A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.
TL;DR: The expanded CMap is reported, made possible by a new, low-cost, high-throughput reduced representation expression profiling method that is shown to be highly reproducible, comparable to RNA sequencing, and suitable for computational inference of the expression levels of 81% of non-measured transcripts.
About: This article is published in Cell.The article was published on 2017-11-30 and is currently open access. It has received 1943 citations till now.
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Henry Ford Health System1, Harvard University2, Stanford University3, University of Hasselt4, University of Texas MD Anderson Cancer Center5, Nencki Institute of Experimental Biology6, École Polytechnique Fédérale de Lausanne7, Sage Bionetworks8, Université libre de Bruxelles9, Poznan University of Medical Sciences10, George Washington University11, Cold Spring Harbor Laboratory12, University of Kansas13, University of California, Santa Cruz14, University of North Carolina at Chapel Hill15, Van Andel Institute16
TL;DR: Novel stemness indices for assessing the degree of oncogenic dedifferentiation are provided and it is found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors.
1,099 citations
Cites methods from "A Next Generation Connectivity Map:..."
...To further investigate about mechanism of actions (MoA) and drug-target we performed specific analysis within Connectivity Map tools (https://clue.io/) (Subramanian et al., 2017)....
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...Connectivity Map (CMap) was recently updated (September 2017) (Subramanian et al., 2017), providing the end-users new functionalities and new graphical interface as web-server, previous registration (https://clue.io/) allowing easily the extraction of druginteraction knowledge using as input a…...
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TL;DR: A resistance program expressed by malignant cells that is associated with T cell exclusion and immune evasion is identified, and this study provides a high-resolution landscape of ICI-resistant cell states, identifies clinically predictive signatures, and suggests new therapeutic strategies to overcome immunotherapy resistance.
794 citations
Cites background or methods from "A Next Generation Connectivity Map:..."
...Moreover, there is a significant overlap between the perturbations that reverse the expression of the program’s repressed and induced components (p = 4.353 10 6, hypergeometric test), including the overexpression of IFN-g and IFN-b and the knockdown of MYC and CDK7 (Subramanian et al., 2017)....
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...Three genes (CDKN2C/ p18, CDKN1B/p27, andCDKN1A/p21) that inhibit CDK4 repress the program when overexpressed (Subramanian et al., 2017) (STARMethods), and the program ismore pronounced in cycling cells (Figures 1E, 2C, and S2E), where CDK4/6 are active....
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...The latter mirrors the significantly large number of Myc and CDK7 (direct) targets (Oki et al., 2018; Subramanian et al., 2005) in the program (p < 1 3 10 17, hypergeometric test)....
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...Indeed, the programs are enriched for Myc targets, even after removing RP genes (p 7.18 3 10 10) and are predicted to be repressed byMYC knockdown according to the Connectivity Map (Subramanian et al., 2017)....
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...353 10 (6), hypergeometric test), including the overexpression of IFN-g and IFN-b and the knockdown of MYC and CDK7 (Subramanian et al., 2017)....
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TL;DR: The extent, origins and consequences of genetic variation within human cell lines are studied, providing a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.
Abstract: Human cancer cell lines are the workhorse of cancer research. Although cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here we use genomic analyses of 106 human cell lines grown in two laboratories to show extensive clonal diversity. Further comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic diversification. Similar results were obtained with multiple strains of 13 additional cell lines. Notably, genetic changes were associated with differential activation of gene expression programs and marked differences in cell morphology and proliferation. Barcoding experiments showed that cell line evolution occurs as a result of positive clonal selection that is highly sensitive to culture conditions. Analyses of single-cell-derived clones demonstrated that continuous instability quickly translates into heterogeneity of the cell line. When the 27 MCF7 strains were tested against 321 anti-cancer compounds, we uncovered considerably different drug responses: at least 75% of compounds that strongly inhibited some strains were completely inactive in others. This study documents the extent, origins and consequences of genetic variation within cell lines, and provides a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.
601 citations
01 Dec 2016
TL;DR: Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions, and posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation.
Abstract: Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes-such as transcriptional profiles-at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS). Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions. We posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation. By decomposing many high content measurements into the effects of perturbations, their interactions, and diverse cell metadata, Perturb-seq dramatically increases the scope of pooled genomic assays.
539 citations
TL;DR: The current state-of-the art of AI-assisted pharmaceutical discovery is discussed, including applications in structure- and ligand-based virtual screening, de novo drug design, physicochemical and pharmacokinetic property prediction, drug repurposing, and related aspects.
Abstract: Artificial intelligence (AI), and, in particular, deep learning as a subcategory of AI, provides opportunities for the discovery and development of innovative drugs. Various machine learning approaches have recently (re)emerged, some of which may be considered instances of domain-specific AI which have been successfully employed for drug discovery and design. This review provides a comprehensive portrayal of these machine learning techniques and of their applications in medicinal chemistry. After introducing the basic principles, alongside some application notes, of the various machine learning algorithms, the current state-of-the art of AI-assisted pharmaceutical discovery is discussed, including applications in structure- and ligand-based virtual screening, de novo drug design, physicochemical and pharmacokinetic property prediction, drug repurposing, and related aspects. Finally, several challenges and limitations of the current methods are summarized, with a view to potential future directions for AI-assisted drug discovery and design.
425 citations
References
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01 Dec 2016
TL;DR: Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions, and posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation.
Abstract: Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes-such as transcriptional profiles-at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS). Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions. We posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation. By decomposing many high content measurements into the effects of perturbations, their interactions, and diverse cell metadata, Perturb-seq dramatically increases the scope of pooled genomic assays.
539 citations
TL;DR: Experimental validation that an antiulcer drug and an antiepileptic can be reused for lung cancer and inflammatory bowel disease reinforces the promise of the computational approach to discover new drug therapies for IBD in silico.
Abstract: Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract for which there are few safe and effective therapeutic options for long-term treatment and disease maintenance. Here, we applied a computational approach to discover new drug therapies for IBD in silico, using publicly available molecular data reporting gene expression in IBD samples and 164 small-molecule drug compounds. Among the top compounds predicted to be therapeutic for IBD by our approach were prednisolone, a corticosteroid used to treat IBD, and topiramate, an anticonvulsant drug not previously described to have efficacy for IBD or any related disorders of inflammation or the gastrointestinal tract. Using a trinitrobenzenesulfonic acid (TNBS)–induced rodent model of IBD, we experimentally validated our topiramate prediction in vivo. Oral administration of topiramate significantly reduced gross pathological signs and microscopic damage in primary affected colon tissue in the TNBS-induced rodent model of IBD. These findings suggest that topiramate might serve as a therapeutic option for IBD in humans and support the use of public molecular data and computational approaches to discover new therapeutic options for disease.
525 citations
"A Next Generation Connectivity Map:..." refers background in this paper
..., 2009), and new therapeutic hypotheses for the treatment of inflammatory bowel disease (Dudley et al., 2011) and cancer (Singh et al....
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TL;DR: It is discovered that Celastrol, a pentacyclic triterpene extracted from the roots of Tripterygium Wilfordi (thunder god vine) plant, is a powerful anti-obesity agent and a promising agent for the pharmacological treatment of obesity.
502 citations
"A Next Generation Connectivity Map:..." refers background in this paper
..., 2015), celastrol as a leptin sensitizer (Liu et al., 2015), compounds targeting COX2 and ADRA2A as potential diabetes treatments (Zhang et al....
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TL;DR: It is found that the number of CRISPR/Cas9-induced DNA breaks dictates a gene-independent antiproliferative response in cells, which has practical implications for using CRISpr/cas9 to interrogate cancer gene function and illustrate that cancer cells are highly sensitive to site-specific DNA damage, which may provide a path to novel therapeutic strategies.
Abstract: The CRISPR-Cas9 system enables genome editing and somatic cell genetic screens in mammalian cells. We performed genome scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation/survival and found a strong correlation between increased gene copy number and decreased cell viability after genome editing. Within regions of copy number gain, CRISPR-Cas9 targeting of both expressed and unexpressed genes, as well as intergenic loci, led to significantly decreased cell proliferation through induction of a G2 cell cycle arrest. By examining single guide RNAs that map to multiple genomic sites, we found that this cell response to CRISPR-Cas9 editing correlated strongly with the number of target loci. These observations indicate that genome targeting by CRISPR-Cas9 elicits a gene-independent anti-proliferative cell response. This effect has important practical implications for interpretation of CRISPR-Cas9 screening data and confounds the use of this technology for identification of essential genes in amplified regions.
494 citations
"A Next Generation Connectivity Map:..." refers background in this paper
...First, we and others have shown that CRISPR/Cas9-based genome editing results in non-specific toxicity directly proportional to the number of cuts to the genome (Aguirre et al., 2016)....
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TL;DR: The continued MAPK signaling-based resistance identified in patients suggests that alternative dosing of current agents, more potent RAF/MEK inhibitors, and/or inhibition of the downstream kinase ERK may be needed for durable control of BRAF-mutant melanoma.
Abstract: Treatment of BRAF-mutant melanoma with combined dabrafenib and trametinib, which target RAF and the downstream MAP-ERK kinase (MEK)1 and MEK2 kinases, respectively, improves progression-free survival and response rates compared with dabrafenib monotherapy. Mechanisms of clinical resistance to combined RAF/MEK inhibition are unknown. We performed whole-exome sequencing (WES) and whole-transcriptome sequencing (RNA-seq) on pretreatment and drug-resistant tumors from five patients with acquired resistance to dabrafenib/trametinib. In three of these patients, we identified additional mitogen-activated protein kinase (MAPK) pathway alterations in the resistant tumor that were not detected in the pretreatment tumor, including a novel activating mutation in MEK2 (MEK2(Q60P)). MEK2(Q60P) conferred resistance to combined RAF/MEK inhibition in vitro, but remained sensitive to inhibition of the downstream kinase extracellular signal-regulated kinase (ERK). The continued MAPK signaling-based resistance identified in these patients suggests that alternative dosing of current agents, more potent RAF/MEK inhibitors, and/or inhibition of the downstream kinase ERK may be needed for durable control of BRAF-mutant melanoma.
438 citations
"A Next Generation Connectivity Map:..." refers background in this paper
...Analysis at the time of relapse showed that several patients showed strong negative connectivity to these same CMap perturbations, suggestive of reactivation of the MAP kinase pathway—a known mechanism of drug resistance in melanoma (Wagle et al., 2014)....
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