1
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Yao D, Tycko J, Oh JW, Bounds LR, Gosai SJ, Lataniotis L, Mackay-Smith A, Doughty BR, Gabdank I, Schmidt H, Guerrero-Altamirano T, Siklenka K, Guo K, White AD, Youngworth I, Andreeva K, Ren X, Barrera A, Luo Y, Yardımcı GG, Tewhey R, Kundaje A, Greenleaf WJ, Sabeti PC, Leslie C, Pritykin Y, Moore JE, Beer MA, Gersbach CA, Reddy TE, Shen Y, Engreitz JM, Bassik MC, Reilly SK. Multicenter integrated analysis of noncoding CRISPRi screens. Nat Methods 2024; 21:723-734. [PMID: 38504114 PMCID: PMC11009116 DOI: 10.1038/s41592-024-02216-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/18/2024] [Indexed: 03/21/2024]
Abstract
The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE-gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome.
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Affiliation(s)
- David Yao
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
| | - Jin Woo Oh
- Departments of Biomedical Engineering and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lexi R Bounds
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Sager J Gosai
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Center for System Biology, Harvard University, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
| | - Lazaros Lataniotis
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
| | - Ava Mackay-Smith
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA
| | | | - Idan Gabdank
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Henri Schmidt
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tania Guerrero-Altamirano
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA
- Department of Biology, Duke University, Durham, NC, USA
| | - Keith Siklenka
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Katherine Guo
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alexander D White
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | | | - Kalina Andreeva
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Xingjie Ren
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Center for System Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christina Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuri Pritykin
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael A Beer
- Departments of Biomedical Engineering and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Timothy E Reddy
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Yin Shen
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jesse M Engreitz
- Department of Genetics, Stanford University, Stanford, CA, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Steven K Reilly
- Department of Genetics, Yale University, New Haven, CT, USA.
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Wang H, Canasto-Chibuque C, Kim JH, Hohl M, Leslie C, Reis-Filho JS, Petrini JH. Chronic Interferon Stimulated Gene Transcription Promotes Oncogene Induced Breast Cancer. bioRxiv 2023:2023.10.16.562529. [PMID: 37905095 PMCID: PMC10614814 DOI: 10.1101/2023.10.16.562529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The Mre11 complex (comprising Mre11, Rad50, Nbs1) is integral to the maintenance of genome stability. We previously showed that a hypomorphic Mre11 mutant mouse strain ( Mre11 ATLD1/ATLD1 ) was highly susceptible to oncogene induced breast cancer. Here we used a mammary organoid system to examine which Mre11 dependent responses are tumor suppressive. We found that Mre11 ATLD1/ATLD1 organoids exhibited an elevated interferon stimulated gene (ISG) signature and sustained changes in chromatin accessibility. This Mre11 ATLD1/ATLD1 phenotype depended on DNA binding of a nuclear innate immune sensor, IFI205. Ablation of Ifi205 in Mre11 ATLD1/ATLD1 organoids restored baseline and oncogene-induced chromatin accessibility patterns to those observed in WT . Implantation of Mre11 ATLD1/ATLD1 organoids and activation of oncogene led to aggressive metastatic breast cancer. This outcome was reversed in implanted Ifi205 -/- Mre11 ATLD1/ATLD1 organoids. These data reveal a connection between innate immune signaling and tumor suppression in mammary epithelium. Given the abundance of aberrant DNA structures that arise in the context of genome instability syndromes, the data further suggest that cancer predisposition in those contexts may be partially attributable to tonic innate immune transcriptional programs.
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Herrejon Chavez F, Luo H, Cifani P, Pine A, Chu KL, Joshi S, Barin E, Schurer A, Chan M, Chang K, Han GYQ, Pierson AJ, Xiao M, Yang X, Kuehm LM, Hong Y, Nguyen DTT, Chiosis G, Kentsis A, Leslie C, Vu LP, Kharas MG. RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells. Nat Commun 2023; 14:2290. [PMID: 37085479 PMCID: PMC10121618 DOI: 10.1038/s41467-023-38001-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 04/11/2023] [Indexed: 04/23/2023] Open
Abstract
Tissue homeostasis is maintained after stress by engaging and activating the hematopoietic stem and progenitor compartments in the blood. Hematopoietic stem cells (HSCs) are essential for long-term repopulation after secondary transplantation. Here, using a conditional knockout mouse model, we revealed that the RNA-binding protein SYNCRIP is required for maintenance of blood homeostasis especially after regenerative stress due to defects in HSCs and progenitors. Mechanistically, we find that SYNCRIP loss results in a failure to maintain proteome homeostasis that is essential for HSC maintenance. SYNCRIP depletion results in increased protein synthesis, a dysregulated epichaperome, an accumulation of misfolded proteins and induces endoplasmic reticulum stress. Additionally, we find that SYNCRIP is required for translation of CDC42 RHO-GTPase, and loss of SYNCRIP results in defects in polarity, asymmetric segregation, and dilution of unfolded proteins. Forced expression of CDC42 recovers polarity and in vitro replating activities of HSCs. Taken together, we uncovered a post-transcriptional regulatory program that safeguards HSC self-renewal capacity and blood homeostasis.
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Affiliation(s)
- Florisela Herrejon Chavez
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Alli Pine
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karen L Chu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell School of Medical Sciences, New York, NY, USA
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ersilia Barin
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Program of the Weill Cornell Graduate School of Medicine Sciences, New York, NY, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mandy Chan
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn Chang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Grace Y Q Han
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aspen J Pierson
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Xiao
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Xuejing Yang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yuning Hong
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Diu T T Nguyen
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA
| | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ly P Vu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Michael G Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Ladewig E, Nazir A, Leslie C, Sawyers C. Abstract 2048: Mutations in FOXA1 alter chromatin remodeling and cell fate in prostate organoids. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-2048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Genomic analysis of targeted patient tumor sequencing identified frequent mutations, 41% in prostate cancer (Li, et al., 2020) in the gene FOXA1, a developmentally important pioneer transcription factor (TF) in mammary and prostate tissues. Previous work by our group and others has shown that these FOXA1 mutations alter global chromatin accessibility and promote growth in prostate cells (Adams, 2019), but the underlying molecular details, including the identity of partner TFs, remain unclear. To address this topic, we generated mouse prostate organoids expressing Foxa1 alleles harboring three distinct classes of mutations: (i) overexpression of WT Foxa1 (reflecting focal gene amplification seen in tumors), (ii) a series of mutants within the Wing2region of the forkhead binding domain (FHBD) and (iii) a mutant bearing a stop codon after the FHBD to represent a series of C-terminal truncation mutants. We performed single nucleus multiome sequencing to obtain gene expression (snRNA-seq) and chromatin accessibility (snATAC-seq) readouts from the same individual nuclei. Whereas each Foxa1 mutant has distinct, often mutant-specific features, several themes emerge. These include alterations in the relative proportion of stem-like (L2) luminal cells vs secretory (L1) luminal cells as well as changes in luminal or basal gene signatures, increased androgen receptor signaling output, and enrichment for motifs of distinct classes of partner TFs. For example, cells expressing the truncation mutant show gain in the accessibility of Gata3 and Pou2f1 TF binding motifs, as well as enhanced numbers of L1-like luminal cells. Functional studies demonstrate that Pou2f1 is specifically required for the pro-luminal phenotype in cells expressing the truncation mutant whereas Gata3 plays a more general pro-luminal role. Correlations in motif accessibility and transcription factor expression across single cells further revealed a composite androgen receptor (AR)-FOXA1 motif enriched in the pro-luminal truncation mutant, while the canonical AR motif was enriched in pro-basal cell mutants. Finally, Foxa1 mutants cooperative with Trp53 and Pten loss in orthotopic prostate tumorigenicity assays, most strikingly manifest by reversion of the basal-like features characteristic of Trp53/Pten loss tumors to Ck8+ luminal adenocarcinoma histology, mirroring that seen in Foxa1-mutant human prostate cancer tumors in mice. Thus, mutant Foxa1 alleles cooperate with canonical prostate cancer tumor suppressors and alter the histologic phenotype of prostate cancers in mice through the activation of basal or luminal lineage differentiation programs.
Citation Format: Erik Ladewig, Abbas Nazir, Christina Leslie, Charles Sawyers. Mutations in FOXA1 alter chromatin remodeling and cell fate in prostate organoids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2048.
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Affiliation(s)
- Erik Ladewig
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abbas Nazir
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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5
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Kshirsagar M, Yuan H, Ferres JL, Leslie C. BindVAE: Dirichlet variational autoencoders for de novo motif discovery from accessible chromatin. Genome Biol 2022; 23:174. [PMID: 35971180 PMCID: PMC9380350 DOI: 10.1186/s13059-022-02723-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
We present a novel unsupervised deep learning approach called BindVAE, based on Dirichlet variational autoencoders, for jointly decoding multiple TF binding signals from open chromatin regions. BindVAE can disentangle an input DNA sequence into distinct latent factors that encode cell-type specific in vivo binding signals for individual TFs, composite patterns for TFs involved in cooperative binding, and genomic context surrounding the binding sites. On the task of retrieving the motifs of expressed TFs in a given cell type, BindVAE is competitive with existing motif discovery approaches.
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Affiliation(s)
| | - Han Yuan
- Calico Life Sciences, South San Francisco, CA, USA
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6
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Ladewig E, Michelini F, Jhaveri K, Castel P, Carmona J, Fairchild L, Zuniga AG, Arruabarrena-Aristorena A, Cocco E, Blawski R, Kittane S, Zhang Y, Sallaku M, Baldino L, Hristidis V, Chandarlapaty S, Abdel-Wahab O, Leslie C, Scaltriti M, Toska E. The oncogenic PI3K-induced transcriptomic landscape reveals key functions in splicing and gene expression regulation. Cancer Res 2022; 82:2269-2280. [PMID: 35442400 DOI: 10.1158/0008-5472.can-22-0446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
The PI3K pathway regulates proliferation, survival, and metabolism and is frequently activated across human cancers. A comprehensive elucidation of how this signaling pathway controls transcriptional and co-transcriptional processes could provide new insights into the key functions of PI3K signaling in cancer. Here, we undertook a transcriptomic approach to investigate genome-wide gene expression and transcription factor (TF) activity changes, as well as splicing and isoform usage dynamics, downstream of PI3K. These analyses uncovered widespread alternatively spliced (AS) isoforms linked to proliferation, metabolism, and splicing in PIK3CA mutant cells, which were reversed by inhibition of PI3Kα. Analysis of paired tumor biopsies from PIK3CA-mutated breast cancer patients undergoing treatment with PI3Kα inhibitors identified widespread splicing alterations that affect specific isoforms in common with the preclinical models, and these alterations, namely PTK2/FRNK and AFMID isoforms, were validated as functional drivers of cancer cell growth or migration. Mechanistically, isoform-specific splicing factors mediated PI3K-dependent RNA splicing. Treatment with splicing inhibitors rendered breast cancer cells more sensitive to the PI3Kα inhibitor alpelisib, resulting in greater growth inhibition than alpelisib alone. This study provides the first comprehensive analysis of widespread splicing alterations driven by oncogenic PI3K in breast cancer. The atlas of PI3K-mediated splicing programs establishes a key role for the PI3K pathway in regulating splicing, opening new avenues for exploiting PI3K signaling as a therapeutic vulnerability in breast cancer.
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Affiliation(s)
- Erik Ladewig
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Komal Jhaveri
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
| | - Pau Castel
- NYU Langone, New York, NY, United States
| | - Javier Carmona
- Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Lauren Fairchild
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Adler G Zuniga
- Johns Hopkins University School of Medicine, United States
| | | | | | - Ryan Blawski
- Johns Hopkins University School of Medicine, United States
| | - Srushti Kittane
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Yuhan Zhang
- Johns Hopkins University, Baltimore, United States
| | | | - Laura Baldino
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | | | - Omar Abdel-Wahab
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Christina Leslie
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Eneda Toska
- Johns Hopkins University, Baltimore, United States
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7
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Akagbosu B, Tayyebi Z, Shibu G, Paucar Iza YA, Deep D, Parisotto YF, Fisher L, Pasolli HA, Thevin V, Elmentaite R, Knott M, Hemmers S, Jahn L, Friedrich C, Verter J, Wang ZM, van den Brink M, Gasteiger G, Grünewald TGP, Marie JC, Leslie C, Rudensky AY, Brown CC. Novel antigen-presenting cell imparts T reg-dependent tolerance to gut microbiota. Nature 2022; 610:752-760. [PMID: 36070798 PMCID: PMC9605865 DOI: 10.1038/s41586-022-05309-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/01/2022] [Indexed: 01/21/2023]
Abstract
Establishing and maintaining tolerance to self-antigens or innocuous foreign antigens is vital for the preservation of organismal health. Within the thymus, medullary thymic epithelial cells (mTECs) expressing autoimmune regulator (AIRE) have a critical role in self-tolerance through deletion of autoreactive T cells and promotion of thymic regulatory T (Treg) cell development1-4. Within weeks of birth, a separate wave of Treg cell differentiation occurs in the periphery upon exposure to antigens derived from the diet and commensal microbiota5-8, yet the cell types responsible for the generation of peripheral Treg (pTreg) cells have not been identified. Here we describe the identification of a class of RORγt+ antigen-presenting cells called Thetis cells, with transcriptional features of both mTECs and dendritic cells, comprising four major sub-groups (TC I-TC IV). We uncover a developmental wave of Thetis cells within intestinal lymph nodes during a critical window in early life, coinciding with the wave of pTreg cell differentiation. Whereas TC I and TC III expressed the signature mTEC nuclear factor AIRE, TC IV lacked AIRE expression and was enriched for molecules required for pTreg generation, including the TGF-β-activating integrin αvβ8. Loss of either major histocompatibility complex class II (MHCII) or ITGB8 by Thetis cells led to a profound impairment in intestinal pTreg differentiation, with ensuing colitis. By contrast, MHCII expression by RORγt+ group 3 innate lymphoid cells (ILC3) and classical dendritic cells was neither sufficient nor required for pTreg generation, further implicating TC IV as the tolerogenic RORγt+ antigen-presenting cell with an essential function in early life. Our studies reveal parallel pathways for the establishment of tolerance to self and foreign antigens in the thymus and periphery, respectively, marked by the involvement of shared cellular and transcriptional programmes.
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Affiliation(s)
- Blossom Akagbosu
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Zakieh Tayyebi
- grid.51462.340000 0001 2171 9952Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XTri-Institutional Program in Computational Biology and Medicine, Weill Cornell Graduate School, New York, NY USA
| | - Gayathri Shibu
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA ,grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA
| | - Yoselin A. Paucar Iza
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA ,grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA
| | - Deeksha Deep
- grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA ,grid.51462.340000 0001 2171 9952Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XTri-Institutional MD-PhD Program, Weill Cornell Medicine, The Rockefeller University and Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Yollanda Franco Parisotto
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Logan Fisher
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA ,grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA
| | - H. Amalia Pasolli
- grid.134907.80000 0001 2166 1519Electron Microscopy Resource Center, The Rockefeller University, New York, NY USA
| | - Valentin Thevin
- grid.462282.80000 0004 0384 0005Tumor Escape Resistance Immunity Department, CRCL, INSERM U1052, CNRS 5286, Centre Léon Bérard, Université de Lyon, Lyon, France ,Equipe Labellisée Ligue Nationale contre le Cancer, Lyon, France
| | - Rasa Elmentaite
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton UK
| | - Maximilian Knott
- grid.5252.00000 0004 1936 973XInstitute of PathologyFaculty of Medicine, LMU Munich, Munich, Germany
| | - Saskia Hemmers
- grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA ,grid.51462.340000 0001 2171 9952Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.26009.3d0000 0004 1936 7961Present Address: Department of Immunology, Duke University, Durham, NC USA
| | - Lorenz Jahn
- grid.51462.340000 0001 2171 9952Department of Immunology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Christin Friedrich
- grid.8379.50000 0001 1958 8658Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Jacob Verter
- grid.51462.340000 0001 2171 9952Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Zhong-Min Wang
- grid.51462.340000 0001 2171 9952Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Marcel van den Brink
- grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA ,grid.51462.340000 0001 2171 9952Department of Immunology, Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Georg Gasteiger
- grid.8379.50000 0001 1958 8658Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Thomas G. P. Grünewald
- grid.510964.fHopp—Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Julien C. Marie
- grid.462282.80000 0004 0384 0005Tumor Escape Resistance Immunity Department, CRCL, INSERM U1052, CNRS 5286, Centre Léon Bérard, Université de Lyon, Lyon, France ,Equipe Labellisée Ligue Nationale contre le Cancer, Lyon, France
| | - Christina Leslie
- grid.51462.340000 0001 2171 9952Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Alexander Y. Rudensky
- grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA ,grid.51462.340000 0001 2171 9952Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Chrysothemis C. Brown
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA ,grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA ,grid.51462.340000 0001 2171 9952Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.51462.340000 0001 2171 9952Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY USA
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8
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Abstract
Artificial intelligence and machine learning techniques are breaking into biomedical research and health care, which importantly includes cancer research and oncology, where the potential applications are vast. These include detection and diagnosis of cancer, subtype classification, optimization of cancer treatment and identification of new therapeutic targets in drug discovery. While big data used to train machine learning models may already exist, leveraging this opportunity to realize the full promise of artificial intelligence in both the cancer research space and the clinical space will first require significant obstacles to be surmounted. In this Viewpoint article, we asked four experts for their opinions on how we can begin to implement artificial intelligence while ensuring standards are maintained so as transform cancer diagnosis and the prognosis and treatment of patients with cancer and to drive biological discovery.
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Affiliation(s)
- Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| | - Christina Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Johan Lundin
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden.
- Institute for Molecular Medicine Finland - FIMM, University of Helsinki, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
| | - Georgia Tourassi
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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9
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Kim JK, Marco MR, Choi S, Qu X, Chen C, Elkabets M, Fairchild L, Chow O, Barriga FM, Dow LE, O’Rourke K, Szeglin B, Yarilin D, Fujisawa S, Manova‐Todorova K, Paty PB, Shia J, Leslie C, Joshua Smith J, Lowe S, Pelossof R, Sanchez‐Vega F, Garcia‐Aguilar J. KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix. Mol Oncol 2021; 15:2766-2781. [PMID: 33817986 PMCID: PMC8486594 DOI: 10.1002/1878-0261.12960] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 02/05/2023] Open
Abstract
Somatic mutations in the KRAS oncogene are associated with poor outcomes in locally advanced rectal cancer but the underlying biologic mechanisms are not fully understood. We profiled mRNA in 76 locally advanced rectal adenocarcinomas from patients that were enrolled in a prospective clinical trial and investigated differences in gene expression between KRAS mutant (KRAS-mt) and KRAS-wild-type (KRAS-wt) patients. We found that KRAS-mt tumors display lower expression of genes related to the tumor stroma and remodeling of the extracellular matrix. We validated our findings using samples from The Cancer Genome Atlas (TCGA) and also by performing immunohistochemistry (IHC) and immunofluorescence (IF) in orthogonal cohorts. Using in vitro and in vivo models, we show that oncogenic KRAS signaling within the epithelial cancer cells modulates the activity of the surrounding fibroblasts in the tumor microenvironment.
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Affiliation(s)
- Jin K. Kim
- Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Michael R. Marco
- Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Seo‐Hyun Choi
- Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Xuan Qu
- Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Chin‐Tung Chen
- Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Moshe Elkabets
- Shraga Segal Department of Microbiology and ImmunologyThe Cancer Research CentreFaculty of Health SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Lauren Fairchild
- Department of Computational and Systems BiologyMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Oliver Chow
- Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Francisco M. Barriga
- Department of Cancer Biology and GeneticsMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Lukas E. Dow
- Department of Cancer Biology and GeneticsMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Department of MedicineWeill‐Cornell Medical CollegeNew YorkNYUSA
| | - Kevin O’Rourke
- Department of Cancer Biology and GeneticsMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Department of MedicineWeill‐Cornell Medical CollegeNew YorkNYUSA
| | - Bryan Szeglin
- Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Dmitry Yarilin
- Molecular Cytology Core FacilityMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Sho Fujisawa
- Molecular Cytology Core FacilityMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | | | - Philip B. Paty
- Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Jinru Shia
- Department of PathologyMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Christina Leslie
- Department of Computational and Systems BiologyMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - J. Joshua Smith
- Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Human Oncology and Pathogenesis ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Scott Lowe
- Department of Cancer Biology and GeneticsMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Howard Hughes Medical InstituteMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Raphael Pelossof
- Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Francisco Sanchez‐Vega
- Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Department of Epidemiology and BiostatisticsMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
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10
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Nguyen D, Prieto C, Liu Z, Wheat J, Perez A, Gourkanti S, Chou T, Barin E, Velleca A, Rohwetter T, Chow A, Taggart J, Savino A, Hoskova K, Dhodapkar M, Schurer A, Barlowe T, Leslie C, Vu L, Steidl U, Rabandan R, Kharas M. 2007 – TRANSCRIPTIONAL CONTROL OF CBX5 BY THE RNA BINDING PROTEINS RBMX AND RBMXL1 MAINTAINS CHROMATIN STATE IN MYELOID LEUKEMIA. Exp Hematol 2021. [DOI: 10.1016/j.exphem.2021.12.372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Prieto C, Nguyen DTT, Liu Z, Wheat J, Perez A, Gourkanti S, Chou T, Barin E, Velleca A, Rohwetter T, Chow A, Taggart J, Savino AM, Hoskova K, Dhodapkar M, Schurer A, Barlowe TS, Vu LP, Leslie C, Steidl U, Rabadan R, Kharas MG. Transcriptional control of CBX5 by the RNA binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia. Nat Cancer 2021; 2:741-757. [PMID: 34458856 PMCID: PMC8388313 DOI: 10.1038/s43018-021-00220-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 05/11/2021] [Indexed: 01/08/2023]
Abstract
RNA binding proteins (RBPs) are key arbiters of post-transcriptional regulation and are found to be found dysregulated in hematological malignancies. Here, we identify the RBP RBMX and its retrogene RBMXL1 to be required for murine and human myeloid leukemogenesis. RBMX/L1 are overexpressed in acute myeloid leukemia (AML) primary patients compared to healthy individuals, and RBMX/L1 loss delayed leukemia development. RBMX/L1 loss lead to significant changes in chromatin accessibility, as well as chromosomal breaks and gaps. We found that RBMX/L1 directly bind to mRNAs, affect transcription of multiple loci, including CBX5 (HP1α), and control the nascent transcription of the CBX5 locus. Forced CBX5 expression rescued the RBMX/L1 depletion effects on cell growth and apoptosis. Overall, we determine that RBMX/L1 control leukemia cell survival by regulating chromatin state through their downstream target CBX5. These findings identify a mechanism for RBPs directly promoting transcription and suggest RBMX/L1, as well as CBX5, as potential therapeutic targets in myeloid malignancies.
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Affiliation(s)
- Camila Prieto
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diu T T Nguyen
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhaoqi Liu
- Program for Mathematical Genomics, Department of Systems Biology, Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Justin Wheat
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY USA
| | - Alexendar Perez
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Saroj Gourkanti
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy Chou
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ersilia Barin
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthony Velleca
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thomas Rohwetter
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arthur Chow
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James Taggart
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angela M Savino
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katerina Hoskova
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Dhodapkar
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Trevor S Barlowe
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ly P Vu
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC, Canada; Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY USA
| | - Raul Rabadan
- Program for Mathematical Genomics, Department of Systems Biology, Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - Michael G Kharas
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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12
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Abstract
BACKGROUND Evidence increasingly acknowledges the impact of social isolation and loneliness on the lives of military veterans and the wider Armed Forces Community. AIMS The study gathered expert consensus to (i) understand if veterans are considered 'unique' in their experiences of social isolation and loneliness; (ii) examine perceived factors leading to social isolation and loneliness of veterans; (iii) identify ways to tackle veterans' social isolation and loneliness. METHODS This study adopted a three-phase Delphi method. Phase 1 utilized a qualitative approach and Phase 2 and Phase 3 utilized a mixed-methods approach. RESULTS Several outcomes were identified across the three phases. Transition out of the military was viewed as a period to build emotional resilience and raise awareness of relevant services. It was also concluded that veterans would benefit from integrating into services within the wider community, and that social prescribing services could be a vehicle to link veterans to relevant services. Furthermore, access to, and the content of, programmes was also of importance. CONCLUSIONS These findings illustrate various important interventional aspects to consider when funding and implementing programmes focussed on tackling social isolation and loneliness.
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Affiliation(s)
- C Leslie
- Faculty of Health and Life Sciences, Department of Psychology, Northumbria University, Newcastle-upon-Tyne, UK
| | - G McGill
- Faculty of Health and Life Sciences, Department of Nursing, Midwifery and Health, Northumbria University, Newcastle-upon-Tyne, UK
| | - M D Kiernan
- Faculty of Health and Life Sciences, Department of Nursing, Midwifery and Health, Northumbria University, Newcastle-upon-Tyne, UK
| | - G Wilson
- Faculty of Health and Life Sciences, Department of Nursing, Midwifery and Health, Northumbria University, Newcastle-upon-Tyne, UK
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13
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Wesely J, Kotini AG, Izzo F, Luo H, Yuan H, Sun J, Georgomanoli M, Zviran A, Deslauriers AG, Dusaj N, Nimer SD, Leslie C, Landau DA, Kharas MG, Papapetrou EP. Acute Myeloid Leukemia iPSCs Reveal a Role for RUNX1 in the Maintenance of Human Leukemia Stem Cells. Cell Rep 2021; 31:107688. [PMID: 32492433 DOI: 10.1016/j.celrep.2020.107688] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/12/2020] [Accepted: 05/04/2020] [Indexed: 12/19/2022] Open
Abstract
Leukemia stem cells (LSCs) are believed to have more distinct vulnerabilities than the bulk acute myeloid leukemia (AML) cells, but their rarity and the lack of universal markers for their prospective isolation hamper their study. We report that genetically clonal induced pluripotent stem cells (iPSCs) derived from an AML patient and characterized by exceptionally high engraftment potential give rise, upon hematopoietic differentiation, to a phenotypic hierarchy. Through fate-tracking experiments, xenotransplantation, and single-cell transcriptomics, we identify a cell fraction (iLSC) that can be isolated prospectively by means of adherent in vitro growth that resides on the apex of this hierarchy and fulfills the hallmark features of LSCs. Through integrative genomic studies of the iLSC transcriptome and chromatin landscape, we derive an LSC gene signature that predicts patient survival and uncovers a dependency of LSCs, across AML genotypes, on the RUNX1 transcription factor. These findings can empower efforts to therapeutically target AML LSCs.
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Affiliation(s)
- Josephine Wesely
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andriana G Kotini
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Franco Izzo
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Han Yuan
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jun Sun
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Maria Georgomanoli
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Asaf Zviran
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA
| | - André G Deslauriers
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Biotech Research and Innovation Center, University of Copenhagen, Denmark; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neville Dusaj
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dan A Landau
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA
| | - Michael G Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eirini P Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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14
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Wang T, Pine AR, Kotini AG, Yuan H, Zamparo L, Starczynowski DT, Leslie C, Papapetrou EP. Sequential CRISPR gene editing in human iPSCs charts the clonal evolution of myeloid leukemia and identifies early disease targets. Cell Stem Cell 2021; 28:1074-1089.e7. [PMID: 33571445 DOI: 10.1016/j.stem.2021.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/20/2020] [Accepted: 01/14/2021] [Indexed: 12/20/2022]
Abstract
Human cancers arise through the sequential acquisition of somatic mutations that create successive clonal populations. Human cancer evolution models could help illuminate this process and inform therapeutic intervention at an early disease stage, but their creation has faced significant challenges. Here, we combined induced pluripotent stem cell (iPSC) and CRISPR-Cas9 technologies to develop a model of the clonal evolution of acute myeloid leukemia (AML). Through the stepwise introduction of three driver mutations, we generated iPSC lines that, upon hematopoietic differentiation, capture distinct premalignant stages, including clonal hematopoiesis (CH) and myelodysplastic syndrome (MDS), culminating in a transplantable leukemia, and recapitulate transcriptional and chromatin accessibility signatures of primary human MDS and AML. By mapping dynamic changes in transcriptomes and chromatin landscapes, we characterize transcriptional programs driving specific transitions between disease stages. We identify cell-autonomous dysregulation of inflammatory signaling as an early and persistent event in leukemogenesis and a promising early therapeutic target.
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Affiliation(s)
- Tiansu Wang
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Allison R Pine
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andriana G Kotini
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Han Yuan
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lee Zamparo
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel T Starczynowski
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eirini P Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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15
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Dhara S, Chhangawala S, Chintalapudi H, Massa AL, Aveson V, Askan G, Zhang L, Nicolle R, Makohon-Moore AP, Sinha S, Gui J, Moffitt R, Yu KH, Balachandran V, Chandwani R, Leslie C, Leach SD. Abstract LB-263: Pancreatic cancer prognosis is predicted by chromatin accessibility microarray. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-lb-263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Personalized therapy is the future of cancer care. Almost half of the cancer patients do not respond to chemotherapy. For instance, pancreatic ductal adenocarcinoma (PDAC) patients with the limited local disease and with no detectable metastasis typically have their primary tumor surgically resected, but the disease recurs in approximately 50% of cases within 1 year of surgery, in spite of adjuvant chemotherapy. Although gene expression signatures correlating prognosis have been described in PDAC, the therapeutic utility of these signatures has been limited based in part on a large number of genes displaying an altered expression. On the other hand, regulatory regions common to these genes might be amenable to collective epigenetic reprogramming using epigenetic drugs. We interrogated genome-wide chromatin accessibility using Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) on EpCAM+ PDAC malignant cells sorted from a cohort of 54 treatment-naïve resected tumors, in hopes of defining a tumor-intrinsic chromatin signature associated with recurrence. We discovered a signature of 1092 loci that were differentially accessible between recurrent (disease-free survival (DFS) < 1 year) and non-recurrent patients (DFS > 1 year). Through transcription factor (TF) binding motif analysis, we identified candidate TFs whose accessible motifs were differentially associated with recurrence. Nuclear localization of two such TFs, ZKSCAN1 and HNF1b, were assessed by immunostaining on tissue microarrays (TMA) representing 40 out of 54 patients. Nuclear staining of HNF1b was strong in tumor tissue from non-recurrent patients and weak or absent in recurrent patients, but ZKSCAN1 staining patterns were not significantly associated with recurrence. In a TMA representing an independent PDAC cohort (n=97) preselected for 52 long (OS 6 years)- and 45 short (OS 6 months)- term survivors, the number of nuclear positive cells for HNF1b was 52-fold higher in the long-term compared to the short-term survivors and that for ZKSCAN1 was 5.3-fold higher in the short-term compared to the long-term survivors. We further validated the 1092 chromatin accessibility signature by a novel microarray-based platform technology that we termed “ATAC-Array”, where the differentially accessible regions from the signatures were probed on a glass slide and then hybridized with fluorescent-labeled ATAC-libraries. This is a cost-effective, easy-to-use platform technology avoiding the time and cost of next-generation ATAC library sequencing. ATAC-array is the only microarray that reads chromatin accessibility. We have compared ATAC-array side-by-side with ATAC-seq (n=30) and found significant correlation (Pearson's median r= 0.64, range= 0.50- 0.77). By performing ATAC-array on the PDAC cohort (n=38), we have independently re-classified the patients who recurred early and the ones who did not (Gehan-Breslow-Wilcoxon test p=0.0076). ATAC-array, as the technology itself, has enormous potential for a wide range of applications, and we propose to develop it as a clinically validated theragnostic tool to predict and stratify cancer patients for epigenetic therapy.
Citation Format: Surajit Dhara, Sagar Chhangawala, Himanshu Chintalapudi, Alexandra L. Massa, Victoria Aveson, Gokce Askan, Liguo Zhang, Remy Nicolle, Alvin P. Makohon-Moore, Smrita Sinha, Jiang Gui, Richard Moffitt, Kenneth H. Yu, Vinod Balachandran, Rohit Chandwani, Christina Leslie, Steven D. Leach. Pancreatic cancer prognosis is predicted by chromatin accessibility microarray [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-263.
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Affiliation(s)
- Surajit Dhara
- 1Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, NH
| | | | | | | | | | - Gokce Askan
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - Liguo Zhang
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - Remy Nicolle
- 3Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | | | - Smrita Sinha
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jiang Gui
- 1Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, NH
| | | | - Kenneth H. Yu
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Steven D. Leach
- 1Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, NH
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Leslie C. Abstract IA20: Chromatin state and scRNA-seq analysis defines a common differentiation trajectory towards T-cell exhaustion. Cancer Immunol Res 2020. [DOI: 10.1158/2326-6074.tumimm19-ia20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
We will describe a unified chromatin state and single cell expression analysis underlying T-cell differentiation to “exhaustion.” Numerous studies in chronic viral infection and tumor models have shown that most T cells progress to a terminally dysfunctional (“exhausted”) state from which they cannot be rescued by current immunotherapies. We performed a systematic analysis of over 280 ATAC-seq and RNA-seq experiments from eight published studies of CD8 T cell dysfunction, using a statistical batch correction to define a common differentiation trajectory to terminal exhaustion in all settings of chronic antigen exposure and to identify transcription factors involved in this progression. We further performed scRNA-seq analysis of CD8 T cells at multiple time points during acute and chronic viral infection and in adoptive cell transfer studies to elucidate this trajectory at single-cell resolution.
Citation Format: Christina Leslie. Chromatin state and scRNA-seq analysis defines a common differentiation trajectory towards T-cell exhaustion [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr IA20.
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Brown CC, Gudjonson H, Pritykin Y, Deep D, Lavallée VP, Mendoza A, Fromme R, Mazutis L, Ariyan C, Leslie C, Pe'er D, Rudensky AY. Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity. Cell 2019; 179:846-863.e24. [PMID: 31668803 PMCID: PMC6838684 DOI: 10.1016/j.cell.2019.09.035] [Citation(s) in RCA: 298] [Impact Index Per Article: 59.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/12/2019] [Accepted: 09/27/2019] [Indexed: 12/24/2022]
Abstract
Dendritic cells (DCs) play a critical role in orchestrating adaptive immune responses due to their unique ability to initiate T cell responses and direct their differentiation into effector lineages. Classical DCs have been divided into two subsets, cDC1 and cDC2, based on phenotypic markers and their distinct abilities to prime CD8 and CD4 T cells. While the transcriptional regulation of the cDC1 subset has been well characterized, cDC2 development and function remain poorly understood. By combining transcriptional and chromatin analyses with genetic reporter expression, we identified two principal cDC2 lineages defined by distinct developmental pathways and transcriptional regulators, including T-bet and RORγt, two key transcription factors known to define innate and adaptive lymphocyte subsets. These novel cDC2 lineages were characterized by distinct metabolic and functional programs. Extending our findings to humans revealed conserved DC heterogeneity and the presence of the newly defined cDC2 subsets in human cancer. Single-cell analyses reveal novel dendritic cell subsets Major cDC2 subsets differentially express T-bet and RORγt Distinct pro- and anti-inflammatory potential of T-bet+ and Tbet– cDC2s Transcriptional basis for cDC2 heterogeneity conserved across mouse and human
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Affiliation(s)
- Chrysothemis C Brown
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Infection, Inflammation and Rheumatology Section, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK.
| | - Herman Gudjonson
- Infection, Inflammation and Rheumatology Section, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Yuri Pritykin
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Deeksha Deep
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vincent-Philippe Lavallée
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alejandra Mendoza
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rachel Fromme
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Linas Mazutis
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Charlotte Ariyan
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christina Leslie
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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Jackson J, Leslie C, Cotto J, Korth C, Mah M, Hor K, Cripe L, Camino E, Al-Zaidy S, Hassan S, Vannatta K, Lowes L, Iammarino M, Miller N, Alfano L, Lehman K, Mendell J. DMD BRAIN. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Osmanbeyoglu HU, Shimizu F, Rynne-Vidal A, Yeung TL, Jelinic P, Mok SC, Chiosis G, Levine DA, Leslie C. Abstract 3370: Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epigenomic data on transcription factor occupancy and chromatin accessibility can elucidate the developmental origin of cancer cells and reveal the enhancer landscape of key oncogenic transcriptional regulators. We develop a computational strategy called PSIONIC (patient-specific inference of networks informed by chromatin) to combine cell line chromatin accessibility data with large tumor expression data sets and model the effect of enhancers on transcriptional programs in multiple cancers. We generated a new ATAC-seq data set profiling chromatin accessibility in gynecologic and basal breast cancer cell lines and applied PSIONIC to 723 patient and 96 cell line RNA-seq profiles from ovarian, uterine, and basal breast cancers. Our computational framework enables us to share information across tumors to learn patient-specific TF activities, revealing regulatory differences between and within tumor types. Many of theidentified TFs were significantly associated with survival outcome in basal breast, uterine serous and endometrioid carcinomas. To validate one PSIONIC-derived prognostic TF, we performed immunohistochemical analyses in 31 uterine serous tumors for ETV6 and confirmed that the corresponding protein expression pattern was also significantly associated with prognosis. Moreover, PSIONIC-predicted activity for MTF1 in cell line models correlated with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy.
Citation Format: Hatice Ulku Osmanbeyoglu, Fumiko Shimizu, Angela Rynne-Vidal, Tsz-Lun Yeung, Petar Jelinic, Samuel C. Mok, Gabriela Chiosis, Douglas A. Levine, Christina Leslie. Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3370.
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Affiliation(s)
| | | | | | - Tsz-Lun Yeung
- 3The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Petar Jelinic
- 4New York University Langone Medical Center, New York, NY
| | - Samuel C. Mok
- 3The University of Texas MD Anderson Cancer Center, Houston, TX
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Ladewig E, Fairchild L, Scaltriti M, Leslie C, Toska E, Baselga J. Abstract 4346: PI3K pathway mediated splicing defects in ER+ breast cancers. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Activating mutations in PIK3CA, the gene encoding for the catalytic subunit (p100a), are the most common oncogenic alterations in estrogen receptor-positive (ER+). The majority of PIK3CA mutations occur within two hot spots; exons 9 and exon 20 which encode the helical (E545K) and kinase domains (H1047R), respectively. These mutations result in hyperactivation of the PI3K/AKT/mTOR pathway and provide the rationale for the development of inhibitors targeting the PI3K pathway. To this end, PI3K α-specific inhibitors are showing antitumor activity in patients with PIK3CA-mutant, ER-positive breast cancer. Evidence of alternative mRNA regulation and splicing in various cancers has been described in the literature. Although, the majority of events appear to have unknown clinical significance, there is evidence alternative splicing can lead to drug resistance. The role of the PI3K pathway on transcriptional regulation and mRNA processing is not well studied. Through transcriptome analysis and cell assays in mouse MEF and human MCF10A cells we demonstrate splicing defects accrue as a result of the PI3K pathway activation by the PIK3CA H1047R mutation. PI3Ka pathway inhibitors were able to restore wildtype exon inclusion levels in these mutants, suggesting a potential clinical benefit. We propose that PIK3CA H1047R imposes mRNA differential isoform regulation by acting through the most commonly mutated PI3K pathway in ER+ breast cancers and that such mutations are targetable with PI3K pathway inhibitors.
Citation Format: Erik Ladewig, Lauren Fairchild, Maurizio Scaltriti, Christina Leslie, Eneda Toska, Jose Baselga. PI3K pathway mediated splicing defects in ER+ breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4346.
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Pritykin Y, Leslie C. Abstract 3384: Genome-wide epigenetic and transcriptional comparison of CD8 T cell functional states between mouse models of cancer and chronic viral infection. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent studies in mouse models of cancer and chronic viral infection applied genomic assays to profile various states of impaired T cell function and demonstrated that T cell dysfunction is epigenetically imprinted. However, comprehensive characterization of T cell dysfunction across models based on their epigenetic and transcriptional profiles is lacking. We reanalyzed a large collection of recently published chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data sets. After batch effect correction, we observed that epigenetic profiles of dysfunctional tumor-infiltrating T cells and exhausted T cells in chronic viral infection were surprisingly extremely similar. Furthermore, we observed that temporal progression towards dysfunction in chronic infection resembles that in tumorigenesis, and found that T cells committed to becoming dysfunctional early after activation. Motif analysis using generalized linear modeling allowed us to find candidate transcription factors associated with development of dysfunction in both immune settings. This analysis provides a better systematic understanding of cell-intrinsic mechanisms driving different functional states of CD8 T cells and demonstrates the power of systems biology approaches in cancer immunology.
Citation Format: Yuri Pritykin, Christina Leslie. Genome-wide epigenetic and transcriptional comparison of CD8 T cell functional states between mouse models of cancer and chronic viral infection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3384.
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Affiliation(s)
- Yuri Pritykin
- Memorial Sloan Kettering Cancer Center, New York, NY
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Toska E, Xu G, Chhangawala S, Cocco E, Razavi P, Otto J, Cai Y, Chan C, Avino DRD, Collings C, Levine RL, Scaltriti M, Reis-Filho JS, Kadoch C, Leslie C, Baselga J. Abstract 949: ARID1A is a critical regulator of luminal identity and therapeutic response in estrogen receptor-positive breast cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mutations in ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, are the most common somatic alteration of the SWI/SNF complex across all cancers including estrogen receptor positive (ER)+ breast cancer. We have recently reported that ARID1A inactivating mutations are present at a high frequency in advanced endocrine resistant ER+ breast cancer. However, the mechanisms whereby disruption of ARID1A influences breast cancer progression and/or endocrine therapy resistance are unknown. In order to elucidate mechanisms of resistance to endocrine therapy, we performed an epigenome CRISPR/CAS9 knockout screen that identified ARID1A as the top candidate whose loss determines resistance to the ER degrader, fulvestrant. ARID1A knockout cells were found to be less responsive to endocrine therapy compared to intact ARID1A cells in vitro and in vivo. These observations led us to undertake a comprehensive chromatin-based mechanistic characterization of ARID1A loss in ER+ breast cancer and its role in endocrine therapy response. ARID1A disruption in ER+ breast cancer cells led to widespread changes in chromatin accessibility converging on the master transcription factors (TFs) that regulate gene expression programs critical for luminal (ER+) lineage identity. Global transcriptome profiling of ARID1A knockout cell lines and patient samples harboring ARID1A inactivating mutations revealed an enrichment for basal-like (ER-) gene expression signatures. The state of increased cellular plasticity of luminal cells that acquire a basal-like phenotype upon ARID1A inactivation is enabled by loss of ARID1A-dependent SWI/SNF complex targeting to genomic sites of the major luminal-lineage determining transcription factors including ER, FOXA1, and GATA3. Thus, through widespread chromatin reprograming and functional regulation of mater luminal TFs, tumor cells alter lineage fidelity and become less responsive to luminal-specific anti-ER therapy. We also show that ARID1A regulates genome-wide ER-chromatin interactions and ER-dependent transcription. Altogether, we uncover a critical role for ARID1A in the determination of breast luminal cell identity and endocrine therapeutic response in breast cancer.
Citation Format: Eneda Toska, Guotai Xu, Sagar Chhangawala, Emiliano Cocco, Pedram Razavi, Jordan Otto, Yanyan Cai, Carmen Chan, Drew R. D' Avino, Clayton Collings, Ross L. Levine, Maurizo Scaltriti, Jorge S. Reis-Filho, Cigall Kadoch, Christina Leslie, Jose Baselga. ARID1A is a critical regulator of luminal identity and therapeutic response in estrogen receptor-positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 949.
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Affiliation(s)
- Eneda Toska
- 1Mem. Sloan Kettering Cancer Ctr., New York, NY
| | - Guotai Xu
- 1Mem. Sloan Kettering Cancer Ctr., New York, NY
| | | | | | | | - Jordan Otto
- 2Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Yanyan Cai
- 1Mem. Sloan Kettering Cancer Ctr., New York, NY
| | - Carmen Chan
- 1Mem. Sloan Kettering Cancer Ctr., New York, NY
| | - Drew R. D' Avino
- 2Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | | | | | | | | | - Cigall Kadoch
- 2Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | | | - Jose Baselga
- 3Vall d'Hebron Institute of Oncology, Barcelona, Spain
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Pritykin Y, Leslie C. Abstract B038: A unified genome-wide analysis of dysfunctional T-cell states in cancer and chronic viral infection. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-b038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Tumor-specific T-cells that have differentiated into a terminal dysfunctional state exist in the tumor microenvironment. A systematic understanding of the requirements of immunotherapeutic rescue of these cells is critically needed to improve clinical results in patients. Mouse models of chronic infection and cancer have been studied to elucidate biologic mechanisms of persistent antigen stimulation resulting in T-cell dysfunction, or “exhaustion.” Recently, chromatin accessibility imprinting has been associated with T-cells falling back into the dysfunctional state after temporary rescue by checkpoint blockade, suggesting epigenetic mechanisms in control of T-cell dysfunction. However, comprehensive characterization of T-cell dysfunction across models based on their epigenetic and transcriptional profiles is lacking.We collected 106 chromatin accessibility (ATAC-seq) samples and 87 gene expression (RNA-seq) samples from seven recent publications. We analyzed these data by first applying batch effect correction using generalized linear modeling. This enabled mapping profiles of chromatin accessibility peaks in gene promoters and enhancers from different studies into the same space. We observed that epigenetic profiles of dysfunctional tumor-infiltrating T-cells and dysfunctional T-cells in chronic viral infection were, surprisingly, extremely similar. Furthermore, a recently characterized discrete distinction between epigenetic profiles of early (day 7-8) and late (day 28-35) dysfunction in the tumor was recapitulated in the model of chronic infection. Overall we observed across mouse models that T-cells committed to becoming dysfunctional early after an immune challenge, rather than first mounting and then loosing an effector response. These observations were also largely recapitulated in gene expression analysis. Differentially expressed genes with massive differential accessibility of their promoter and enhancer peaks during development of dysfunction, observed consistently across models, including transcription factors (TF) well studied in immunity such as Tcf7, Lef1, Satb1, Ikzf2, Tox, are good candidates for further targeted analysis.We then turned to TF binding analysis. We associated absolute levels of chromatin accessibility in peaks of each sample with TF binding (predicted by motif analysis) using regularized negative binomial regression with cross-validation. We estimated the effect of each TF in each sample, which allowed us to map chromatin accessibility profiles into the TF activity space of much lower dimensionality. This mapping largely preserved the hierarchy of relative similarities between samples. We identified key TFs whose binding was associated with open or closed chromatin in functional and dysfunctional cell states. For example, not surprisingly, binding of well known effector factors Eomes and Batf was associated with closed chromatin in naive cells and open chromatin in effector cells. Strikingly, the strongest association with closing chromatin in dysfunction, consistently across mouse models, was observed for Tcf7/Lef1 binding, further suggesting the role of these TFs in establishing the terminal CD8 T-cell dysfunctional state. Notably, we found two large groups of TFs anti-correlated to each other whose predicted binding sites had higher accessibility in either functional or dysfunctional cells. This suggested that coordinated activity of a broad range of TFs (not necessarily binding at the same sites) might be responsible for establishing and maintaining T-cell functional states, and focusing on one or a handful of TFs is not sufficient to explain them. This analysis provides a better systematic understanding of cell-intrinsic mechanisms driving different functional states of CD8 T-cells, and the developed computational methods are broadly applicable in other experimental setups where diverse cell states are profiled by high-throughput genomic assays.
Citation Format: Yuri Pritykin, Christina Leslie. A unified genome-wide analysis of dysfunctional T-cell states in cancer and chronic viral infection [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B038.
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Affiliation(s)
- Yuri Pritykin
- Memorial Sloan Kettering Cancer Center, New York, NY
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Park SM, Cho H, Thornton AM, Barlowe TS, Chou T, Chhangawala S, Fairchild L, Taggart J, Chow A, Schurer A, Gruet A, Witkin MD, Kim JH, Shevach EM, Krivtsov A, Armstrong SA, Leslie C, Kharas MG. IKZF2 Drives Leukemia Stem Cell Self-Renewal and Inhibits Myeloid Differentiation. Cell Stem Cell 2019; 24:153-165.e7. [PMID: 30472158 PMCID: PMC6602096 DOI: 10.1016/j.stem.2018.10.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/06/2018] [Accepted: 10/10/2018] [Indexed: 01/08/2023]
Abstract
Leukemias exhibit a dysregulated developmental program mediated through both genetic and epigenetic mechanisms. Although IKZF2 is expressed in hematopoietic stem cells (HSCs), we found that it is dispensable for mouse and human HSC function. In contrast to its role as a tumor suppressor in hypodiploid B-acute lymphoblastic leukemia, we found that IKZF2 is required for myeloid leukemia. IKZF2 is highly expressed in leukemic stem cells (LSCs), and its deficiency results in defective LSC function. IKZF2 depletion in acute myeloid leukemia (AML) cells reduced colony formation, increased differentiation and apoptosis, and delayed leukemogenesis. Gene expression, chromatin accessibility, and direct IKZF2 binding in MLL-AF9 LSCs demonstrate that IKZF2 regulates a HOXA9 self-renewal gene expression program and inhibits a C/EBP-driven differentiation program. Ectopic HOXA9 expression and CEBPE depletion rescued the effects of IKZF2 depletion. Thus, our study shows that IKZF2 regulates the AML LSC program and provides a rationale to therapeutically target IKZF2 in myeloid leukemia.
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MESH Headings
- Animals
- Cell Differentiation
- Cell Self Renewal
- Chromatin/genetics
- Chromatin/metabolism
- DNA-Binding Proteins/physiology
- Female
- Gene Expression Regulation, Leukemic
- Hematopoiesis
- Leukemia, Experimental/genetics
- Leukemia, Experimental/metabolism
- Leukemia, Experimental/pathology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Transcription Factors/physiology
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Affiliation(s)
- Sun-Mi Park
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hyunwoo Cho
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angela M Thornton
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Trevor S Barlowe
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy Chou
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sagar Chhangawala
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lauren Fairchild
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James Taggart
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arthur Chow
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandria Schurer
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Antoine Gruet
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Witkin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jun Hyun Kim
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ethan M Shevach
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Andrei Krivtsov
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael G Kharas
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Dhara S, Chhangawala S, Askan G, Liguo Z, Sinha S, Glassman D, Yu K, Balachandran V, Leslie C, Leach S. Abstract LB-238: Genome wide cis-regulatory elements accessibility signature predicts early recurrence of the treatment-naïve resected subset of PDAC: A new paradigm for precision oncology. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
We have recently discovered a set of 1092 cis-regulatory elements in the human genome that are differentially accessible in the treatment-naïve resected subset of pancreatic ductal adenocarcinoma (PDAC) recurring within first 12 months of surgery. Recurrence, even after complete removal of the primary tumor, is a pressing issue in PDAC. We hypothesized that malignant cells of the recurrent and the non-recurrent PDAC tumors possessed differential accessibility patterns of cis-regulatory elements in the genome. To test this hypothesis, we interrogated genome wide chromatin accessibility landscape of EpCAM-sorted “pure” PDAC malignant cells (KRAS mutant allele frequency 45+22%) from 54 freshly resected tumors followed by the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). We identified a near-saturating total number of 126661 open chromatin peaks from duplicate ATAC-seq libraries from each of 40 (out of 54) patients (80 libraries with Irreproducible Discovery Rate (IDR)-cut-off <0.01). We found 1092 peaks differentially represented (p<0.001) in patients who recurred within first 12 months of surgery compared to the patients who didn't. We identified 62 transcription-factor binding motifs by MEME curated CisBP transcription factor binding motifs (TBFM) and FIMO that were differentially enriched in recurrent and non-recurrent patients (P < 1x10-4). We selected the top listed two transcription factors, HNF1b and ZKSCAN1, from the non-recurrent and recurrent groups respectively, for further validation by immunohistochemistry (IHC) and immunofluorescence (IF) staining of tissue microarrays (TMA) prepared from formalin-fixed paraffin blocks of these tumors (N=40). With the blinded subjective scoring (0-3 scale) method using the combination of HNF1b and ZKSCAN1 we could predict recurrence with 83.33% accuracy. HNF1b nuclear staining pattern was completely absent from 7, weak in 4 and strong in 1 out of 12 recurrent patients. As opposed to that, strong nuclear staining of ZKSCAN1 in 3, moderate staining in 5, weak to moderate in 3 and no staining in 1 out of 12 patients was observed. Among the rest 28 patients, only 3 (10.7%) showed a clear cut opposite staining pattern, i.e., strong HNF1b and weak ZKSCAN1 nuclear staining, 7 patients showed the recurrence signature of staining and other 18 patients showed ambivalent patterns. Altogether, from the current study we conclude that epigenetic reprogramming, by increasing or decreasing accessibility of the cis-regulatory elements in the genome, regulates binding of the specific transcription factors, which in turn might control the PDAC heterogeneity of recurrence and chemoresistance.
Citation Format: Surajit Dhara, Sagar Chhangawala, Gokce Askan, Zhang Liguo, Smrita Sinha, Danielle Glassman, Kenneth Yu, Vinod Balachandran, Christina Leslie, Steven Leach. Genome wide cis-regulatory elements accessibility signature predicts early recurrence of the treatment-naïve resected subset of PDAC: A new paradigm for precision oncology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-238.
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Affiliation(s)
- Surajit Dhara
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Gokce Askan
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zhang Liguo
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Smrita Sinha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Kenneth Yu
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Steven Leach
- Memorial Sloan Kettering Cancer Center, New York, NY
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Osmanbeyoglu HU, Jelinic P, Douglas D, Leslie C. Abstract 282: Inferring transcriptional regulatory programs in gynecological cancers. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer cells acquire genetic and epigenetic alterations that often lead to dysregulation of oncogenic signal transduction pathways, which in turn alter downstream transcriptional programs. Transcription factors (TFs) are the main link between signaling pathways and the transcriptional regulatory programs. The Cancer Genome Atlas (TCGA) has studied several of the most common and aggressive gynecologic tumors including high-grade serous ovarian carcinomas (HGSOC), uterine carcinosarcoma (UCS), and the serous-like subset of endometrial cancer (UCEC), together with basal breast cancer, which shares many genomic features with serous ovarian tumors. TFs impacts on gene regulation have not been well characterized in gynecological and basal breast cancers. The majority of these tumors lack accurate predictors of response and resistance and share an unmet need for adequate treatment of recurrent disease. We developed a multitask learning framework for integrating regulatory sequence from ATAC-mapped promoters and enhancers from cell line models with RNA-seq data from patient tumors in order to infer transcription factor (TF) regulatory activities and explore similarities and differences between uterine, ovarian, and basal breast tumors. We showed that our multitask learning framework enables us to selectively share the information across tumors and strongly improves the accuracy of gene expression prediction models for gynecological and basal breast tumors. Our analysis identified histologic type specific and common TF regulators of gene expression as well as predicted distinct dysregulated transcriptional regulators downstream of somatic alterations in these different cancers. Moreover, many of the identified TF regulators were significantly associated with survival outcome within the histological subtype. Computationally dissecting the role of TFs in these cancers may ultimately lead to new therapeutics tailored to groups of subtypes or individuals.
Citation Format: Hatice U. Osmanbeyoglu, Petar Jelinic, Douglas Douglas, Christina Leslie. Inferring transcriptional regulatory programs in gynecological cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 282.
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Affiliation(s)
| | - Petar Jelinic
- 2New York University Langone Medical Center, New York, NY
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Downs L, Leslie C, Houghton D, Amanuel B. Comparison of PD-L1 expression in cytology and non-cytology samples. Pathology 2018. [DOI: 10.1016/j.pathol.2017.11.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Osmanbeyoglu HU, Leslie C. Abstract LB-010: Modeling the impact of mutations in ubiquitin pathway genes across human cancers. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A number of ubiquitin pathway genes show a strikingly high frequency of somatic alterations across diverse human cancers. While several ubiquitin ligase genes with recurrent mutations or copy number alterations been studied in individual cancers, their role in many malignancies remains poorly understood. To better model the impact of ubiquitin pathway alterations, we developed a computational strategy for exploiting parallel phosphoproteomics and mRNA sequencing data for large tumor sets to link dysregulation of upstream signaling pathways with altered transcriptional response through the transcriptional circuitry. Our modeling allows us to interpret the impact of mutations and copy number events in terms of altered signaling and transcription factor (TF) activity. We used a multi-task learning strategy to jointly train phosphoprotein-TF interaction models across 10 human cancers for which large reverse-phase protein array and RNA-seq data sets are available through TCGA. We then applied a novel algorithmic approach to extract networks of signaling proteins and TFs whose inferred activities are correlated across tumors and whose dysregulation is associated with specific somatically altered ubiquitin pathway genes. Our analysis revealed both known and novel interactions of ubiquitin ligase genes with signaling pathways and transcriptional programs in a pan-cancer context.
Citation Format: Hatice U. Osmanbeyoglu, Christina Leslie. Modeling the impact of mutations in ubiquitin pathway genes across human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-010. doi:10.1158/1538-7445.AM2017-LB-010
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Vu LP, Prieto C, Amin EM, Chhangawala S, Krivtsov A, Calvo-Vidal MN, Chou T, Chow A, Minuesa G, Park SM, Barlowe TS, Taggart J, Tivnan P, Deering RP, Chu LP, Kwon JA, Meydan C, Perales-Paton J, Arshi A, Gönen M, Famulare C, Patel M, Paietta E, Tallman MS, Lu Y, Glass J, Garret-Bakelman FE, Melnick A, Levine R, Al-Shahrour F, Järås M, Hacohen N, Hwang A, Garippa R, Lengner CJ, Armstrong SA, Cerchietti L, Cowley GS, Root D, Doench J, Leslie C, Ebert BL, Kharas MG. Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells. Nat Genet 2017; 49:866-875. [PMID: 28436985 PMCID: PMC5508533 DOI: 10.1038/ng.3854] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 03/31/2017] [Indexed: 12/15/2022]
Abstract
The identity of the RNA-binding proteins (RBPs) that govern cancer stem cells remains poorly characterized. The MSI2 RBP is a central regulator of translation of cancer stem cell programs. Through proteomic analysis of the MSI2-interacting RBP network and functional shRNA screening, we identified 24 genes required for in vivo leukemia. Syncrip was the most differentially required gene between normal and myeloid leukemia cells. SYNCRIP depletion increased apoptosis and differentiation while delaying leukemogenesis. Gene expression profiling of SYNCRIP-depleted cells demonstrated a loss of the MLL and HOXA9 leukemia stem cell program. SYNCRIP and MSI2 interact indirectly though shared mRNA targets. SYNCRIP maintains HOXA9 translation, and MSI2 or HOXA9 overexpression rescued the effects of SYNCRIP depletion. Altogether, our data identify SYNCRIP as a new RBP that controls the myeloid leukemia stem cell program. We propose that targeting these RBP complexes might provide a novel therapeutic strategy in leukemia.
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Affiliation(s)
- Ly P Vu
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Camila Prieto
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
| | - Elianna M Amin
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sagar Chhangawala
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA.,Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andrei Krivtsov
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - M Nieves Calvo-Vidal
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medical College, New York, New York, USA
| | - Timothy Chou
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Arthur Chow
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gerard Minuesa
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sun Mi Park
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Trevor S Barlowe
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - James Taggart
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Patrick Tivnan
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Lisa P Chu
- Division of Hematology, Brigham and Woman's Hospital, Boston, Massachusetts, USA
| | | | - Cem Meydan
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
| | - Javier Perales-Paton
- Translational Bioinformatics Unit, Clinical Research Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Arora Arshi
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christopher Famulare
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Minal Patel
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Elisabeth Paietta
- Department of Medicine, Montefiore Medical Center, Bronx, New York, USA
| | - Martin S Tallman
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Hospital, New York, New York, USA
| | - Yuheng Lu
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jacob Glass
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Hospital, New York, New York, USA
| | - Francine E Garret-Bakelman
- Department of Medicine and Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA.,Division of Hematology and Medical Oncology, Departments of Medicine and Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Ari Melnick
- Division of Hematology and Medical Oncology, Departments of Medicine and Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Fatima Al-Shahrour
- Translational Bioinformatics Unit, Clinical Research Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Marcus Järås
- Department of Clinical Genetics, Lund University, Lund, Sweden
| | - Nir Hacohen
- Harvard Medical School, Boston, Massachusetts, USA
| | - Alexia Hwang
- RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ralph Garippa
- RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christopher J Lengner
- Department of Animal Biology, Department of Cell and Developmental Biology, and Institute for Regenerative Medicine, Schools of Veterinary Medicine and Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Leandro Cerchietti
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Glenn S Cowley
- Discovery Sciences, Janssen Research and Development, Spring House, Pennsylvania, USA
| | - David Root
- Broad Institute, Boston, Massachusetts, USA
| | | | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Benjamin L Ebert
- Division of Hematology, Brigham and Woman's Hospital, Boston, Massachusetts, USA
| | - Michael G Kharas
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, and Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Toska E, Osmanbeyoglu H, Elkabets M, Chan C, Castel P, Dickler M, Armstrong S, Leslie C, Scaltriti M, José B. Abstract 885: Epigenetic regulation of estrogen receptor transcription by the PI3K pathway in breast cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mutations in the PIK3CA gene are the most frequent genomic alterations in estrogen receptor (ER)-positive breast cancers. Direct pharmacological inhibition of PI3K signaling is therefore an attractive clinical strategy and a number of PI3K pathway inhibitors are currently under clinical development. Unfortunately, although the majority of ER-positive PIK3CA-mutant patients respond, mechanisms of resistance to these inhibitors inevitably emerge. By studying both mouse models and human samples, our laboratory has previously uncovered that inhibition of PI3K pathway increases ER transcriptional activity, which in turn renders cells more susceptible to endocrine therapy. The mechanisms by which ER and PI3K signaling pathway regulate each other in breast cancer cells, however, remain elusive.
To better understand the cross-talk between the PI3K pathway and the ER transcriptional program, we developed an unbiased transposon activation mutagenesis screen with the goal of identifying modulators of resistance to PI3K inhibitors in ER-positive tumors. Among the genes identified, we found a number of key regulators of ER function including the pioneer transcription factors FOXA1 and PBX1. We further confirmed that FOXA1 and PBX1 expression and transcriptional activity was enhanced upon PI3K inhibition and validated these observations in both xenograft models and samples from patients undergoing treatment with the PI3Ká inhibitor BYL719. Moreover, chromatin imunoprecipitation (ChIP)-sequencing against ER and FOXA1 demonstrated that these factors occupy the same genomic regions, and their binding is increased upon PI3K inhibition. Silencing FOXA1 or PBX1 impaired the activation of the ER-dependent transcriptional program following PI3K blockade and sensitized cells to PI3K inhibition.
To better understand the role of FOXA1 and PBX1 in the ER-PI3K crosstalk, we have then studied in detail the chromatin changes upon BYL719 treatment using transposase-accessible chromatin using high-throughput sequencing (ATAC-seq) in breast cancer cells. Epigenomic profiling using ATAC-seq is also being done on patient samples collected before BYL719 administration (pre-treatment) and during therapy (on-treatment). ATAC-seq and RNA-seq data from the same patients will be integrated using novel computational approaches.
These analyses will help to dissect the ER-dependent epigenetic changes occurring upon PI3K inhibition and how the cells use these chromatin modifications to adapt to the pharmacological stress. Elucidating the interconnection between the PI3K pathway and ER activity may uncover novel mechanisms of resistance to either PI3K inhibitors or endocrine therapy in ER-positive breast cancer patients.
Citation Format: Eneda Toska, Hatice Osmanbeyoglu, Moshe Elkabets, Carmen Chan, Pau Castel, Maura Dickler, Scott Armstrong, Christina Leslie, Maurizio Scaltriti, Baselga José. Epigenetic regulation of estrogen receptor transcription by the PI3K pathway in breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 885.
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Affiliation(s)
- Eneda Toska
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Carmen Chan
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pau Castel
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maura Dickler
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Baselga José
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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Pelossof R, Elkatebts M, Chow O, Fairchild L, O’Rourke K, Smith JJ, Chen CT, Brook S, Scaltriti M, Shia J, Paty P, Leslie C, Lowe S, Baselga J, Garcia-Aguilar J. Abstract 4078: KRAS mutation status is associated with stromal inactivation in colorectal cancer and predicts poor response to neoadjuvant chemoradiotherapy. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Treatment for locally advanced rectal cancer (LARC) consists of neoadjuvant chemoradiotherapy (NCRT) followed by radical excision. Patients with tumors carrying a mutant KRAS are less likely to respond to NCRT compared to KRAS wild type tumors. We hypothesized that an RNA-based signature differentiating KRAS mutant and wild type patients could serve as an indicator of the biological process associated with response to NCRT. We found that the RNA-based signature is enriched for stromal and immune genes. Furthermore, the stromal component of the signature is a predictor of response to NCRT.
Methods: Tumors from 120 LARC patients enrolled in a multicenter phase 2 trial studying response to NCRT were tested for KRAS status by Sanger Sequencing or Memorial Sloan Kettering (MSK)-IMPACT assay and gene expression was quantified by sequencing. Colorectal cancer (CRC) patients from MSK (n = 95) and TCGA (n = 261), previously annotated for KRAS mutation status and gene expression, were used for validation. A KRAS-inducible mouse model and CRC patient-derived xenografts (PDXs) were utilized to determine the cell of origin for the gene expression signature. Stromal enrichment was assessed with the ESTIMATE stromal gene signature. Immunohistochemistry (IHC) was completed for Periostin (POSTN), a stromal marker from the RNA-signature. Variant Allele Frequency (VAF) was used to measure the abundance of KRAS, TP53 and Adenomatous Polyposis Coli (APC) mutant alleles in tumors, and was quantified by targeted exome sequencing with the MSK-IMPACT assay.
Results: Analysis of the KRAS-associated gene signature showed significant stromal inactivation in KRAS mutant patients. The signature was validated in the MSK and TCGA cohorts. The stromal signature was recapitulated in a KRAS inducible mouse model. Human CRC PDXs in mouse indicated that the signature arose from murine stroma and not human epithelium. Consistent with the stromal signature, IHC for POSTN, a stromal marker, was significantly lower in the KRAS mutant tumors compared with the KRAS wild type tumors (p<0.05) and was absent from the epithelium. The stromal enrichment in mutant KRAS tumors was inversely correlated with the KRAS VAF (p<0.01). This finding was not observed for TP53 or APC VAF indicating specificity for stromal inactivation in KRAS mutant tumors. Furthermore, the stromal component of the signature is associated with poor response to NCRT in LARC.
Conclusions: This study shows that a KRAS mutation in CRC is associated with a lower expression of a stromal signature and that this signature is derived from the tumor microenvironment. This study indicates that CRC KRAS mutant tumors and a stromal subtype are closely related. Understanding this relationship may play a key role in elucidating the mechanism by which a KRAS mutant tumor is resistant to standard therapy.
Citation Format: Raphael Pelossof, Moshe Elkatebts, Oliver Chow, Lauren Fairchild, Kevin O’Rourke, Jesse J. Smith, Chin-Tung Chen, Samuel Brook, Maurizio Scaltriti, Jinru Shia, Philip Paty, Christina Leslie, Scott Lowe, Jose Baselga, Julio Garcia-Aguilar. KRAS mutation status is associated with stromal inactivation in colorectal cancer and predicts poor response to neoadjuvant chemoradiotherapy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4078.
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Affiliation(s)
| | | | - Oliver Chow
- 3Beth Israel Deaconess Medical Center, Boston, MA
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Osmanbeyoglu HU, Toska E, Baselga J, Leslie C. Abstract 781: Modeling the impact of somatic alterations across human cancers. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Large-scale cancer genomics projects like The Cancer Genome Atlas have generated a comprehensive catalog of somatic mutations and copy number aberrations across many tumor types, but the role of most frequently altered genes remains obscure. To better model the impact of these alterations, we developed a novel computational strategy for exploiting parallel phosphoproteomics and mRNA sequencing data for large tumor sets by linking dysregulation of upstream signaling pathways with altered transcriptional response through the transcriptional circuitry. Our modeling allows us to interpret the impact of somatic alterations in terms of functional outcomes such as altered signaling and transcription factor (TF) activity.
We used this novel machine learning strategy to train phosphoprotein-TF interaction models across 12 human cancers for which large reverse-phase protein array and RNA-seq data sets are available through TCGA. First, we used this approach to identify shared and cancer-specific roles of TF/signaling regulators across cancer types. Then we performed a statistical analysis to associate frequent somatic aberrations with alterations in inferred TF and signaling protein activities. From our analysis, we gained many novel insights into cancer biology. We identified both known (e.g FOXO1 for breast cancer) and novel TF regulators of cancer (e.g. ELK1 for head and neck cancer). Many of these identified TF regulators were significantly associated with survival outcome in bladder urothelial, renal cell clear and endometrial carcinoma.
Next we performed a comprehensive cross-cancer analysis and identified relationships between somatic alterations and downstream transcriptional effects and signaling pathway activation. We observed that specific molecular aberrations have different functional consequences in different cancer types. For example, PIK3CA mutations are associated with altered activities of a diverse set of TFs across cancers that are involved in cell cycle, apoptosis, metabolism and MAPK/ERK signaling. Notably, in cell line models, we validated some of the altered TFs predicted by our model. We showed that PIK3CA mutation leads to ELK1 activation in breast and head and neck cancer models. We further found that different set of TFs are associated with a specific mutation in different cancers due to the different background of genomic aberrations in each cancer. For example, KRAS mutations are associated with a distinct set of TFs depending of cancer-specific co-mutation profiles (e.g. co-mutations of KRAS and TP53 in lung adenocarcinoma and co-mutations of KRAS and APC in colorectal cancer).
Our analysis revealed both known and novel interactions of frequently altered genes with signaling pathways and transcriptional programs in a pan-cancer context. Patterns of co-alterations across cancers may provide new insights relevant to targeted therapy and may be crucial to optimizing combination therapies.
Citation Format: Hatice U. Osmanbeyoglu, Eneda Toska, José Baselga, Christina Leslie. Modeling the impact of somatic alterations across human cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 781.
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Affiliation(s)
| | - Eneda Toska
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - José Baselga
- Memorial Sloan Kettering Cancer Center, New York, NY
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Philip M, Fairchild L, Sun L, Viale A, Leslie C, Schietinger A. Deciphering the epigenetic programming underlying CD8 T cell dysfunction in solid tumors. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.144.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Tumor-specific CD8 T cells in progressive solid tumors express inhibitory receptors and fail to proliferate and produce effector cytokines. Using a mouse model (ASTxCre-ERT2) in which tamoxifen (TAM) treatment induces an oncogenic driver neoantigen, SV40 large T antigen (Tag) in hepatocytes, we previously showed that tumor-specific CD8 T cells (TCRSV40-I) become unresponsive quite early during the pre-/early malignant phase. While the dysfunctional state is initially plastic, TCRSV40-I cells soon enter a fixed dysfunctional state with the phenotypic, functional, and molecular hallmarks of T cells from late-stage human tumors. To define the epigenetic programs associated with plasticity and imprinting of tumor-specific T cell dysfunction, we used the “Assay for Transposase-Accessible Chromatin using Sequencing” (ATAC-Seq) to map chromatin accessibility in TCRSV40-I cells isolated from pre/early malignant lesions as well as in TCRSV40-I differentiating to the normal effector and memory states. Chromatin accessibility changes underlying TCRSV40-I activation and differentiation in pre-malignant lesions diverged from that in normal differentiation, and we observed 2 distinct chromatin accessibility patterns in dysfunctional TCRSV40-I correlating with the plastic and fixed dysfunctional states. Surprisingly, memory TCRSV40-I transferred into mice with late-stage established Tag-expressing hepatocellular carcinomas displayed these same 2 chromatin accessibility profiles, thus regardless of the initial CD8 T cell epigenetic state, epigenetic remodeling drives tumor-specific T cell differentiation to the dysfunctional state in both pre-malignant lesions and late established solid tumors.
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Taggart J, Ho TC, Amin E, Xu H, Barlowe TS, Perez AR, Durham BH, Tivnan P, Okabe R, Chow A, Vu L, Park SM, Prieto C, Famulare C, Patel M, Lengner CJ, Verma A, Roboz G, Guzman M, Klimek VM, Abdel-Wahab O, Leslie C, Nimer SD, Kharas MG. MSI2 is required for maintaining activated myelodysplastic syndrome stem cells. Nat Commun 2016; 7:10739. [PMID: 26898884 PMCID: PMC4764878 DOI: 10.1038/ncomms10739] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/14/2016] [Indexed: 12/22/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are driven by complex genetic and epigenetic alterations. The MSI2 RNA-binding protein has been demonstrated to have a role in acute myeloid leukaemia and stem cell function, but its role in MDS is unknown. Here, we demonstrate that elevated MSI2 expression correlates with poor survival in MDS. Conditional deletion of Msi2 in a mouse model of MDS results in a rapid loss of MDS haematopoietic stem and progenitor cells (HSPCs) and reverses the clinical features of MDS. Inversely, inducible overexpression of MSI2 drives myeloid disease progression. The MDS HSPCs remain dependent on MSI2 expression after disease initiation. Furthermore, MSI2 expression expands and maintains a more activated (G1) MDS HSPC. Gene expression profiling of HSPCs from the MSI2 MDS mice identifies a signature that correlates with poor survival in MDS patients. Overall, we identify a role for MSI2 in MDS representing a therapeutic target in this disease. Several studies have recently demonstrated the role of the MSI2 RNA binding protein in normal and malignant haematopoietc stem cells. In this study, the authors show that MSI2 is required for maintaining myelodysplastic syndrome stem cells in mice and that MSI2 expression predicts poor prognosis in patients affected by this disease.
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Affiliation(s)
- James Taggart
- Molecular Pharmacology and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Tzu-Chieh Ho
- Molecular Pharmacology and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Elianna Amin
- Molecular Pharmacology and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Haiming Xu
- Memorial Sloan Kettering Cancer Center, Cancer Biology Program, New York, New York 10065, USA
| | - Trevor S Barlowe
- Molecular Pharmacology and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Alexendar R Perez
- Computational Biology Program Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Institute, New York, New York 10065, USA
| | - Benjamin H Durham
- Memorial Sloan Kettering Cancer Center, Human Oncology and Pathogenesis Program, New York, New York 10065, USA
| | - Patrick Tivnan
- Molecular Pharmacology and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Rachel Okabe
- Molecular Pharmacology and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Arthur Chow
- Molecular Pharmacology and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ly Vu
- Molecular Pharmacology and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Sun Mi Park
- Molecular Pharmacology and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Camila Prieto
- Molecular Pharmacology and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christopher Famulare
- Memorial Sloan Kettering Cancer Center, Department of Medicine, Leukemia Service, New York, New York 10065, USA
| | - Minal Patel
- Memorial Sloan Kettering Cancer Center, Department of Medicine, Leukemia Service, New York, New York 10065, USA
| | - Christopher J Lengner
- Department of Animal Biology, Department of Cell and Developmental Biology and Institute for Regenerative Medicine, Schools of Veterinary Medicine and Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Amit Verma
- Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Gail Roboz
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Monica Guzman
- Division of Hematology and Medical Oncology, Department of Medicine and Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York 10065, USA
| | - Virginia M Klimek
- Memorial Sloan Kettering Cancer Center, Department of Medicine, Leukemia Service, New York, New York 10065, USA
| | - Omar Abdel-Wahab
- Memorial Sloan Kettering Cancer Center, Human Oncology and Pathogenesis Program, New York, New York 10065, USA
| | - Christina Leslie
- Computational Biology Program Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Institute, New York, New York 10065, USA
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer Center, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Michael G Kharas
- Molecular Pharmacology and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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Osmanbeyoglu HU, Leslie C. Abstract LB-C04: Modeling the impact of somatic alterations across human cancers. Mol Cancer Ther 2015. [DOI: 10.1158/1535-7163.targ-15-lb-c04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Modeling the impact of somatic alterations across human cancers
Hatice U. Osmanbeyoglu1, Christina S. Leslie1,*
1Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
Abstract
Large-scale cancer genomics projects like The Cancer Genome Atlas have generated a comprehensive catalog of somatic mutations and copy number aberrations across many tumor types, but the role of some frequently altered genes remains obscure. To better model the impact of these alterations, we developed a computational strategy for exploiting parallel phosphoproteomics and mRNA sequencing data for large tumor sets to link dysregulation of upstream signaling pathways with altered transcriptional response through the transcriptional circuitry. Our modeling allows us to interpret the impact of mutations and copy number events in terms of altered signaling and transcription factor (TF) activity. We used a novel machine learning strategy to train phosphoprotein-TF interaction models across 10 human cancers for which large reverse-phase protein array and RNA-seq data sets are available through TCGA. We then applied a novel algorithmic approach to extract networks of signaling proteins and TFs whose inferred activities are correlated across tumors and whose dysregulation is associated with specific somatically altered genes. Our analysis revealed both known and novel interactions of frequently altered genes with signaling pathways and transcriptional programs in a pan-cancer context. Moreover, our algorithmic approach provides a general strategy for modeling the impact of recurrent mutations and copy number alterations on signaling pathways and transcriptional programs through pan-cancer analysis.
Citation Format: Hatice U. Osmanbeyoglu, Christina Leslie. Modeling the impact of somatic alterations across human cancers. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-C04.
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Zhang L, Tran NT, Su H, Wang R, Lu Y, Tang H, Aoyagi S, Guo A, Khodadadi-Jamayran A, Zhou D, Qian K, Hricik T, Côté J, Han X, Zhou W, Laha S, Abdel-Wahab O, Levine RL, Raffel G, Liu Y, Chen D, Li H, Townes T, Wang H, Deng H, Zheng YG, Leslie C, Luo M, Zhao X. Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing. eLife 2015; 4:07938. [PMID: 26575292 PMCID: PMC4775220 DOI: 10.7554/elife.07938] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 11/16/2015] [Indexed: 12/24/2022] Open
Abstract
RBM15, an RNA binding protein, determines cell-fate specification of many tissues including blood. We demonstrate that RBM15 is methylated by protein arginine methyltransferase 1 (PRMT1) at residue R578, leading to its degradation via ubiquitylation by an E3 ligase (CNOT4). Overexpression of PRMT1 in acute megakaryocytic leukemia cell lines blocks megakaryocyte terminal differentiation by downregulation of RBM15 protein level. Restoring RBM15 protein level rescues megakaryocyte terminal differentiation blocked by PRMT1 overexpression. At the molecular level, RBM15 binds to pre-messenger RNA intronic regions of genes important for megakaryopoiesis such as GATA1, RUNX1, TAL1 and c-MPL. Furthermore, preferential binding of RBM15 to specific intronic regions recruits the splicing factor SF3B1 to the same sites for alternative splicing. Therefore, PRMT1 regulates alternative RNA splicing via reducing RBM15 protein concentration. Targeting PRMT1 may be a curative therapy to restore megakaryocyte differentiation for acute megakaryocytic leukemia. DOI:http://dx.doi.org/10.7554/eLife.07938.001 The many different cell types in an adult animal all develop from a single fertilized egg. The development of cells into more specialized cell types is called ‘differentiation’. Proteins and other molecules from both inside and outside of the cells regulate the differentiation process. RNA is a molecule that is similar to DNA, and performs several important roles inside cells. Perhaps most importantly, RNA molecules act as messengers and carry genetic instructions during gene expression. RBM15 is an RNA-binding protein that is found throughout nature, and is involved in a number of developmental processes. Previous research has linked the incorrect control of RBM15 with an increased risk of certain cancers, including megakaryocytic leukemia. However, it is not clear what role RNA-binding proteins such as RBM15 play during differentiation. Now, Zhang, Tran, Su et al. have investigated the role of RBM15 during the development of large cells found in human bone marrow (called megakaryocytes). First, the experiments demonstrated that an enzyme called PRMT1 modifies RBM15. This enzyme adds a chemical mark called a methyl group at a specific site (an arginine amino acid) on the RNA-binding protein. Next, Zhang, Tran, Su et al. showed that the addition of this methyl group earmarks RBM15 for destruction. This means that an increase in PRMT1 levels reduces the amount of RBM15 in cells, while decreases in PRMT1 have the opposite effect. Further experiments showed that RBM15 normally processes the RNA messengers that carry the genetic instructions needed for the differentiation of bone marrow cells. An excess of PRMT1 enzyme leads to a lack of this RNA-binding protein. This in turn interferes with the differentiation process, and can contribute to the development of cancers such as megakaryocytic leukemia. Future work will therefore explore whether targeting PRMT1 with drugs could represent an effective treatment for these kinds of cancers. DOI:http://dx.doi.org/10.7554/eLife.07938.002
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Affiliation(s)
- Li Zhang
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
| | - Ngoc-Tung Tran
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
| | - Hairui Su
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
| | - Rui Wang
- Program of Molecular Pharmacology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Yuheng Lu
- Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Haiping Tang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Sayura Aoyagi
- Cell Signaling Technology, Inc., Danvers, United States
| | - Ailan Guo
- Cell Signaling Technology, Inc., Danvers, United States
| | - Alireza Khodadadi-Jamayran
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
| | - Dewang Zhou
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
| | - Kun Qian
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia, Athens, United States
| | - Todd Hricik
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Jocelyn Côté
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
| | - Xiaosi Han
- Department of Neurology, Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, United States
| | - Wenping Zhou
- Department of Internal Medicine, Zhengzhou - Henan Cancer Hospital, Zhengzhou, China
| | - Suparna Laha
- Division of Hematology and Oncology, University of Massachusetts Medical School, Worcester, United States
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Glen Raffel
- Division of Hematology and Oncology, University of Massachusetts Medical School, Worcester, United States
| | - Yanyan Liu
- Department of Internal Medicine, Zhengzhou - Henan Cancer Hospital, Zhengzhou, China
| | - Dongquan Chen
- Division of Preventive Medicine, The University of Alabama at Birmingham, Birmingham, United States
| | - Haitao Li
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Tim Townes
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
| | - Hengbin Wang
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia, Athens, United States
| | - Christina Leslie
- Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Minkui Luo
- Program of Molecular Pharmacology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Xinyang Zhao
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, The University of Alabama at Birmingham, Birmingham, United States
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Han YC, Vidigal JA, Mu P, Yao E, Singh I, González AJ, Concepcion CP, Bonetti C, Ogrodowski P, Carver B, Selleri L, Betel D, Leslie C, Ventura A. An allelic series of miR-17 ∼ 92-mutant mice uncovers functional specialization and cooperation among members of a microRNA polycistron. Nat Genet 2015; 47:766-75. [PMID: 26029871 PMCID: PMC4485521 DOI: 10.1038/ng.3321] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 05/04/2015] [Indexed: 01/07/2023]
Abstract
Polycistronic microRNA clusters are a common feature of vertebrate genomes. The coordinated expression of miRNAs belonging to different seed families from a single transcription unit suggests functional cooperation, but this hypothesis has not been experimentally tested. Here we report the characterization of an allelic series of genetically engineered mice harboring selective targeted deletions of individual components of miR-17~92. Our results demonstrate the co-existence of functional cooperation and specialization among members of this cluster, identify a novel function for the miR-17 seed family in controlling axial patterning in vertebrates, and show that loss of miR-19 selectively impairs Myc-driven tumorigenesis in two models of human cancer. By integrating phenotypic analysis and gene expression profiling, we provide a genome-wide view of how components of a polycistronic miRNA-cluster affect gene expression in vivo. The reagents and datasets reported here will accelerate exploration of the complex biological functions of this important miRNA cluster.
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Affiliation(s)
- Yoon-Chi Han
- 1] Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA. [2] Oncology Research Unit, Pfizer, Inc., Pearl River, New York, USA
| | - Joana A Vidigal
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ping Mu
- 1] Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA. [2] Weill Cornell Graduate School of Medical Sciences of Cornell University, New York, New York, USA
| | - Evelyn Yao
- 1] Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA. [2] Weill Cornell Graduate School of Medical Sciences of Cornell University, New York, New York, USA
| | - Irtisha Singh
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alvaro J González
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Carla P Concepcion
- 1] Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA. [2] Weill Cornell Graduate School of Medical Sciences of Cornell University, New York, New York, USA
| | - Ciro Bonetti
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Paul Ogrodowski
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Brett Carver
- 1] Human Oncology and Pathogenesis Program. Memorial Sloan Kettering Cancer Center, New York, New York, USA. [2] Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Licia Selleri
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, USA
| | - Doron Betel
- 1] Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York, USA. [2] Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Luo C, Osmanbeyoglu H, Leslie C, Li M. Essential role of the Ets transcription factor GABP in control of T cell responses to antigen stimulation (IRM15P.454). The Journal of Immunology 2015. [DOI: 10.4049/jimmunol.194.supp.199.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Upon antigen stimulation, naive T cells transition from cellular quiescence into cell cycle progression and initiate functional differentiation. Such a coordinated response is orchestrated by numerous transcriptional programs, among which include Ets protein-dependent regulation. The Ets family of transcription factors, characterized by an evolutionarily conserved DNA-binding domain, is modulated by T cell receptor (TCR) signaling; yet the specific Ets member that is crucial for antigen receptor-mediated response remains elusive. GA-binding protein (GABP), which is composed of GABPα and GABPβ, is the only obligate multimeric complex among Ets factors. T cell-specific ablation of Gabpa gene in mice leads to a profound reduction in peripheral T cells. In response to antigen stimulation in vitro, GABPα-deficient T cells show diminished proliferation, dysregulation of reactive oxygen species and impaired cell survival. In addition, mice lacking GABPα fail to mount an antigen-specific T cell response to Listeria Monocytogenes infection. Transcriptome analysis coupled with chromatin immunoprecipitation sequencing identifies GABPα as a key regulator of the folate-dependent one carbon metabolism as well as cellular balance of redox. Our findings reveal critical functions of GABP-dependent transcriptional program in the control of TCR-stimulated metabolic reprogramming.
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Affiliation(s)
- Chong Luo
- 1Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY
- 2Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Hatice Osmanbeyoglu
- 3Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Christina Leslie
- 3Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Ming Li
- 2Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY
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Park SM, Gönen M, Vu L, Minuesa G, Tivnan P, Barlowe TS, Taggart J, Lu Y, Deering RP, Hacohen N, Figueroa ME, Paietta E, Fernandez HF, Tallman MS, Melnick A, Levine R, Leslie C, Lengner CJ, Kharas MG. Musashi2 sustains the mixed-lineage leukemia-driven stem cell regulatory program. J Clin Invest 2015; 125:1286-98. [PMID: 25664853 DOI: 10.1172/jci78440] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 01/05/2015] [Indexed: 01/15/2023] Open
Abstract
Leukemia stem cells (LSCs) are found in most aggressive myeloid diseases and contribute to therapeutic resistance. Leukemia cells exhibit a dysregulated developmental program as the result of genetic and epigenetic alterations. Overexpression of the RNA-binding protein Musashi2 (MSI2) has been previously shown to predict poor survival in leukemia. Here, we demonstrated that conditional deletion of Msi2 in the hematopoietic compartment results in delayed leukemogenesis, reduced disease burden, and a loss of LSC function in a murine leukemia model. Gene expression profiling of these Msi2-deficient animals revealed a loss of the hematopoietic/leukemic stem cell self-renewal program and an increase in the differentiation program. In acute myeloid leukemia patients, the presence of a gene signature that was similar to that observed in Msi2-deficent murine LSCs correlated with improved survival. We determined that MSI2 directly maintains the mixed-lineage leukemia (MLL) self-renewal program by interacting with and retaining efficient translation of Hoxa9, Myc, and Ikzf2 mRNAs. Moreover, depletion of MLL target Ikzf2 in LSCs reduced colony formation, decreased proliferation, and increased apoptosis. Our data provide evidence that MSI2 controls efficient translation of the oncogenic LSC self-renewal program and suggest MSI2 as a potential therapeutic target for myeloid leukemia.
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Sevenich L, Bowman R, Mason S, Quail D, Rapaport F, Elie B, Brogi E, Brastianos P, Hahn W, Holsinger L, Massagué J, Leslie C, Joyce JA. Abstract IA18: A brain metastasis-promoting role for cathepsin S identified from analysis of tumor- and stroma-supplied proteolytic networks. Cancer Res 2015. [DOI: 10.1158/1538-7445.chtme14-ia18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer cells in an aggressive primary tumor are adept at exploiting their local tissue microenvironment. In contrast, when metastatic cells leave these favorable surroundings, they must possess or acquire traits that will allow them to survive and colonize foreign, potentially hostile tissue environments. The obstacles that metastasizing tumor cells encounter vary from organ to organ, and are highly influenced by non-cancerous stromal cells of the tumor microenvironment. For example, the blood-brain barrier, composed of endothelial cells, astrocytes and pericytes, presents a far more formidable structure for tumor cells to penetrate, compared to the fenestrated capillaries in the bone marrow.
While the primary tumor microenvironment has emerged as an important regulator of cancer progression, it is less well understood how different tissue environments influence metastatic processes. We used a dual species-specific microarray platform to uncover tumor-stroma interactions that modulate organ tropism of brain, bone and lung metastasis in animal models of cancer. Among the differentially regulated tumor- and stroma-specific genes, we identified cathepsin S as a novel regulator of breast-to-brain metastasis. In breast cancer patients, high cathepsin S expression at the primary site correlated with decreased brain metastasis-free survival. Both macrophages and tumor cells produce cathepsin S, and only the combined depletion significantly reduced brain metastasis in experimental models in vivo. We show that cathepsin S specifically mediates blood-brain barrier transmigration via proteolytic processing of the junctional adhesion molecule (JAM)-B. Pharmacological inhibition of cathepsin S significantly reduced experimental brain metastasis, supporting its consideration as a therapeutic target for this disease.
Citation Format: Lisa Sevenich, Robert Bowman, Steve Mason, Daniela Quail, Franck Rapaport, Benelita Elie, Edi Brogi, Priscilla Brastianos, William Hahn, Leslie Holsinger, Joan Massagué, Christina Leslie, Johanna A. Joyce. A brain metastasis-promoting role for cathepsin S identified from analysis of tumor- and stroma-supplied proteolytic networks. [abstract]. In: Abstracts: AACR Special Conference on Cellular Heterogeneity in the Tumor Microenvironment; 2014 Feb 26-Mar 1; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(1 Suppl):Abstract nr IA18. doi:10.1158/1538-7445.CHTME14-IA18
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Affiliation(s)
- Lisa Sevenich
- 1Memorial Sloan-Kettering Cancer Center, New York, NY,
| | - Robert Bowman
- 1Memorial Sloan-Kettering Cancer Center, New York, NY,
| | - Steve Mason
- 1Memorial Sloan-Kettering Cancer Center, New York, NY,
| | - Daniela Quail
- 1Memorial Sloan-Kettering Cancer Center, New York, NY,
| | | | - Benelita Elie
- 1Memorial Sloan-Kettering Cancer Center, New York, NY,
| | - Edi Brogi
- 1Memorial Sloan-Kettering Cancer Center, New York, NY,
| | | | | | | | - Joan Massagué
- 1Memorial Sloan-Kettering Cancer Center, New York, NY,
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Park C, Yalcin S, Carty M, Shin J, Miller R, Leslie C. Anti-aging interventions reverse hematopoietic stem cell aging via regulation of micrornas. Exp Hematol 2014. [DOI: 10.1016/j.exphem.2014.07.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Furman RR, Cheng S, Lu P, Setty M, Perez AR, Guo A, Racchumi J, Xu G, Wu H, Ma J, Steggerda SM, Coleman M, Leslie C, Wang YL. Ibrutinib resistance in chronic lymphocytic leukemia. N Engl J Med 2014; 370:2352-4. [PMID: 24869597 PMCID: PMC4512173 DOI: 10.1056/nejmc1402716] [Citation(s) in RCA: 226] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
MESH Headings
- Adenine/analogs & derivatives
- Agammaglobulinaemia Tyrosine Kinase
- Drug Resistance, Neoplasm/genetics
- Female
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Middle Aged
- Phosphorylation
- Piperidines
- Point Mutation
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/chemistry
- Protein-Tyrosine Kinases/metabolism
- Pyrazoles/metabolism
- Pyrazoles/therapeutic use
- Pyrimidines/metabolism
- Pyrimidines/therapeutic use
- Receptors, Antigen, B-Cell/metabolism
- Recurrence
- Sequence Analysis, DNA
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Park SM, Deering RP, Lu Y, Tivnan P, Lianoglou S, Al-Shahrour F, Ebert BL, Hacohen N, Leslie C, Daley GQ, Lengner CJ, Kharas MG. Musashi-2 controls cell fate, lineage bias, and TGF-β signaling in HSCs. ACTA ACUST UNITED AC 2014; 211:71-87. [PMID: 24395885 PMCID: PMC3892968 DOI: 10.1084/jem.20130736] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Musashi-2 is an important regulator of the hematopoietic stem cell translatome and balances HSC homeostasis and lineage bias. Hematopoietic stem cells (HSCs) are maintained through the regulation of symmetric and asymmetric cell division. We report that conditional ablation of the RNA-binding protein Msi2 results in a failure of HSC maintenance and engraftment caused by a loss of quiescence and increased commitment divisions. Contrary to previous studies, we found that these phenotypes were independent of Numb. Global transcriptome profiling and RNA target analysis uncovered Msi2 interactions at multiple nodes within pathways that govern RNA translation, stem cell function, and TGF-β signaling. Msi2-null HSCs are insensitive to TGF-β–mediated expansion and have decreased signaling output, resulting in a loss of myeloid-restricted HSCs and myeloid reconstitution. Thus, Msi2 is an important regulator of the HSC translatome and balances HSC homeostasis and lineage bias.
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Affiliation(s)
- Sun-Mi Park
- Molecular Pharmacology and Chemistry Program, 2 Center for Cell Engineering, and 3 Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
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Loeb G, Canner D, Khan A, Darnell R, Leslie C, Rudensky A. Context specific regulation of microRNA targets in the immune system (P1142). The Journal of Immunology 2013. [DOI: 10.4049/jimmunol.190.supp.64.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
MicroRNAs (miRNAs) are key gene expression regulators—their misexpression can cause both immune dysfunction and cancer. However, most miRNA targets remain unknown, limiting mechanistic insight. Combining genetic and biochemical approaches we generated a transcriptome-wide map of miR-155 targets in T cells. High throughput sequencing of cross-linked immunoprecipitated (HITS-CLIP) Argonaute bound transcript fragments in miR-155 sufficient and deficient cells identified hundreds of direct targets for this miRNA in T cells. This map shed insight on known and novel miRNA phenotypes and demonstrated that miRNAs directly regulate transcripts without canonical target motifs. In addition to T cells, miR-155 is expressed in many innate and adaptive immune cells following activation and its deletion leads to varied cell-type specific phenotypes. We hypothesized that miRNAs have diverse functions in different contexts through regulation of different targets. To reveal the extent and mechanism of context specific miRNA targeting, we employed RNA-seq and HITS-CLIP in wild type and miR-155 deficient T cells, B cells, and dendritic cells. Furthermore, we employed polyA-seq to determine how alternative polyadenylation affects context specific targeting. Immune system complexity is generated from a limited set of genes; by revealing how regulatory factors are repurposed in different cell types, our studies will provide insight into fundamental mechanisms of immunological gene regulation.
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Affiliation(s)
- Gabriel Loeb
- 1Memorial Sloan-Kettering Cancer Center, New York, NY
| | - David Canner
- 1Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Aly Khan
- 1Memorial Sloan-Kettering Cancer Center, New York, NY
- 3University of Chicago, Chicago, IL
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Kobos R, Nagai M, Tsuda M, Merl MY, Saito T, Laé M, Mo Q, Olshen A, Lianoglou S, Leslie C, Ostrovnaya I, Antczak C, Djaballah H, Ladanyi M. Combining integrated genomics and functional genomics to dissect the biology of a cancer-associated, aberrant transcription factor, the ASPSCR1-TFE3 fusion oncoprotein. J Pathol 2013; 229:743-754. [PMID: 23288701 DOI: 10.1002/path.4158] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 12/07/2012] [Accepted: 12/13/2012] [Indexed: 12/30/2022]
Abstract
Oncogenic rearrangements of the TFE3 transcription factor gene are found in two distinct human cancers. These include ASPSCR1-TFE3 in all cases of alveolar soft part sarcoma (ASPS) and ASPSCR1-TFE3, PRCC-TFE3, SFPQ-TFE3 and others in a subset of paediatric and adult RCCs. Here we examined the functional properties of the ASPSCR1-TFE3 fusion oncoprotein, defined its target promoters on a genome-wide basis and performed a high-throughput RNA interference screen to identify which of its transcriptional targets contribute to cancer cell proliferation. We first confirmed that ASPSCR1-TFE3 has a predominantly nuclear localization and functions as a stronger transactivator than native TFE3. Genome-wide location analysis performed on the FU-UR-1 cell line, which expresses endogenous ASPSCR1-TFE3, identified 2193 genes bound by ASPSCR1-TFE3. Integration of these data with expression profiles of ASPS tumour samples and inducible cell lines expressing ASPSCR1-TFE3 defined a subset of 332 genes as putative up-regulated direct targets of ASPSCR1-TFE3, including MET (a previously known target gene) and 64 genes as down-regulated targets of ASPSCR1-TFE3. As validation of this approach to identify genuine ASPSCR1-TFE3 target genes, two up-regulated genes bound by ASPSCR1-TFE3, CYP17A1 and UPP1, were shown by multiple lines of evidence to be direct, endogenous targets of transactivation by ASPSCR1-TFE3. As the results indicated that ASPSCR1-TFE3 functions predominantly as a strong transcriptional activator, we hypothesized that a subset of its up-regulated direct targets mediate its oncogenic properties. We therefore chose 130 of these up-regulated direct target genes to study in high-throughput RNAi screens, using FU-UR-1 cells. In addition to MET, we provide evidence that 11 other ASPSCR1-TFE3 target genes contribute to the growth of ASPSCR1-TFE3-positive cells. Our data suggest new therapeutic possibilities for cancers driven by TFE3 fusions. More generally, this work establishes a combined integrated genomics/functional genomics strategy to dissect the biology of oncogenic, chimeric transcription factors.
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Affiliation(s)
- Rachel Kobos
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Makoto Nagai
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Masumi Tsuda
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Man Yee Merl
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Tsuyoshi Saito
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Marick Laé
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Qianxing Mo
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Adam Olshen
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Steven Lianoglou
- Computational Biology Program, Sloan-Kettering Institute, New York, USA
| | - Christina Leslie
- Computational Biology Program, Sloan-Kettering Institute, New York, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Christophe Antczak
- High-throughput Screening Core Facility, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Hakim Djaballah
- High-throughput Screening Core Facility, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Marc Ladanyi
- Department of Pathology and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, USA
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46
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Abstract
Gene regulatory programs in distinct cell types are maintained in large part through the cell-type–specific binding of transcription factors (TFs). The determinants of TF binding include direct DNA sequence preferences, DNA sequence preferences of cofactors, and the local cell-dependent chromatin context. To explore the contribution of DNA sequence signal, histone modifications, and DNase accessibility to cell-type–specific binding, we analyzed 286 ChIP-seq experiments performed by the ENCODE Consortium. This analysis included experiments for 67 transcriptional regulators, 15 of which were profiled in both the GM12878 (lymphoblastoid) and K562 (erythroleukemic) human hematopoietic cell lines. To model TF-bound regions, we trained support vector machines (SVMs) that use flexible k-mer patterns to capture DNA sequence signals more accurately than traditional motif approaches. In addition, we trained SVM spatial chromatin signatures to model local histone modifications and DNase accessibility, obtaining significantly more accurate TF occupancy predictions than simpler approaches. Consistent with previous studies, we find that DNase accessibility can explain cell-line–specific binding for many factors. However, we also find that of the 10 factors with prominent cell-type–specific binding patterns, four display distinct cell-type–specific DNA sequence preferences according to our models. Moreover, for two factors we identify cell-specific binding sites that are accessible in both cell types but bound only in one. For these sites, cell-type–specific sequence models, rather than DNase accessibility, are better able to explain differential binding. Our results suggest that using a single motif for each TF and filtering for chromatin accessible loci is not always sufficient to accurately account for cell-type–specific binding profiles.
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Affiliation(s)
- Aaron Arvey
- Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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47
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Arvey A, Tempera I, Tsai K, Chen HS, Tikhmyanova N, Klichinsky M, Leslie C, Lieberman PM. An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactions. Cell Host Microbe 2013; 12:233-45. [PMID: 22901543 DOI: 10.1016/j.chom.2012.06.008] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 04/13/2012] [Accepted: 06/01/2012] [Indexed: 02/06/2023]
Abstract
Epstein-Barr virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly available high-throughput sequencing data sets for human lymphoblastoid cell lines mapped to the EBV genome. We found that viral lytic genes are coexpressed with cellular cancer-associated pathways, suggesting that the lytic cycle may play an unexpected role in virus-mediated oncogenesis. Host regulators of viral oncogene expression and chromosome structure were identified and validated, revealing a role for the B cell-specific protein Pax5 in viral gene regulation and the cohesin complex in regulating higher order chromatin structure. Our findings provide a deeper understanding of latent viral persistence in oncogenesis and establish a valuable viral genomics resource for future exploration.
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Affiliation(s)
- Aaron Arvey
- Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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48
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Basso K, Schneider C, Shen Q, Holmes AB, Setty M, Leslie C, Dalla-Favera R. BCL6 positively regulates AID and germinal center gene expression via repression of miR-155. ACTA ACUST UNITED AC 2012; 209:2455-65. [PMID: 23166356 PMCID: PMC3526356 DOI: 10.1084/jem.20121387] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The BCL6 proto-oncogene encodes a transcriptional repressor that is required for germinal center (GC) formation and whose de-regulation is involved in lymphomagenesis. Although substantial evidence indicates that BCL6 exerts its function by repressing the transcription of hundreds of protein-coding genes, its potential role in regulating gene expression via microRNAs (miRNAs) is not known. We have identified a core of 15 miRNAs that show binding of BCL6 in their genomic loci and are down-regulated in GC B cells. Among BCL6 validated targets, miR-155 and miR-361 directly modulate AID expression, indicating that via repression of these miRNAs, BCL6 up-regulates AID. Similarly, the expression of additional genes relevant for the GC phenotype, including SPI1, IRF8, and MYB, appears to be sustained via BCL6-mediated repression of miR-155. These findings identify a novel mechanism by which BCL6, in addition to repressing protein coding genes, promotes the expression of important GC functions by repressing specific miRNAs.
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Affiliation(s)
- Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY 10027, USA.
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49
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Samstein RM, Arvey A, Josefowicz SZ, Peng X, Reynolds A, Sandstrom R, Neph S, Sabo P, Kim JM, Liao W, Li MO, Leslie C, Stamatoyannopoulos JA, Rudensky AY. Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Cell 2012; 151:153-66. [PMID: 23021222 PMCID: PMC3493256 DOI: 10.1016/j.cell.2012.06.053] [Citation(s) in RCA: 355] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/06/2012] [Accepted: 06/29/2012] [Indexed: 12/13/2022]
Abstract
Regulatory T (Treg) cells, whose identity and function are defined by the transcription factor Foxp3, are indispensable for immune homeostasis. It is unclear whether Foxp3 exerts its Treg lineage specification function through active modification of the chromatin landscape and establishment of new enhancers or by exploiting a pre-existing enhancer landscape. Analysis of the chromatin accessibility of Foxp3-bound enhancers in Treg and Foxp3-negative T cells showed that Foxp3 was bound overwhelmingly to preaccessible enhancers occupied by its cofactors in precursor cells or a structurally related predecessor. Furthermore, the bulk of Foxp3-bound Treg cell enhancers lacking in Foxp3(-) CD4(+) cells became accessible upon T cell receptor activation prior to Foxp3 expression, and only a small subset associated with several functionally important genes were exclusively Treg cell specific. Thus, in a late cellular differentiation process, Foxp3 defines Treg cell functionality in an "opportunistic" manner by largely exploiting the preformed enhancer network instead of establishing a new enhancer landscape.
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Affiliation(s)
- Robert M Samstein
- Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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50
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Pastar I, Khan AA, Stojadinovic O, Lebrun EA, Medina MC, Brem H, Kirsner RS, Jimenez JJ, Leslie C, Tomic-Canic M. Induction of specific microRNAs inhibits cutaneous wound healing. J Biol Chem 2012; 287:29324-35. [PMID: 22773832 DOI: 10.1074/jbc.m112.382135] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Chronic nonhealing wounds, such as venous ulcers (VUs), are a widespread and serious medical problem with high morbidity and mortality. The molecular pathology of VUs remains poorly understood, impeding the development of effective treatment strategies. Using mRNA expression profiling of VUs biopsies and computational analysis, we identified a candidate set of microRNAs with lowered target gene expression. Among these candidates, miR-16, -20a, -21, -106a -130a, and -203 were confirmed to be aberrantly overexpressed in a cohort study of 10 VU patients by quantitative PCR and in situ hybridizations. These microRNAs were predicted to target multiple genes important for wound healing, including early growth response factor 3, vinculin, and leptin receptor (LepR). Overexpression of the top up-regulated miRNAs, miR-21 and miR-130a, in primary human keratinocytes down-regulated expression of the endogenous LepR and early growth response factor 3. The luciferase reporter assay verified LepR as a direct target for miR-21 and miR-130a. Both miR-21 and miR-130a delayed epithelialization in an acute human skin wound model. Furthermore, in vivo overexpression of miR-21 inhibited epithelialization and granulation tissue formation in a rat wound model. Our results identify a novel mechanism in which overexpression of specific set of microRNAs inhibits wound healing, resulting in new potential molecular markers and targets for therapeutic intervention.
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Affiliation(s)
- Irena Pastar
- Wound Healing and Regenerative Medicine Research Program, Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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