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162 articles

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Jan 2020 • Clinical Cancer Research

Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms for the CIMAC-CIDC network

Zexian Zeng, Jingxin Fu, Carrie Cibulskis, Aashna Jhaveri, Curtis Gumbs, Biswajit Das, Beatriz Sanchez-Espiridion, Sylvie Janssens, Len Taing, Jin Wang, James Lindsay, Tomas Vilimas, Jianhua Zhang, Collin Tokheim, Avinash Das Sahu, Peng Jiang, Chunhua Yan, Dzifa Y Duose, Ethan Cerami, Li Chen, David Cohen, Qing-Rong Chen, Rebecca A Enos, Xin Huang, J Jack Lee, Yang Liu, Donna S Neuberg, Cu Nguyen, Candace Patterson, Sachet A Shukla, Ming Tang, Junko Tsuji, Mohamed Uduman, Xiaoman Wang, Jason L Weirather, Jijun Yu, Joyce Yu, Jianjun Zhang, Jiexin Zhang, Daoud Meerzaman, Magdalena Thurin, P Andrew Futreal, Chris Karlovich, Stacey B Gabriel, Ignacio I Wistuba, Xiaole Shirley Liu, Catherine Wu

Purpose: Whole-exome (WES) and RNA-sequencing (RNA-seq) are key components of cancer immunogenomic analyses. To evaluate the consistency of tumor WES and RNA-seq profiling platforms across different centers, the Cancer Immune Monitoring and Analysis Centers (CIMACs) and the Cancer Immunologic Data Commons (CIDC) conducted a systematic harmonization study. Experimental Design: DNA and RNA were centrally extracted from fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) non-small cell lung carcinoma (NSCLC) tumors and distributed to three centers for WES and RNA-seq profiling. In addition, two 10-plex HapMap cell-line pools with known mutations were used to evaluate the accuracy of the WES platforms. Results: The WES platforms achieved high precision (> 0.98) and recall (> 0.87) on the HapMap pools when evaluated on loci using > 50X common coverage. Non …

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2020 • Mol Cell

Synthetic lethal and resistance interaction with BET Bromodomain inhibitors in triple-negative breast cancer

BET bromodomain inhibitors (BBDIs) are candidate therapeutic agents for triple-negative breast cancer (TNBC) and other cancer types, but inherent and acquired resistance to BBDIs limits their potential clinical use. Using CRISPR and small-molecule inhibitor screens combined with comprehensive molecular profiling of BBDI response and resistance, we identified synthetic lethal interactions with BBDIs and genes that, when deleted, confer resistance. We observed synergy with regulators of cell cycle progression, YAP, AXL, and SRC signaling, and chemotherapeutic agents. We also uncovered functional similarities and differences among BRD2, BRD4, and BRD7. Although deletion of BRD2 enhances sensitivity to BBDIs, BRD7 loss leads to gain of TEAD-YAP chromatin binding and luminal features associated with BBDI resistance. Single-cell RNA-seq, ATAC-seq, and cellular barcoding analysis of BBDI …

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2020 • Genome Biology

Integrative analyses of single-cell transcriptome and regulome using MAESTRO

Liu XS Wang C, Sun D, Huang X, Wan C, Li Z, Han Y, Qin Q, Fan J, Qiu X, Xie Y, Meyer C, Brown M, Tang M, Long H, Liu T


2020 • Bioinformatics for Cancer Immunotherapy, 249-262, 2020

Computational deconvolution of tumor-infiltrating immune components with bulk tumor gene expression data

Bo Li, Taiwen Li, Jun S Liu, X Shirley Liu

Tumor-infiltrating immune cells play critical roles in immune-mediated tumor rejection and/or progression, and are key targets of immunotherapies. Estimation of different immune subsets becomes increasingly important with the decreased cost of high-throughput molecular profiling and the rapidly growing amount of cancer genomics data. Here, we present Tumor IMmune Estimation Resource (TIMER), an in silico deconvolution method for inference of tumor-infiltrating immune components. TIMER takes bulk tissue gene expression profiles measured with RNA-seq or microarray to evaluate the abundance of six immune cell types in the tumor microenvironment: B cell, CD4+ T cell, CD8+ T cell, neutrophil, macrophage, and dendritic cell. We further introduce its associated webserver for convenient, user-friendly analysis of tumor immune infiltrates across multiple cancer types.

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2020 • Nat Commun

Determinants of transcription factor regulatory range

Liu XS*# Chen C#, Zheng R, Tokheim C#, Dong X, Fan J, Wan C, Tang Q, Brown M, Liu JS, Meyer C


2020 • Genome Medicine

Large-scale public data reuse to model immunotherapy response and resistance

Liu XS* 215. Fu J, Li K, Zhang W, Wan C, Zhang J*, Jiang P*


2020 • Frontiers in Genetics

ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants

Mohith Manjunath, Yi Zhang, Shilu Zhang, Sushmita Roy, Pablo Perez-Pinera, Jun S Song

Over the past decade, hundreds of genome-wide association studies (GWAS) have implicated genetic variants in various diseases, including cancer. However, only few of these variants have been functionally characterized to date, mainly owing to the fact that the majority of the variants reside in noncoding regions of the human genome with unknown function. A comprehensive functional annotation of the candidate variants is thus necessary to fill the gap between the correlative findings of GWAS and the development of therapeutic strategies. By integrating large-scale multi-omics datasets such as the Cancer Genome Atlas (TCGA) and the Encyclopedia of DNA Elements (ENCODE), we performed multivariate linear regression analysis of expression quantitative trait loci, sequence permutation test of transcription factor binding perturbation, and modeling of three-dimensional chromatin interactions to analyze the potential molecular functions of 2,813 single nucleotide variants in 93 genomic loci associated with estrogen receptor-positive breast cancer. To facilitate rapid progress in functional genomics of breast cancer, we have created “Analysis of Breast Cancer GWAS” (ABC-GWAS), an interactive database of functional annotation of estrogen receptor-positive breast cancer GWAS variants. Our resource includes expression quantitative trait loci, long-range chromatin interaction predictions, and transcription factor binding motif analyses to prioritize putative target genes, causal variants and transcription factors. An embedded genome browser also facilitates convenient visualization of the GWAS loci in genomic and epigenomic context. ABC …

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2020 • Cell Res

ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells

Meng F Liu X, Liu T, Shang Y, Dai P, Zhang W, Lee BJ, Huang M, Yang D, Wu Q, Liu DL, Zheng X, Zhou BO, Dong J, Yeap L, Hu J, Xiao T, Zha S, Casellas R, Liu XS

Programmed DNA recombination in mammalian cells occurs predominantly in a directional manner. While random DNA breaks are typically repaired both by deletion and by inversion at approximately equal proportions, V (D) J and class switch recombination (CSR) of immunoglobulin heavy chain gene overwhelmingly delete intervening sequences to yield productive rearrangement. What factors channel chromatin breaks to deletional CSR in lymphocytes is unknown. Integrating CRISPR knockout and chemical perturbation screening we here identify the Snf2-family helicase-like ERCC6L2 as one such factor. We show that ERCC6L2 promotes double-strand break end-joining and facilitates optimal CSR in mice. At the cellular levels, ERCC6L2 rapidly engages in DNA repair through its C-terminal domains. Mechanistically, ERCC6L2 interacts with other end-joining factors and plays a functionally redundant role …

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2020 • Genomics Proteomics Bioinformatics

CRISPR screens identify essential cell growth mediators in BRAF inhibitor-resistant melanoma

Liu XS Li Z, Wang B, Gu S, Peng J, Sahu A, Chen C, Han T, Shi S, Wang X, Traugh N, Liu H, Liu Y, Wu Q, Brown M, Xiao T, Boland G

BRAF is a serine/threonine kinase that harbors activating mutations in ∼7% of human malignancies and ∼60% of melanomas. Despite initial clinical responses to BRAF inhibitors, patients frequently develop drug resistance. To identify candidate therapeutic targets for BRAF inhibitor resistant melanoma, we conduct CRISPR screens in melanoma cells harboring an activating BRAF mutation that had also acquired resistance to BRAF inhibitors. To investigate the mechanisms and pathways enabling resistance to BRAF inhibitors in melanomas, we integrate expression, ATAC-seq, and CRISPR screen data. We identify the JUN family transcription factors and the ETS family transcription factor ETV5 as key regulators of CDK6, which together enable resistance to BRAF inhibitors in melanoma cells. Our findings reveal genes contributing to resistance to a selective BRAF inhibitor PLX4720, providing new insights into …

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2020 • iScience

Loss of H3K36 Methyltransferase SETD2 Impairs V(D)J Recombination during Lymphoid Development

Armstrong SA 214. Chu SH, Chabon JR, Matovina CN, Chen BR, Zhang J, Kumar V, Xiong Y, Callen E, Hung PJ, Feng Z, Koche RP, Liu XS, Chaudhuri J, Nussenzweig A, Sleckman BP

Repair of DNA double-stranded breaks (DSBs) during lymphocyte development is essential for V(D)J recombination and forms the basis of immunoglobulin variable region diversity. Understanding of this process in lymphogenesis has historically been centered on the study of RAG1/2 recombinases and a set of classical non-homologous end-joining factors. Much less has been reported regarding the role of chromatin modifications on this process. Here, we show a role for the non-redundant histone H3 lysine methyltransferase, Setd2, and its modification of lysine-36 trimethylation (H3K36me3), in the processing and joining of DNA ends during V(D)J recombination. Loss leads to mis-repair of Rag-induced DNA DSBs, especially when combined with loss of Atm kinase activity. Furthermore, loss reduces immune repertoire and a severe block in lymphogenesis as well as causes post-mitotic neuronal apoptosis …

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Oct 2019 • Journal of vision

Contributions of foveal and non-foveal retina to the human eye's focusing response

Vivek Labhishetty, Steven A Cholewiak, Martin S Banks

The human eye changes focus—accommodates—to minimize blur in the retinal image. Previous work has shown that stimulation of nonfoveal retina can produce accommodative responses when no competing stimulus is presented to the fovea. In everyday situations it is very common for the fovea and other parts of the retina to be stimulated simultaneously. We examined this situation by asking how nonfoveal retina contributes to accommodation when the fovea is also stimulated. There were three experimental conditions.(a) Real change in which stimuli of different sizes, centered on the fovea, were presented at different optical distances. Accommodation was, as expected, robust because there was no conflicting stimulation of other parts of the retina.(b) Simulated change, no conflict in which stimuli of different sizes, again centered on the fovea, were presented at different simulated distances using rendered chromatic blur. Accommodation was robust in this condition because there was no conflict between the central and peripheral stimuli.(c) Simulated change, conflict in which a central disk (of different diameters) was presented along with an abutting peripheral annulus. The disk and annulus underwent opposite changes in simulated distance. Here we observed a surprisingly consistent effect of the peripheral annulus. For example, when the diameter of the central stimulus was 8 (thereby stimulating the fovea and parafovea), the abutting peripheral annulus had a significant effect on accommodation. We discuss how these results may help us understand other situations in which nonfixated targets affect the ability to focus on a fixated target …

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Oct 2019 • European journal of immunology

Guidelines for the use of flow cytometry and cell sorting in immunological studies

Andrea Cossarizza, Hyun‐Dong Chang, Andreas Radbruch, Andreas Acs, Dieter Adam, Sabine Adam‐Klages, William W Agace, Nima Aghaeepour, Mübeccel Akdis, Matthieu Allez, Larissa Nogueira Almeida, Giorgia Alvisi, Graham Anderson, Immanuel Andrä, Francesco Annunziato, Achille Anselmo, Petra Bacher, Cosima T Baldari, Sudipto Bari, Vincenzo Barnaba, Joana Barros‐Martins, Luca Battistini, Wolfgang Bauer, Sabine Baumgart, Nicole Baumgarth, Dirk Baumjohann, Bianka Baying, Mary Bebawy, Burkhard Becher, Wolfgang Beisker, Vladimir Benes, Rudi Beyaert, Alfonso Blanco, Dominic A Boardman, Christian Bogdan, Jessica G Borger, Giovanna Borsellino, Philip E Boulais, Jolene A Bradford, Dirk Brenner, Ryan R Brinkman, Anna ES Brooks, Dirk H Busch, Martin Büscher, Timothy P Bushnell, Federica Calzetti, Garth Cameron, Ilenia Cammarata, Xuetao Cao, Susanna L Cardell, Stefano Casola, Marco A Cassatella, Andrea Cavani, Antonio Celada, Lucienne Chatenoud, Pratip K Chattopadhyay, Sue Chow, Eleni Christakou, Luka Čičin‐Šain, Mario Clerici, Federico S Colombo, Laura Cook, Anne Cooke, Andrea M Cooper, Alexandra J Corbett, Antonio Cosma, Lorenzo Cosmi, Pierre G Coulie, Ana Cumano, Ljiljana Cvetkovic, Van Duc Dang, Chantip Dang‐Heine, Martin S Davey, Derek Davies, Sara De Biasi, Genny Del Zotto, Gelo Victoriano Dela Cruz, Michael Delacher, Silvia Della Bella, Paolo Dellabona, Günnur Deniz, Mark Dessing, James P Di Santo, Andreas Diefenbach, Francesco Dieli, Andreas Dolf, Thomas Dörner, Regine J Dress, Diana Dudziak, Michael Dustin, Charles‐Antoine Dutertre, Friederike Ebner, Sidonia BG Eckle, Matthias Edinger, Pascale Eede, Götz RA Ehrhardt, Marcus Eich, Pablo Engel, Britta Engelhardt, Anna Erdei, Charlotte Esser, Bart Everts, Maximilien Evrard, Christine S Falk, Todd A Fehniger, Mar Felipo‐Benavent, Helen Ferry, Markus Feuerer, Andrew Filby, Kata Filkor, Simon Fillatreau, Marie Follo, Irmgard Förster, John Foster, Gemma A Foulds, Britta Frehse, Paul S Frenette, Stefan Frischbutter, Wolfgang Fritzsche, David W Galbraith, Anastasia Gangaev, Natalio Garbi, Brice Gaudilliere, Ricardo T Gazzinelli, Jens Geginat, Wilhelm Gerner, Nicholas A Gherardin, Kamran Ghoreschi, Lara Gibellini, Florent Ginhoux, Keisuke Goda, Dale I Godfrey, Christoph Goettlinger, Jose M González‐Navajas, Carl S Goodyear, Andrea Gori, Jane L Grogan, Daryl Grummitt, Andreas Grützkau, Claudia Haftmann, Jonas Hahn, Hamida Hammad, Günter Hämmerling, Leo Hansmann, Goran Hansson, Christopher M Harpur, Susanne Hartmann, Andrea Hauser, Anja E Hauser, David L Haviland

These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer‐reviewed by leading experts in the field, making this an essential research companion.

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Sep 2019 • Journal of Vision

Real-time blur with chromatic aberration drives accommodation and depth perception

Steven A Cholewiak, Peter Shirley, Morgan McGuire, Martin S Banks

In computer-generated imagery and vision science, defocus blur is often rendered to simulate objects closer or farther than the focal plane. But depth-dependent optical effects, like longitudinal chromatic aberration (LCA), are not implemented in a physically correct manner. Recent evidence has shown that incorporating LCA into rendered images produces a powerful cue for driving accommodation and depth perception. But implementing correct LCA effects is computationally expensive. Applied implementations of defocus blur with LCA are possible, but require approximations in order to run in real-time. We investigated whether real-time implementation of blur with LCA using approximate blur kernels and simplified treatment of occlusions can still drive accommodation and improve perceived depth compared to conventional methods that do not incorporate LCA. We measured accommodative responses with an …

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Jul 2019 • Frontiers in Genetics, section Bioinformatics and Computational Biology

The cancer-associated genetic variant rs3903072 modulates immune cells in the tumor microenvironment

Y. Zhang, M. Manjunath, J. Yan, B.A. Baur, S. Zhang, S. Roy, J.S Song

Genome-wide association studies (GWAS) have hitherto identified several germline variants associated with cancer susceptibility, but the molecular functions of these risk modulators remain largely uncharacterized. Recent studies have begun to uncover the regulatory potential of non-coding GWAS SNPs by using epigenetic information in corresponding cancer cell types and matched normal tissues. However, this approach does not explore the potential effect of risk germline variants on other important cell types that constitute the microenvironment of tumor or its precursor. This paper presents evidence that the breast cancer-associated variant rs3903072 may regulate the expression of CTSW in tumor infiltrating lymphocytes. CTSW is a candidate tumor-suppressor gene, with expression highly specific to immune cells and also positively correlated with breast cancer patient survival. Integrative analyses suggest a putative causative variant in a GWAS-linked enhancer in lymphocytes that loops to the 3’ end of CTSW through three-dimensional chromatin interaction. Our work thus poses the possibility that a cancer-associated genetic variant could regulate a gene not only in the cell of cancer origin, but also in immune cells in the microenvironment, thereby modulating the immune surveillance by T lymphocytes and natural killer cells and affecting the clearing of early cancer initiating cells.

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Jul 2019 • Investigative Ophthalmology & Visual Science

Peripheral stimulation can override foveal stimulation in driving accommodation

Vivek Labhishetty, Steven Cholewiak, Martin S Banks

Purpose: Experiments suggest that hyperopic focus in the peripheral retina increases the risk of developing myopia. This implies that signed defocus can trigger eye growth. But does this mean blur in the periphery affects other oculomotor mechanisms such as accommodation? Stimulation of the human peripheral retina when no foveal stimulus is present elicits accommodation. But in natural viewing, the fovea and periphery are nearly always both stimulated. We investigated accommodative responses when the fovea and periphery are both stimulated, but with different signs of defocus.Methods: 10 participants (18-25 yrs) viewed black-white textures monocularly. The stimuli varied in depth (±1.5 D) sinusoidally (0.1, 0.2, 0.5, or 1.0 Hz). Three conditions were tested: Real Blur, Defocus+ LCA, and Defocus+ LCA Conflict. In Real Blur, the optical distance of the textures (disks subtending 1, 2, 4, 6, 8, or 14) was varied …

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Jul 2019 • Nucleic acids research

Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks

Shaojuan Li, Changxin Wan, Rongbin Zheng, Jingyu Fan, Xin Dong, Clifford A Meyer, X Shirley Liu

Characterizing the ontologies of genes directly regulated by a transcription factor (TF), can help to elucidate the TF’s biological role. Previously, we developed a widely used method, BETA, to integrate TF ChIP-seq peaks with differential gene expression (DGE) data to infer direct target genes. Here, we provide Cistrome-GO, a website implementation of this method with enhanced features to conduct ontology analyses of gene regulation by TFs in human and mouse. Cistrome-GO has two working modes: solo mode for ChIP-seq peak analysis; and ensemble mode, which integrates ChIP-seq peaks with DGE data. Cistrome-GO is freely available at http://go.cistrome.org/.

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Jun 2019 • Nature genetics

Publisher Correction: Landscape of B cell immunity and related immune evasion in human cancers

Xihao Hu, Jian Zhang, Jin Wang, Jingxin Fu, Taiwen Li, Xiaoqi Zheng, Binbin Wang

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Jun 2019 • Oncoimmunology

Localization-associated immune phenotypes of clonally expanded tumor-infiltrating T cells and distribution of their target antigens in rectal cancer

Livius Penter, Kerstin Dietze, Julia Ritter, Maria Fernanda Lammoglia Cobo, Josefin Garmshausen, Felix Aigner, Lars Bullinger, Holger Hackstein, Sandra Wienzek-Lischka, Thomas Blankenstein, Michael Hummel, Klaus Dornmair, Leo Hansmann

The degree and type of T cell infiltration influence rectal cancer prognosis regardless of classical tumor staging. We asked whether clonal expansion and tumor infiltration are restricted to selected-phenotype T cells; which clones are accessible in peripheral blood; and what the spatial distribution of their target antigens is.From five rectal cancer patients, we isolated paired tumor-infiltrating T cells (TILs) and T cells from unaffected rectum mucosa (TUM) using 13-parameter FACS single cell index sorting. TCRαβ sequences, cytokine, and transcription factor expression were determined with single cell sequencing. TILs and TUM occupied distinct phenotype compartments and clonal expansion predominantly occurred within CD8+ T cells. Expanded TIL clones identified by paired TCRαβ sequencing and exclusively detectable in the tumor showed characteristic PD-1 and TIM-3 expression. TCRβ repertoire sequencing …

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May 2019 • University of Illinois at Urbana-Champaign, 2019

Functional interpretation of cancer-associated genetic variants

Yi Zhang

Genome-wide association studies have hitherto identified several common genetic variants that may significantly modulate cancer susceptibility. However, the precise molecular mechanisms behind these associations remain largely uncharacterized, creating barriers to understanding the biological processes behind oncogenesis. This thesis presents an integrated computational method for identifying functional regulatory variants associated with cancer and for revealing their precise gene-regulation role by combining analyses of heterogeneous high-throughput sequencing data. Application of the method to breast cancer susceptibility regions reveals functional variants and their perturbation on cis-regulatory elements that act on cancer-associated genes. It is also shown that a cancer-associated variant may interact with the tumor microenvironment. Overall, these computational methods built on multi-omics data have helped move toward the goal of understanding the genotype-phenotype association for personalized medicine.

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Mar 2019 • Cancer cell

ARv7 represses Tumor-Suppressor genes in Castration-Resistant prostate cancer

Laura Cato, Jonas de Tribolet-Hardy, Irene Lee, Jaice T Rottenberg, Ilsa Coleman, Diana Melchers, René Houtman, Tengfei Xiao, Wei Li, Takuma Uo, Shihua Sun, Nane C Kuznik, Bettina Göppert, Fatma Ozgun, Martin E Van Royen, Adriaan B Houtsmuller, Raga Vadhi, Prakash K Rao, Lewyn Li, Steven P Balk, Robert B Den, Bruce J Trock, R Jeffrey Karnes, Robert B Jenkins, Eric A Klein, Elai Davicioni, Friederike J Gruhl, Henry W Long, X Shirley Liu, Andrew CB Cato, Nathan A Lack, Peter S Nelson, Stephen R Plymate, Anna C Groner, Myles Brown

Androgen deprivation therapy for prostate cancer (PCa) benefits patients with early disease, but becomes ineffective as PCa progresses to a castration-resistant state (CRPC). Initially CRPC remains dependent on androgen receptor (AR) signaling, often through increased expression of full-length AR (ARfl) or expression of dominantly active splice variants such as ARv7. We show in ARv7-dependent CRPC models that ARv7 binds together with ARfl to repress transcription of a set of growth-suppressive genes. Expression of the ARv7-repressed targets and ARv7 protein expression are negatively correlated and predicts for outcome in PCa patients. Our results provide insights into the role of ARv7 in CRPC and define a set of potential biomarkers for tumors dependent on ARv7.

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Mar 2019 • Nature protocols

Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute

Binbin Wang, Mei Wang, Wubing Zhang, Tengfei Xiao, Chen-Hao Chen, Alexander Wu, Feizhen Wu, Nicole Traugh, Xiaoqing Wang, Ziyi Li, Shenglin Mei, Yingbo Cui, Sailing Shi, Jesse Jonathan Lipp, Matthias Hinterndorfer, Johannes Zuber, Myles Brown, Wei Li, X Shirley Liu

Genome-wide screening using CRISPR coupled with nuclease Cas9 (CRISPR–Cas9) is a powerful technology for the systematic evaluation of gene function. Statistically principled analysis is needed for the accurate identification of gene hits and associated pathways. Here, we describe how to perform computational analysis of CRISPR screens using the MAGeCKFlute pipeline. MAGeCKFlute combines the MAGeCK and MAGeCK-VISPR algorithms and incorporates additional downstream analysis functionalities. MAGeCKFlute is distinguished from other currently available tools by its comprehensive pipeline, which contains a series of functions for analyzing CRISPR screen data. This protocol explains how to use MAGeCKFlute to perform quality control (QC), normalization, batch effect removal, copy-number bias correction, gene hit identification and downstream functional enrichment analysis for CRISPR …

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