts, when you first hear them, are scary, but once you accept that these days, “medicine is more of an art than a science,” you are able to sit back and think with a clear head. And thinking with a clear head is paramount to getting what you want.

“Despite what Michael Moore says, the United States has some of the best care in the world,” Cohen writes in her introduction, “And my family and I have been grateful recipients of it on many occasions. But getting that excellent care takes know-how, and I want to share with you what I’ve learned through my reporting and my personal experiences with doctors.”

One such doctor, Sanjay Gupta, who recently appeared on the cover of Life Extension Magazine®, says that The Empowered Patient is “a book no household should be without”. And he’s right. From the starting point of getting the right diagnosis for an ailment, to how to buy the cheapest drugs, to how to beat your insurance company, The Empowered Patient is an invaluable resource.

Elizabeth Cohen is a senior medical correspondent for CNN and author of the popular “empowered patient” column on cnn.com. She received her master’s degree in public health from Boston University and her bachelor’s degree from Columbia University in New York. She lives in Atlanta, Georgia with her husband, Tal Cohen and their four daughters.

*These statements have not been evaluated by the Food and Drug Administration. These products are not intended to diagnose, treat, cure or prevent any disease.

 

Why Most Published Research Findings Are False

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Posted 16 Sep 2011 — by James Street
Category Educational, Fraud, General Cancer Research, Online Research Tools, Open Source Drug Discovery

John P. A. Ioannidis

Abstract Top

Summary

There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this essay, I discuss the implications of these problems for the conduct and interpretation of research.

Citation: Ioannidis JPA (2005) Why Most Published Research Findings Are False. PLoS Med 2(8): e124. doi:10.1371/journal.pmed.0020124

Published: August 30, 2005

Copyright: © 2005 John P. A. Ioannidis. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Competing interests: The author has declared that no competing interests exist.

Abbreviation: PPV, positive predictive value

John P. A. Ioannidis is in the Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece, and Institute for Clinical Research and Health Policy Studies, Department of Medicine, Tufts-New England Medical Center, Tufts University School of Medicine, Boston, Massachusetts, United States of America. E-mail: jioannid@cc.uoi.gr

Published research findings are sometimes refuted by subsequent evidence, with ensuing confusion and disappointment. Refutation and controversy is seen across the range of research designs, from clinical trials and traditional epidemiological studies [1–3] to the most modern molecular research [4,5]. There is increasing concern that in modern research, false findings may be the majority or even the vast majority of published research claims [6–8]. However, this should not be surprising. It can be proven that most claimed research findings are false. Here I will examine the key factors that influence this problem and some corollaries thereof.

Modeling the Framework for False Positive Findings Top

Several methodologists have pointed out [9–11] that the high rate of nonreplication (lack of confirmation) of research discoveries is a consequence of the convenient, yet ill-founded strategy of claiming conclusive research findings solely on the basis of a single study assessed by formal statistical significance, typically for a p-value less than 0.05. Research is not most appropriately represented and summarized by p-values, but, unfortunately, there is a widespread notion that medical research articles should be interpreted based only on p-values. Research findings are defined here as any relationship reaching formal statistical significance, e.g., effective interventions, informative predictors, risk factors, or associations. “Negative” research is also very useful. “Negative” is actually a misnomer, and the misinterpretation is widespread. However, here we will target relationships that investigators claim exist, rather than null findings.

 

It can be proven that most claimed research findings are false

As has been shown previously, the probability that a research finding is indeed true depends on the prior probability of it being true (before doing the study), the statistical power of the study, and the level of statistical significance [10,11]. Consider a 2 × 2 table in which research findings are compared against the gold standard of true relationships in a scientific field. In a research field both true and false hypotheses can be made about the presence of relationships. 1Let R be the ratio of the number of “true relationships” to “no relationships” among those tested in the field. R is characteristic of the field and can vary a lot depending on whether the field targets highly likely relationships or searches for only one or a few true relationships among thousands and millions of hypotheses that may be postulated. Let us also consider, for computational simplicity, circumscribed fields where either there is only one true relationship (among many that can be hypothesized) or the power is similar to find any of the several existing true relationships. The pre-study probability of a relationship being true is R/(R + 1). The probability of a study finding a true relationship reflects the power 1 – β (one minus the Type II error rate). The probability of claiming a relationship when none truly exists reflects the Type I error rate, α. Assuming that c relationships are being probed in the field, the expected values of the 2 × 2 table are given in Table 1. After a research finding has been claimed based on achieving formal statistical significance, the post-study probability that it is true is the positive predictive value, PPV. The PPV is also the complementary probability of what Wacholder et al. have called the false positive report probability [10]. According to the 2 × 2 table, one gets PPV = (1 – β)R/(R – βR + α). A research finding is thus more likely true than false if (1 – β)R > α. Since usually the vast majority of investigators depend on a = 0.05, this means that a research finding is more likely true than false if (1 – β)R > 0.05.

thumbnailTable 1. Research Findings and True Relationships

doi:10.1371/journal.pmed.0020124.t001

What is less well appreciated is that bias and the extent of repeated independent testing by different teams of investigators around the globe may further distort this picture and may lead to even smaller probabilities of the research findings being indeed true. We will try to model these two factors in the context of similar 2 × 2 tables.

Bias Top

First, let us define bias as the combination of various design, data, analysis, and presentation factors that tend to produce research findings when they should not be produced. Let u be the proportion of probed analyses that would not have been “research findings,” but nevertheless end up presented and reported as such, because of bias. Bias should not be confused with chance variability that causes some findings to be false by chance even though the study design, data, analysis, and presentation are perfect. Bias can entail manipulation in the analysis or reporting of findings. Selective or distorted reporting is a typical form of such bias. We may assume that u does not depend on whether a true relationship exists or not. This is not an unreasonable assumption, since typically it is impossible to know which relationships are indeed true. In the presence of bias (Table 2), one gets PPV = ([1 - β]R + uβR)/(R + α − βR + uuα + uβR), and PPV decreases with increasing u, unless 1 − β ≤ α, i.e., 1 − β ≤ 0.05 for most situations. Thus, with increasing bias, the chances that a research finding is true diminish considerably. This is shown for different levels of power and for different pre-study odds in Figure 1. Conversely, true research findings may occasionally be annulled because of reverse bias. For example, with large measurement errors relationships are lost in noise [12], or investigators use data inefficiently or fail to notice statistically significant relationships, or there may be conflicts of interest that tend to “bury” significant findings [13]. There is no good large-scale empirical evidence on how frequently such reverse bias may occur across diverse research fields. However, it is probably fair to say that reverse bias is not as common. Moreover measurement errors and inefficient use of data are probably becoming less frequent problems, since measurement error has decreased with technological advances in the molecular era and investigators are becoming increasingly sophisticated about their data. Regardless, reverse bias may be modeled in the same way as bias above. Also reverse bias should not be confused with chance variability that may lead to missing a true relationship because of chance.

thumbnailFigure 1. PPV (Probability That a Research Finding Is True) as a Function of the Pre-Study Odds for Various Levels of Bias, u

Panels correspond to power of 0.20, 0.50, and 0.80.

doi:10.1371/journal.pmed.0020124.g001

thumbnailTable 2. Research Findings and True Relationships in the Presence of Bias

doi:10.1371/journal.pmed.0020124.t002

Testing by Several Independent Teams Top

Several independent teams may be addressing the same sets of research questions. As research efforts are globalized, it is practically the rule that several research teams, often dozens of them, may probe the same or similar questions. Unfortunately, in some areas, the prevailing mentality until now has been to focus on isolated discoveries by single teams and interpret research experiments in isolation. An increasing number of questions have at least one study claiming a research finding, and this receives unilateral attention. The probability that at least one study, among several done on the same question, claims a statistically significant research finding is easy to estimate. For n independent studies of equal power, the 2 × 2 table is shown in Table 3: PPV = R(1 − βn)/(R + 1 − [1 − α]nRβn) (not considering bias). With increasing number of independent studies, PPV tends to decrease, unless 1 – β < a, i.e., typically 1 − β < 0.05. This is shown for different levels of power and for different pre-study odds in Figure 2. For n studies of different power, the term βn is replaced by the product of the terms βi for i = 1 to n, but inferences are similar.

thumbnailFigure 2. PPV (Probability That a Research Finding Is True) as a Function of the Pre-Study Odds for Various Numbers of Conducted Studies, n

Panels correspond to power of 0.20, 0.50, and 0.80.

doi:10.1371/journal.pmed.0020124.g002

thumbnailTable 3. Research Findings and True Relationships in the Presence of Multiple Studies

doi:10.1371/journal.pmed.0020124.t003

Corollaries Top

A practical example is shown in Box 1. Based on the above considerations, one may deduce several interesting corollaries about the probability that a research finding is indeed true.

Box 1. An Example: Science at Low Pre-Study Odds

Let us assume that a team of investigators performs a whole genome association study to test whether any of 100,000 gene polymorphisms are associated with susceptibility to schizophrenia. Based on what we know about the extent of heritability of the disease, it is reasonable to expect that probably around ten gene polymorphisms among those tested would be truly associated with schizophrenia, with relatively similar odds ratios around 1.3 for the ten or so polymorphisms and with a fairly similar power to identify any of them. Then R = 10/100,000 = 10−4, and the pre-study probability for any polymorphism to be associated with schizophrenia is also R/(R + 1) = 10−4. 1Let us also suppose that the study has 60% power to find an association with an odds ratio of 1.3 at α = 0.05. Then it can be estimated that if a statistically significant association is found with the p-value barely crossing the 0.05 threshold, the post-study probability that this is true increases about 12-fold compared with the pre-study probability, but it is still only 12 × 10−4.

Now let us suppose that the investigators manipulate their design, analyses, and reporting so as to make more relationships cross the p = 0.05 threshold even though this would not have been crossed with a perfectly adhered to design and analysis and with perfect comprehensive reporting of the results, strictly according to the original study plan. Such manipulation could be done, for example, with serendipitous inclusion or exclusion of certain patients or controls, post hoc subgroup analyses, investigation of genetic contrasts that were not originally specified, changes in the disease or control definitions, and various combinations of selective or distorted reporting of the results. Commercially available “data mining” packages actually are proud of their ability to yield statistically significant results through data dredging. In the presence of bias with u = 0.10, the post-study probability that a research finding is true is only 4.4 × 10−4. Furthermore, even in the absence of any bias, when ten independent research teams perform similar experiments around the world, if one of them finds a formally statistically significant association, the probability that the research finding is true is only 1.5 × 10−4, hardly any higher than the probability we had before any of this extensive research was undertaken!

Corollary 1: The smaller the studies conducted in a scientific field, the less likely the research findings are to be true. Small sample size means smaller power and, for all functions above, the PPV for a true research finding decreases as power decreases towards 1 − β = 0.05. Thus, other factors being equal, research findings are more likely true in scientific fields that undertake large studies, such as randomized controlled trials in cardiology (several thousand subjects randomized) [14] than in scientific fields with small studies, such as most research of molecular predictors (sample sizes 100-fold smaller) [15].

Corollary 2: The smaller the effect sizes in a scientific field, the less likely the research findings are to be true. Power is also related to the effect size. Thus research findings are more likely true in scientific fields with large effects, such as the impact of smoking on cancer or cardiovascular disease (relative risks 3–20), than in scientific fields where postulated effects are small, such as genetic risk factors for multigenetic diseases (relative risks 1.1–1.5) [7]. Modern epidemiology is increasingly obliged to target smaller effect sizes [16]. Consequently, the proportion of true research findings is expected to decrease. In the same line of thinking, if the true effect sizes are very small in a scientific field, this field is likely to be plagued by almost ubiquitous false positive claims. For example, if the majority of true genetic or nutritional determinants of complex diseases confer relative risks less than 1.05, genetic or nutritional epidemiology would be largely utopian endeavors.

Corollary 3: The greater the number and the lesser the selection of tested relationships in a scientific field, the less likely the research findings are to be true. As shown above, the post-study probability that a finding is true (PPV) depends a lot on the pre-study odds (R). Thus, research findings are more likely true in confirmatory designs, such as large phase III randomized controlled trials, or meta-analyses thereof, than in hypothesis-generating experiments. Fields considered highly informative and creative given the wealth of the assembled and tested information, such as microarrays and other high-throughput discovery-oriented research [4,8,17], should have extremely low PPV.

Corollary 4: The greater the flexibility in designs, definitions, outcomes, and analytical modes in a scientific field, the less likely the research findings are to be true. Flexibility increases the potential for transforming what would be “negative” results into “positive” results, i.e., bias, u. For several research designs, e.g., randomized controlled trials [18–20] or meta-analyses [21,22], there have been efforts to standardize their conduct and reporting. Adherence to common standards is likely to increase the proportion of true findings. The same applies to outcomes. True findings may be more common when outcomes are unequivocal and universally agreed (e.g., death) rather than when multifarious outcomes are devised (e.g., scales for schizophrenia outcomes) [23]. Similarly, fields that use commonly agreed, stereotyped analytical methods (e.g., Kaplan-Meier plots and the log-rank test) [24] may yield a larger proportion of true findings than fields where analytical methods are still under experimentation (e.g., artificial intelligence methods) and only “best” results are reported. Regardless, even in the most stringent research designs, bias seems to be a major problem. For example, there is strong evidence that selective outcome reporting, with manipulation of the outcomes and analyses reported, is a common problem even for randomized trails [25]. Simply abolishing selective publication would not make this problem go away.

Corollary 5: The greater the financial and other interests and prejudices in a scientific field, the less likely the research findings are to be true. Conflicts of interest and prejudice may increase bias, u. Conflicts of interest are very common in biomedical research [26], and typically they are inadequately and sparsely reported [26,27]. Prejudice may not necessarily have financial roots. Scientists in a given field may be prejudiced purely because of their belief in a scientific theory or commitment to their own findings. Many otherwise seemingly independent, university-based studies may be conducted for no other reason than to give physicians and researchers qualifications for promotion or tenure. Such nonfinancial conflicts may also lead to distorted reported results and interpretations. Prestigious investigators may suppress via the peer review process the appearance and dissemination of findings that refute their findings, thus condemning their field to perpetuate false dogma. Empirical evidence on expert opinion shows that it is extremely unreliable [28].

Corollary 6: The hotter a scientific field (with more scientific teams involved), the less likely the research findings are to be true. This seemingly paradoxical corollary follows because, as stated above, the PPV of isolated findings decreases when many teams of investigators are involved in the same field. This may explain why we occasionally see major excitement followed rapidly by severe disappointments in fields that draw wide attention. With many teams working on the same field and with massive experimental data being produced, timing is of the essence in beating competition. Thus, each team may prioritize on pursuing and disseminating its most impressive “positive” results. “Negative” results may become attractive for dissemination only if some other team has found a “positive” association on the same question. In that case, it may be attractive to refute a claim made in some prestigious journal. The term Proteus phenomenon has been coined to describe this phenomenon of rapidly alternating extreme research claims and extremely opposite refutations [29]. Empirical evidence suggests that this sequence of extreme opposites is very common in molecular genetics [29].

These corollaries consider each factor separately, but these factors often influence each other. For example, investigators working in fields where true effect sizes are perceived to be small may be more likely to perform large studies than investigators working in fields where true effect sizes are perceived to be large. Or prejudice may prevail in a hot scientific field, further undermining the predictive value of its research findings. Highly prejudiced stakeholders may even create a barrier that aborts efforts at obtaining and disseminating opposing results. Conversely, the fact that a field is hot or has strong invested interests may sometimes promote larger studies and improved standards of research, enhancing the predictive value of its research findings. Or massive discovery-oriented testing may result in such a large yield of significant relationships that investigators have enough to report and search further and thus refrain from data dredging and manipulation.

Most Research Findings Are False for Most Research Designs and for Most Fields Top

In the described framework, a PPV exceeding 50% is quite difficult to get. Table 4 provides the results of simulations using the formulas developed for the influence of power, ratio of true to non-true relationships, and bias, for various types of situations that may be characteristic of specific study designs and settings. A finding from a well-conducted, adequately powered randomized controlled trial starting with a 50% pre-study chance that the intervention is effective is eventually true about 85% of the time. A fairly similar performance is expected of a confirmatory meta-analysis of good-quality randomized trials: potential bias probably increases, but power and pre-test chances are higher compared to a single randomized trial. Conversely, a meta-analytic finding from inconclusive studies where pooling is used to “correct” the low power of single studies, is probably false if R ≤ 1:3. Research findings from underpowered, early-phase clinical trials would be true about one in four times, or even less frequently if bias is present. Epidemiological studies of an exploratory nature perform even worse, especially when underpowered, but even well-powered epidemiological studies may have only a one in five chance being true, if R = 1:10. Finally, in discovery-oriented research with massive testing, where tested relationships exceed true ones 1,000-fold (e.g., 30,000 genes tested, of which 30 may be the true culprits) [30,31], PPV for each claimed relationship is extremely low, even with considerable standardization of laboratory and statistical methods, outcomes, and reporting thereof to minimize bias.

thumbnailTable 4. PPV of Research Findings for Various Combinations of Power (1 – ß), Ratio of True to Not-True Relationships (R), and Bias (u)

doi:10.1371/journal.pmed.0020124.t004

Claimed Research Findings May Often Be Simply Accurate Measures of the Prevailing Bias Top

As shown, the majority of modern biomedical research is operating in areas with very low pre- and post-study probability for true findings. Let us suppose that in a research field there are no true findings at all to be discovered. History of science teaches us that scientific endeavor has often in the past wasted effort in fields with absolutely no yield of true scientific information, at least based on our current understanding. In such a “null field,” one would ideally expect all observed effect sizes to vary by chance around the null in the absence of bias. The extent that observed findings deviate from what is expected by chance alone would be simply a pure measure of the prevailing bias.

For example, let us suppose that no nutrients or dietary patterns are actually important determinants for the risk of developing a specific tumor. Let us also suppose that the scientific literature has examined 60 nutrients and claims all of them to be related to the risk of developing this tumor with relative risks in the range of 1.2 to 1.4 for the comparison of the upper to lower intake tertiles. Then the claimed effect sizes are simply measuring nothing else but the net bias that has been involved in the generation of this scientific literature. Claimed effect sizes are in fact the most accurate estimates of the net bias. It even follows that between “null fields,” the fields that claim stronger effects (often with accompanying claims of medical or public health importance) are simply those that have sustained the worst biases.

For fields with very low PPV, the few true relationships would not distort this overall picture much. Even if a few relationships are true, the shape of the distribution of the observed effects would still yield a clear measure of the biases involved in the field. This concept totally reverses the way we view scientific results. Traditionally, investigators have viewed large and highly significant effects with excitement, as signs of important discoveries. Too large and too highly significant effects may actually be more likely to be signs of large bias in most fields of modern research. They should lead investigators to careful critical thinking about what might have gone wrong with their data, analyses, and results.

Of course, investigators working in any field are likely to resist accepting that the whole field in which they have spent their careers is a “null field.” However, other lines of evidence, or advances in technology and experimentation, may lead eventually to the dismantling of a scientific field. Obtaining measures of the net bias in one field may also be useful for obtaining insight into what might be the range of bias operating in other fields where similar analytical methods, technologies, and conflicts may be operating.

How Can We Improve the Situation? Top

Is it unavoidable that most research findings are false, or can we improve the situation? A major problem is that it is impossible to know with 100% certainty what the truth is in any research question. In this regard, the pure “gold” standard is unattainable. However, there are several approaches to improve the post-study probability.

Better powered evidence, e.g., large studies or low-bias meta-analyses, may help, as it comes closer to the unknown “gold” standard. However, large studies may still have biases and these should be acknowledged and avoided. Moreover, large-scale evidence is impossible to obtain for all of the millions and trillions of research questions posed in current research. Large-scale evidence should be targeted for research questions where the pre-study probability is already considerably high, so that a significant research finding will lead to a post-test probability that would be considered quite definitive. Large-scale evidence is also particularly indicated when it can test major concepts rather than narrow, specific questions. A negative finding can then refute not only a specific proposed claim, but a whole field or considerable portion thereof. Selecting the performance of large-scale studies based on narrow-minded criteria, such as the marketing promotion of a specific drug, is largely wasted research. 1Moreover, one should be cautious that extremely large studies may be more likely to find a formally statistical significant difference for a trivial effect that is not really meaningfully different from the null [32–34].

Second, most research questions are addressed by many teams, and it is misleading to emphasize the statistically significant findings of any single team. What matters is the totality of the evidence. Diminishing bias through enhanced research standards and curtailing of prejudices may also help. However, this may require a change in scientific mentality that might be difficult to achieve. In some research designs, efforts may also be more successful with upfront registration of studies, e.g., randomized trials [35]. Registration would pose a challenge for hypothesis-generating research. Some kind of registration or networking of data collections or investigators within fields may be more feasible than registration of each and every hypothesis-generating experiment. Regardless, even if we do not see a great deal of progress with registration of studies in other fields, the principles of developing and adhering to a protocol could be more widely borrowed from randomized controlled trials.

Finally, instead of chasing statistical significance, we should improve our understanding of the range of R values—the pre-study odds—where research efforts operate [10]. Before running an experiment, investigators should consider what they believe the chances are that they are testing a true rather than a non-true relationship. Speculated high R values may sometimes then be ascertained. As described above, whenever ethically acceptable, large studies with minimal bias should be performed on research findings that are considered relatively established, to see how often they are indeed confirmed. I suspect several established “classics” will fail the test [36].

Nevertheless, most new discoveries will continue to stem from hypothesis-generating research with low or very low pre-study odds. We should then acknowledge that statistical significance testing in the report of a single study gives only a partial picture, without knowing how much testing has been done outside the report and in the relevant field at large. Despite a large statistical literature for multiple testing corrections [37], usually it is impossible to decipher how much data dredging by the reporting authors or other research teams has preceded a reported research finding. Even if determining this were feasible, this would not inform us about the pre-study odds. Thus, it is unavoidable that one should make approximate assumptions on how many relationships are expected to be true among those probed across the relevant research fields and research designs. The wider field may yield some guidance for estimating this probability for the isolated research project. Experiences from biases detected in other neighboring fields would also be useful to draw upon. Even though these assumptions would be considerably subjective, they would still be very useful in interpreting research claims and putting them in context.

References Top

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IDIBELL Researchers Discover Why Tumor Cells Change Their Appearance

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Posted 03 Sep 2011 — by James Street
Category Educational, genetic research, MicroRNA, RNAi, Understanding Cancer
September 2, 2011

If environmental conditions of tumors are changed, the process reverses

Like snakes, tumor cells shed their skin. Cancer is not a static disease but during its development the disease accumulates changes to evade natural defenses adapting to new environmental circumstances, protecting against chemotherapy and radiotherapy and invading neighboring organs, eventually causing metastasis.

Until now little was known about the mechanisms involved in these changing processes in a tumor. There is a particularly intriguing way in which a tumor that initially presents a solid state, attached to nearby cells (epithelial), afterwards becomes a semiliquid mass, detached from tissues and more flexible (mesenchymal).

The team led by Manel Esteller, director of the Cancer Epigenetics and Biology Program at the Bellvitge Biomedical Research Institute (IDIBELL), professor of Genetics at the University of Barcelona and ICREA researcher, has identified a mechanism that explains this change. Tumors “shed their skin” because some molecular switches called microRNAs -responsible for maintaining epithelial appearance of cells- turn off. The finding has been published this week in the online version of the international scientific journal Oncogene, Nature group.

“We have discovered that some microRNAs, a group called microRNA-200S, undergoes a chemical inactivation and inhibit their expression. When these cellular appearance drivers are not present, tumor cells change, stretch, stop their inhibition and thus the tumor progresses”, explains Dr. Esteller, adding that “the results from research show that this is a very dynamic process.”

Change involves from the appearance of the tumor to the onset of metastasis, but if we change the environmental circumstances that influence these cells, the process reverses. Dr Esteller compares the process “with a small planet in Darwinian evolution but in an expedited manner.”

The study was conducted mainly in breast and colon tumors. Besides serving to better understand the disease, the results are important because they predict that external intervention is possible in the process. In this sense, drug treatments can reverse the process and move from a highly evolved tumor form to a more primitive form, which would be associated with a slower progression of the disease.

How My Brain Tumor Woke Me Up To Life

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Posted 28 Aug 2011 — by James Street
Category Complementary and Alternative Medicine, Educational, experimental treatments, Support Groups

Posted: 8/28/11 10:27 AM ET

Diagnosed with a brain tumor in 1998 when I was 24 years old, I knew nothing about cancer. Since then, my health and healing journey has taken me to places far and wide.

Within one month I had undergone awake brain surgery at the National Institutes of Health (NIH). I felt my left temporal lobe brain tumor — the center of speech, memory and sound — required awake brain surgery to help protect my cognitive functions. Twelve hours of surgery later — complete with awake speech and memory testing — neurosurgeons removed the brain tumor along with some surrounding tissue. In the ICU, my brain re-routed, my cells repaired, my bones mended, my jaw slowly unlocked, my heart trembled, my body acclimated to new terrain, my soul sung tunes and my spirit held me.

“You need to track brain tumor scientific studies for your tumor type and care for yourself,” said one of my neurosurgeons. I had no concept for any of it. Crisis serves as a powerful teacher and a catalyst for change.

Several opinions from pathologists diagnosed a lower grade stage of a brain tumor. For cancer patients, multiple opinions are necessary. No conventional cancer treatments were recommended. Instead, I had frequent MRI scans at Memorial Sloan Kettering Cancer Center (MSKCC).

Recovering from my surgery and learning about anti-cancer modalities, I built a team of providers and developed self-care strategies. I developed my health and healing map over many years. Some approaches and therapies supporting me involve acupuncture, herbs, holistic medical care, craniosacral treatments, exercise, dietary changes, homeopathy, Shamanic work, energy healing, dental work, psychotherapy and support groups.

Over time, my personal journey and professional cancer work begged the question, “What do people with cancer really need for improved quality of life and survival?” The answer for me has been integrative cancer care. Integrating more than the cancer diagnosis, integrative cancer care addresses the whole person of body, mind and spirit, including social and environmental health. I’ve found studies that show that integrative cancer care can possibly reduce cancer risk, and improve cancer survival and quality of life.

My integrative cancer care plan continues to evolve. In some ways, I began to feel stronger. Some aspects of my health and healing moved forward while other aspects moved backward. Dealing with fatigue and other ailments, I was finally told news about my tumor’s recurrence in February 2004. Not only was I informed about my brain tumor recurrence, I learned that the tumor actually regrew in 2000. Despite my frequent MRI scans, my doctor never informed me. It was a double whammy. Getting copies of medical records, questioning hospitals claiming to offer the best of cancer care, learning about advocacy and self-care — these were only some of the lessons I learned.

Moving toward thinking and creating anew, I added more integrative therapies and made more changes to my life. During the last five years, I completed four major cancer protocols, including three at cancer clinics in Europe and one in New York City. Once again, I became stronger in some ways, but other health problems surfaced simultaneously.

I’ve constantly tried to figure out where I have been and need to go. Now, more than 13 years after my brain tumor diagnosis, surgery, recurrence, more than 30 MRI scans, many cancer therapies, healing modalities, introspection, study and resources, my life contains new knowledge and personal transformation. I embrace adversity as opportunity, seeing healing as a never-ending road and life as a spiritual journey.

But change has occurred once again. A new chapter in my brain tumor journey began three weeks ago. My most recent MRI scan the end of July 2011 showed that my brain tumor requires me to have a second brain surgery. I’ve worked extremely hard trying to heal holistically and trying to avoid another surgery. Yet to stay alive, that is what I must do. On September 1, 2011, I’ll have awake brain surgery at the University of California San Francisco (UCSF) with Mitchel Berger, M.D.

While I live with uncertainty, vulnerability and sometimes pain, my knowledge and strength carries me forward. Eager and open to transforming my challenges into opportunities, I further evolve into my deeper self.

Through my own personal cancer experience and professional cancer work, I’ve identified some essential tips for cancer patients:

1. Self-Care: Make yourself a priority each moment, hour, day and week. Support your own whole person. Definitely sleep, relax, eat healthy, reduce stress, use mind-body support, lean on your spiritual and social connections, live in a clean and green environment and address any other needs you may have.

2. Support Team: Love yourself and receive support. Create a group of family members and friends to help you through your cancer journey. Specific types of support are wide and varied. You can even use Internet-based programs to organize help. Find what works for you. Be open.

3. Advocacy: Self-advocate, and receive help from loved ones and other professionals to navigate your cancer diagnosis, side effects, treatments and journey. Move step by step. Conduct research, ask quality questions, seek multiple opinions, maintain a willingness to change directions when necessary, and use other resources to improve quality of life and cancer survival.

4. Choose Quality Providers And Build A Team: Choose an oncologist with expertise in your specific cancer and access to excellent treatment facilities. I believe that quality cancer care must include other treatments for the cancer diagnosis and your whole person. Identify a group of integrative providers tending to many aspects of your health and healing. The full spectrum of comprehensive integrative cancer care will not come from one professional — instead it will occur through the help of a team.

5. Joy, Love, Passions And Purpose: Focus your attention on what you enjoy and the way that love brings light to your life. Express your passions and purpose in order to strengthen your innate healing capacity. I believe that passions flow through your heart. Purpose feeds from your core through embodiment of heart, soul and spirit.

With these essential tips, many other cancer resources, my personal cancer knowledge and professional cancer work, my commitment is to help people with cancer. You can learn more about integrative cancer care resources for the whole person through my non-profit organization called EmbodiWorks at www.embodiworks.org.