Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance
TL;DR: Data indicate that MCL1 is an important regulator of GC-induced apoptosis and that the combination of rapamycin and glucocorticoids has potential utility in lymphoid malignancies.
About: This article is published in Cancer Cell.The article was published on 2006-10-01 and is currently open access. It has received 503 citations till now. The article focuses on the topics: MCL1.
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TL;DR: Approaches used for drug repurposing (also known as drug repositioning) are presented, the challenges faced by the repurpose community are discussed, and innovative ways by which these challenges could be addressed are recommended to help realize the full potential of drugRepurposing.
Abstract: Given the high attrition rates, substantial costs and slow pace of new drug discovery and development, repurposing of 'old' drugs to treat both common and rare diseases is increasingly becoming an attractive proposition because it involves the use of de-risked compounds, with potentially lower overall development costs and shorter development timelines. Various data-driven and experimental approaches have been suggested for the identification of repurposable drug candidates; however, there are also major technological and regulatory challenges that need to be addressed. In this Review, we present approaches used for drug repurposing (also known as drug repositioning), discuss the challenges faced by the repurposing community and recommend innovative ways by which these challenges could be addressed to help realize the full potential of drug repurposing.
2,365 citations
TL;DR: The Connectivity Map project set out to answer the questions of how the screening process for biomedical research could be systematized and centralized, and hits found and hypotheses generated with something resembling an internet search engine.
Abstract: The ultimate objective of biomedical research is to connect human diseases with the genes that underlie them and drugs that treat them. But this remains a daunting task, and even the most inspired researchers still have to resort to laborious screens of genetic or chemical libraries. What if at least some parts of this screening process could be systematized and centralized? And hits found and hypotheses generated with something resembling an internet search engine? These are the questions the Connectivity Map project set out to answer.
822 citations
Cites background from "Gene expression-based chemical geno..."
...And in the second, we found a drug capable of reversing glucocorticoid resistance in acute lymphoblastic leukaemia (ALL) cell...
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TL;DR: Tests that predict the clinical outcome for patients on the basis of the genes expressed by their tumours are likely to increasingly affect patient management, heralding a new era of personalized medicine.
Abstract: Therapies for patients with cancer have changed gradually over the past decade, moving away from the administration of broadly acting cytotoxic drugs towards the use of more-specific therapies that are targeted to each tumour. To facilitate this shift, tests need to be developed to identify those individuals who require therapy and those who are most likely to benefit from certain therapies. In particular, tests that predict the clinical outcome for patients on the basis of the genes expressed by their tumours are likely to increasingly affect patient management, heralding a new era of personalized medicine.
564 citations
TL;DR: The existence of several “metabolic checkpoints” is proposed, refined molecular mechanisms that sense a panel of metabolic variables and emit one or more signals controlling cell fate, which might allow for the development of novel pharmacological approaches that block or stimulate cell death by inducing specific metabolic alterations.
Abstract: Beyond their contribution to basic metabolism, the major cellular organelles, in particular mitochondria, can determine whether cells respond to stress in an adaptive or suicidal manner. Thus, mitochondria can continuously adapt their shape to changing bioenergetic demands as they are subjected to quality control by autophagy, or they can undergo a lethal permeabilization process that initiates apoptosis. Along similar lines, multiple proteins involved in metabolic circuitries, including oxidative phosphorylation and transport of metabolites across membranes, may participate in the regulated or catastrophic dismantling of organelles. Many factors that were initially characterized as cell death regulators are now known to physically or functionally interact with metabolic enzymes. Thus, several metabolic cues regulate the propensity of cells to activate self-destructive programs, in part by acting on nutrient sensors. This suggests the existence of "metabolic checkpoints" that dictate cell fate in response to metabolic fluctuations. Here, we discuss recent insights into the intersection between metabolism and cell death regulation that have major implications for the comprehension and manipulation of unwarranted cell loss.
519 citations
TL;DR: The current knowledge of the role of BCL2 family members in cancer development and response to therapy, focusing on targeted therapeutics, recent progress in the development of apoptotic biomarkers, and therapeutic strategies designed to overcome deficiencies in apoptosis are summarized.
Abstract: The ability of cancer cells to suppress apoptosis is critical for carcinogenesis. The BCL2 family proteins comprise the sentinel network that regulates the mitochondrial or intrinsic apoptotic response. Recent advances in our understanding of apoptotic signaling pathways have enabled methods to identify cancers that are “primed” to undergo apoptosis, and have revealed potential biomarkers that may predict which cancers will undergo apoptosis in response to specific therapies. Complementary efforts have focused on developing novel drugs that directly target antiapoptotic BCL2 family proteins. In this review, we summarize the current knowledge of the role of BCL2 family members in cancer development and response to therapy, focusing on targeted therapeutics, recent progress in the development of apoptotic biomarkers, and therapeutic strategies designed to overcome deficiencies in apoptosis.
Significance: Apoptosis, long known to be important for response to conventional cytotoxic chemotherapy, has more recently been shown to be essential for the efficacy of targeted therapies. Approaches that increase the likelihood of a cancer to undergo apoptosis following therapy may help improve targeted treatment strategies. Cancer Discov; 5(5); 475–87. ©2015 AACR .
469 citations
Cites background from "Gene expression-based chemical geno..."
...Wei and colleagues (166) used a chemical genomic screen to identify several compounds, including anthracycline chemotherapeutics (e....
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References
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TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Abstract: Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.
34,830 citations
TL;DR: This work has been supported by the Department of the Army and the National Institutes of Health, and the author acknowledges the support and encouragement of the National Cancer Institute.
28,811 citations
"Gene expression-based chemical geno..." refers background in this paper
...Defective apoptosis is a hallmark of cancer (Hanahan and Weinberg, 2000), and the ability to activate the apoptotic program is an important determinant of efficacy for anticancer drugs (Fesik, 2005; Reed, 1995)....
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TL;DR: DNA microarray analysis on primary breast tumours of 117 young patients is used and supervised classification is applied to identify a gene expression signature strongly predictive of a short interval to distant metastases (‘poor prognosis’ signature) in patients without tumour cells in local lymph nodes at diagnosis, providing a strategy to select patients who would benefit from adjuvant therapy.
Abstract: Breast cancer patients with the same stage of disease can have markedly different treatment responses and overall outcome. The strongest predictors for metastases (for example, lymph node status and histological grade) fail to classify accurately breast tumours according to their clinical behaviour. Chemotherapy or hormonal therapy reduces the risk of distant metastases by approximately one-third; however, 70-80% of patients receiving this treatment would have survived without it. None of the signatures of breast cancer gene expression reported to date allow for patient-tailored therapy strategies. Here we used DNA microarray analysis on primary breast tumours of 117 young patients, and applied supervised classification to identify a gene expression signature strongly predictive of a short interval to distant metastases ('poor prognosis' signature) in patients without tumour cells in local lymph nodes at diagnosis (lymph node negative). In addition, we established a signature that identifies tumours of BRCA1 carriers. The poor prognosis signature consists of genes regulating cell cycle, invasion, metastasis and angiogenesis. This gene expression profile will outperform all currently used clinical parameters in predicting disease outcome. Our findings provide a strategy to select patients who would benefit from adjuvant therapy.
9,664 citations
TL;DR: The identification of critical control points in the cell death pathway has yielded fundamental insights for basic biology, as well as provided rational targets for new therapeutics.
4,741 citations
"Gene expression-based chemical geno..." refers background in this paper
...Members of the BCL2 protein family play critical roles in the intrinsic apoptotic program controlling whether an apoptotic signal will result in cell death (Danial and Korsmeyer, 2004)....
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...In response to various apoptotic stimuli, proapoptotic BH3-only members induce activation of BAX and BAK, and cytochrome c release from mitochondria, thus triggering activation of caspases through the apoptosome complex (Danial and Korsmeyer, 2004)....
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...Conversely, antiapoptotic members such BCL2, BCL-XL, or MCL1 antagonize BH3-only proteins, thereby inhibiting BAX and BAK activation and apoptosis (Danial and Korsmeyer, 2004)....
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TL;DR: The first installment of a reference collection of gene-expression profiles from cultured human cells treated with bioactive small molecules is created, and it is demonstrated that this “Connectivity Map” resource can be used to find connections among small molecules sharing a mechanism of action, chemicals and physiological processes, and diseases and drugs.
Abstract: To pursue a systematic approach to the discovery of functional connections among diseases, genetic perturbation, and drug action, we have created the first installment of a reference collection of gene-expression profiles from cultured human cells treated with bioactive small molecules, together with pattern-matching software to mine these data. We demonstrate that this "Connectivity Map" resource can be used to find connections among small molecules sharing a mechanism of action, chemicals and physiological processes, and diseases and drugs. These results indicate the feasibility of the approach and suggest the value of a large-scale community Connectivity Map project.
4,429 citations
"Gene expression-based chemical geno..." refers background or methods in this paper
...scribed (Lamb et al., 2006) and combined to produce a ‘‘connectivity score....
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...To test this hypothesis, we made use of a database of 453 genome-wide expression profiles derived from the treatment of a variety of human cell lines with 164 bioactive small molecules, the majority of which are established pharmaceuticals or compounds with known activities, referred to as the Connectivity Map (Table S1) (Lamb et al., 2006)....
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