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Santoro A, Assenat E, Yau T, Delord JP, Maur M, Knox J, Cattan S, Lee KH, Del Conte G, Springfeld C, Leo E, Xyrafas A, Fairchild L, Mardjuadi F, Chan SL. A phase Ib/II trial of capmatinib plus spartalizumab vs. spartalizumab alone in patients with pretreated hepatocellular carcinoma. JHEP Rep 2024; 6:101021. [PMID: 38617599 PMCID: PMC11009449 DOI: 10.1016/j.jhepr.2024.101021] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 04/16/2024] Open
Abstract
Background & aims This phase Ib/II trial evaluated the safety and efficacy of capmatinib in combination with spartalizumab or spartalizumab alone in patients with advanced hepatocellular carcinoma (HCC). Methods Eligible patients who had progressed or were intolerant to sorafenib received escalating doses of capmatinib 200 mg, 300 mg, and 400 mg twice a day (bid) plus spartalizumab 300 mg every 3 weeks (q3w) in the phase Ib study. Once the recommended phase II dose (RP2D) was determined, the phase II study commenced with randomised 1:1 treatment with either capmatinib + spartalizumab (n = 32) or spartalizumab alone (n = 30). Primary endpoints were safety and tolerability (phase Ib) and investigator-assessed overall response rate per RECIST v1.1 for combination vs. single-agent arms using a Bayesian logistic regression model (phase II). Results In phase Ib, the RP2D for capmatinib in combination with spartalizumab was determined to be 400 mg bid. Dose-limiting toxicity consisting of grade 3 diarrhoea was reported in one patient at the capmatinib 400 mg bid + spartalizumab 300 mg q3w dose level. The primary endpoint in the phase II study was not met. The observed overall response rate in the capmatinib + spartalizumab arm was 9.4% vs. 10% in the spartalizumab arm. The most common any-grade treatment-related adverse events (TRAEs, ≥20%) were nausea (37.5%), asthenia and vomiting (28.1% each), diarrhoea, pyrexia, and decreased appetite (25.0% each) in the combination arm; TRAEs ≥10% were pruritus (23.3%), and rash (10.0%) in the spartalizumab-alone arm. Conclusion Capmatinib at 400 mg bid plus spartalizumab 300 mg q3w was established as the RP2D, with manageable toxicities and no significant safety signals, but the combination did not show superior clinical activity compared with spartalizumab single-agent treatment in patients with advanced HCC who had previously been treated with sorafenib. Impact and implications Simultaneous targeting of MET and programmed cell death protein 1 may provide synergistic clinical benefit in patients with advanced HCC. This is the first trial to report a combination of capmatinib (MET inhibitor) and spartalizumab (programmed cell death protein 1 inhibitor) as second-line treatment after sorafenib for advanced HCC. The combination did not show superior clinical activity compared with spartalizumab single-agent treatment in patients with advanced HCC who had previously been treated with sorafenib. The results indicate that there is a clear need to identify a reliable predictive marker of response for HCC and to identify patients with HCC that would benefit from the combination of checkpoint inhibitor +/- targeted therapy. Clinical trial number NCT02795429.
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Affiliation(s)
- Armando Santoro
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele – Milan, Italy
- IRCCS Humanitas Research Hospital, Humanitas Cancer Center, Via Manzoni 56, Rozzano, Milan, Italy
| | - Eric Assenat
- Hopital Arnaud de Villeneuve Montpellier Cedex 5, Herault, France
| | - Thomas Yau
- Department of Medicine, Queen Mary Hospital, Hong Kong, China
| | | | - Michela Maur
- Oncology Unit, AOU Policlinico Modena and University Study of Modena and Reggio Emilia, Modena, Italy
| | | | | | - Kyung-Hun Lee
- Seoul National University Hospital, Seoul, South Korea
| | - Gianluca Del Conte
- Department of Oncology, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
| | - Christoph Springfeld
- Nat. Centrum f. Tumorerkrankungen, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Elisa Leo
- Novartis Pharma AG, Basel, Switzerland
| | | | - Lauren Fairchild
- Oncology Data Science, Novartis Institutes for BioMedical Research, Cambridge, USA
| | - Feby Mardjuadi
- Novartis Institutes for Biomedical Research Co., Ltd., Shanghai, China
| | - Stephen L. Chan
- State Key Laboratory of Translational Oncology, Department of Clinical Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
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Fairchild L, Whalen J, D'Aco K, Wu J, Gustafson CB, Solovieff N, Su F, Leary RJ, Campbell CD, Balbin OA. Clonal hematopoiesis detection in patients with cancer using cell-free DNA sequencing. Sci Transl Med 2023; 15:eabm8729. [PMID: 36989374 DOI: 10.1126/scitranslmed.abm8729] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
In the context of cancer, clonal hematopoiesis of indeterminate potential (CHIP) is associated with the development of therapy-related myeloid neoplasms and shorter overall survival. Cell-free DNA (cfDNA) sequencing is becoming widely adopted for genomic screening of patients with cancer but has not been used extensively to determine CHIP status because of a requirement for matched blood and tumor sequencing. We present an accurate classification approach to determine the CH status from cfDNA sequencing alone, applying our model to 4324 oncology clinical cfDNA samples. Using this method, we determined that 30.3% of patients in this cohort have evidence of CH, and the incidence of CH varies by tumor type. Matched RNA sequencing data show evidence of increased inflammation, especially neutrophil activation, within the tumors and tumor microenvironments of patients with CH. In addition, patients with CH had evidence of neutrophil activation systemically, pointing to a potential mechanism of action for the worse outcomes associated with CH status. Neutrophil activation may be one of many mechanisms, however, because patients with estrogen receptor-positive breast cancer harboring TET2 frameshift mutations had worse outcomes but similar neutrophil frequencies to patients without CH. Together, these data show the feasibility of detecting CH through cfDNA sequencing alone and an application of this method, demonstrating increased inflammation in patients with CH both systemically and in the tumor microenvironment.
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Affiliation(s)
- Lauren Fairchild
- Novartis Institutes for BioMedical Research Inc., Cambridge, MA 02139, USA
| | - Jeanne Whalen
- Novartis Institutes for BioMedical Research Inc., Cambridge, MA 02139, USA
| | - Katie D'Aco
- Novartis Institutes for BioMedical Research Inc., Cambridge, MA 02139, USA
| | - Jincheng Wu
- Novartis Institutes for BioMedical Research Inc., Cambridge, MA 02139, USA
| | | | - Nadia Solovieff
- Novartis Institutes for BioMedical Research Inc., Cambridge, MA 02139, USA
| | - Fei Su
- Novartis Pharmaceuticals Corporation, East Hanover, NJ 07936, USA
| | - Rebecca J Leary
- Novartis Institutes for BioMedical Research Inc., Cambridge, MA 02139, USA
| | | | - O Alejandro Balbin
- Novartis Institutes for BioMedical Research Inc., Cambridge, MA 02139, USA
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Wolf J, Garon E, Groen H, Tan D, Le Mouhaer S, Riester M, Ji L, Robeva A, Fairchild L, Boran A, Heist R. Capmatinib response in patients with advanced non–small cell lung cancer (NSCLC) harboring focal MET amplifications: Analysis from the phase 2, multicohort GEOMETRY mono-1 study. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)00859-0] [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: 11/28/2022]
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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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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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Abstract
The relationship between physical fitness and field independence was assessed by measuring embedded-figures test performance in the following four groups of children in Grades 4 through 6: (1) 93 boys high in physical fitness, (2) 92 girls high in physical fitness, (3) 67 boys low in physical fitness, and (4) 77 girls low in physical fitness. The group of girls low in physical fitness was significantly more field dependent than the other three groups. No significant differences were found among the other three groups. It appears that skill in physical activities may be related to the embedded-figures test performance of girls, but not boys. In fact, girls skilled in physical activities may be as field independent as boys.
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Heist R, Garon E, Tan D, Groen H, Seto T, Smit E, Nwana N, Fairchild L, Balbin A, Yan M, Wang I, Giovannini M, Sankaran B, Wolf J. B11 Accurate Detection of METex14 Mutations in Non-Small Cell Lung Cancer (NSCLC) with Comprehensive Genomic Sequencing: Results from the GEOMETRY Mono-1 Study. J Thorac Oncol 2020. [DOI: 10.1016/j.jtho.2019.12.080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Heist RS, Garon EB, Tan DS, Groen HJ, Seto T, Smit EF, Fairchild L, Balbin A, Yan M, Giovannini M, Akimov M, Sankaran B, Nwana N, Wolf J. Abstract A029: Biomarker analysis of patients withMETΔex14 mutated non-small-cell lung cancer (NSCLC) treated with capmatinib in the GEOMETRY mono-1 study. Biomarkers 2019. [DOI: 10.1158/1535-7163.targ-19-a029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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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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Pelossof R, Fairchild L, Leslie CS, Fellmann C. Abstract LB-271: SplashRNA, a sequential classification algorithm for ultra-potent RNAi. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-271] [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 present SplashRNA, a sequential classifier - analogous to face detection algorithms - to predict ultra-potent microRNA-based short hairpin RNAs (shRNAs) for virtually any gene. Trained on existing and novel large-scale datasets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a given gene. Combined with the optimized miR-E backbone, >90% of high-scoring SplashRNA predictions trigger >85% protein knockdown when expressed from a single genomic integration. SplashRNA can significantly improve the accuracy of loss-of-function genetics studies and facilitates the generation of compact shRNA libraries. The open source SplashRNA platform completes the RNAi toolkit to harness microRNA-based shRNAs for robust single-gene and multiplexed inducible and reversible target inhibition.
Citation Format: Raphael Pelossof, Lauren Fairchild, Christina S. Leslie, Christof Fellmann. SplashRNA, a sequential classification algorithm for ultra-potent RNAi [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-271. doi:10.1158/1538-7445.AM2017-LB-271
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12
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Philip M, Fairchild L, Sun L, Horste EL, Camara S, Shakiba M, Scott AC, Viale A, Lauer P, Merghoub T, Hellmann MD, Wolchok JD, Leslie CS, Schietinger A. Chromatin states define tumour-specific T cell dysfunction and reprogramming. Nature 2017. [PMID: 28514453 DOI: 10.1038/nature22367.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tumour-specific CD8 T cells in solid tumours are dysfunctional, allowing tumours to progress. The epigenetic regulation of T cell dysfunction and therapeutic reprogrammability (for example, to immune checkpoint blockade) is not well understood. Here we show that T cells in mouse tumours differentiate through two discrete chromatin states: a plastic dysfunctional state from which T cells can be rescued, and a fixed dysfunctional state in which the cells are resistant to reprogramming. We identified surface markers associated with each chromatin state that distinguished reprogrammable from non-reprogrammable PD1hi dysfunctional T cells within heterogeneous T cell populations from tumours in mice; these surface markers were also expressed on human PD1hi tumour-infiltrating CD8 T cells. Our study has important implications for cancer immunotherapy as we define key transcription factors and epigenetic programs underlying T cell dysfunction and surface markers that predict therapeutic reprogrammability.
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Affiliation(s)
- Mary Philip
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Lauren Fairchild
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Liping Sun
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ellen L Horste
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Steven Camara
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Mojdeh Shakiba
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Weill Cornell Medical College, Cornell University, New York, New York 10065, USA
| | - Andrew C Scott
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Weill Cornell Medical College, Cornell University, New York, New York 10065, USA
| | - Agnes Viale
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Peter Lauer
- Aduro Biotech, Inc., Berkeley, California 94720, USA
| | - Taha Merghoub
- Weill Cornell Medical College, Cornell University, New York, New York 10065, USA.,Melanoma and Immunotherapeutics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Matthew D Hellmann
- Weill Cornell Medical College, Cornell University, New York, New York 10065, USA.,Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jedd D Wolchok
- Weill Cornell Medical College, Cornell University, New York, New York 10065, USA.,Melanoma and Immunotherapeutics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Weill Cornell Medical College, Cornell University, New York, New York 10065, USA
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13
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Pelossof R, Fairchild L, Huang CH, Widmer C, Sreedharan VT, Sinha N, Lai DY, Guan Y, Premsrirut PK, Tschaharganeh DF, Hoffmann T, Thapar V, Xiang Q, Garippa RJ, Rätsch G, Zuber J, Lowe SW, Leslie CS, Fellmann C. Prediction of potent shRNAs with a sequential classification algorithm. Nat Biotechnol 2017; 35:350-353. [PMID: 28263295 PMCID: PMC5416823 DOI: 10.1038/nbt.3807] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [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: 10/21/2016] [Accepted: 01/18/2017] [Indexed: 12/31/2022]
Abstract
We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel datasets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a given gene. Combined with an optimized miR-E backbone, >90% of high-scoring SplashRNA predictions trigger >85% protein knockdown when expressed from a single genomic integration. SplashRNA can significantly improve the accuracy of loss-of-function genetics studies and facilitates the generation of compact shRNA libraries.
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Affiliation(s)
- Raphael Pelossof
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lauren Fairchild
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York, USA
| | - Chun-Hao Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York, USA
| | - Christian Widmer
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Machine Learning Group, Department of Computer Science, Berlin Institute of Technology, Berlin, Germany
| | - Vipin T Sreedharan
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | | | | | | | - Darjus F Tschaharganeh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Vishal Thapar
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Qing Xiang
- RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ralph J Garippa
- RNAi Core, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gunnar Rätsch
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Cell and Developmental Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York, USA.,Howard Hughes Medical Institute and Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christof Fellmann
- Mirimus Inc., Woodbury, New York, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
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14
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Philip M, Fairchild L, Sun L, Viale A, Camara S, Horste E, Merghoub T, Wolchok JD, Leslie CS, Schietinger A. Abstract PR09: Identifying the epigenetic code of tumor-specific CD8 T cell dysfunction and therapeutic reprogramming. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6066.imm2016-pr09] [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
Mutant neoantigens are commonly expressed in human solid tumors, and CD8 T cells specific for such antigens are detected in cancer patients. However, we know that these tumor-specific T cells are non-functional because despite their presence, tumors progress and often eventually cause death. Distinct T cell differentiation states are associated with specific epigenetic states that define the T cell's functional and phenotypic properties. It is currently not known what epigenetic changes establish and regulate tumor-specific CD8 T cell dysfunction and whether specific epigenetic modifications in dysfunctional T cells determine the ability to respond to therapeutic interventions such as checkpoint blockade (PD-1 and CTLA-4). Here, for the first time, we (1) characterize the progressive chromatin remodeling underlying T cell differentiation to the dysfunctional state in mouse and human tumors, and (2) provide insights into the epigenetic and transcriptional regulatory mechanisms determining T cell susceptibility to therapeutic reprogramming.
Using a genetic cancer mouse model in which tamoxifen treatment induces expression of an oncogenic driver neoantigen, SV40 large T antigen (Tag), we previously showed that tumor-specific CD8 T cells (TCRSV40-I) become unresponsive early during tumorigenesis, even before the emergence of a pathologically-defined malignant tumor (pre-malignant phase). While CD8 T cell dysfunction was initially reversible, it ultimately became a fixed state that could not be rescued by therapeutic interventions such as PD1 checkpoint blockade.
To identify the hierarchical changes in chromatin states resulting in “dysfunction imprinting,” we used the “Assay for Transposase-Accessible Chromatin using Sequencing” (ATAC-Seq) to map the genome-wide changes in chromatin accessibility in TCRSV40-I cells over the course of tumor development. In parallel, we carried our RNA-Seq on all samples to determine the interplay between chromatin remodeling and transcriptional networks. Substantial chromatin remodeling occurred during early T cell activation in the pre-malignant lesion (day 5), followed by a second wave of chromatin accessibility changes between day 7 and 14. Strikingly, after the second wave, no further CD8 T cell chromatin remodeling occurred during tumorigenesis, even after progression to an advanced late-stage tumor with an immunosuppressive microenvironment. Interestingly, these 2 distinct chromatin accessibility patterns (states 1 and 2) in dysfunctional TCRSV40-I correlated temporally with the plastic and fixed dysfunctional states and susceptibility to therapeutic reprogramming in vivo. To understand the transition from plastic to imprinted dysfunction, we analyzed the differential expression of transcription factors (TF) in conjunction with changes in peak accessibility at TF-binding motifs genome-wide. We identified a network including CD8 T cell regulatory TF such as TCF1, LEF1, BLIMP1, and BACH2 as well as less-well-characterized TF (NR4A2, TOX) potentially controlling differentiation to the dysfunctional state. Moreover, ATAC-Seq analysis of human tumor-infiltrating CD8 T cells revealed similar tumor-associated changes in peak accessibility, and studies are ongoing to assess the associated TF networks.
In this study, we have defined discrete chromatin states and associated transcriptional networks underlying plastic and fixed dysfunction in tumor-specific T cells, thus providing new insights into the genomic control circuitry of T cell differentiation/dysfunction that may point to new strategies for cellular reprogramming of T cells for cancer immunotherapy.
Citation Format: Mary Philip, Lauren Fairchild, Liping Sun, Agnes Viale, Steven Camara, Ellen Horste, Taha Merghoub, Jedd D. Wolchok, Christina S. Leslie, Andrea Schietinger. Identifying the epigenetic code of tumor-specific CD8 T cell dysfunction and therapeutic reprogramming [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr PR09.
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Affiliation(s)
- Mary Philip
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Liping Sun
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Steven Camara
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ellen Horste
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Taha Merghoub
- Memorial Sloan Kettering Cancer Center, New York, NY
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15
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Pelossof R, Chow OS, Fairchild L, Smith JJ, Setty M, Chen CT, Chen Z, Egawa F, Avila K, Leslie CS, Garcia-Aguilar J. Integrated genomic profiling identifies microRNA-92a regulation of IQGAP2 in locally advanced rectal cancer. Genes Chromosomes Cancer 2016; 55:311-321. [PMID: 26865277 DOI: 10.1002/gcc.22329] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 10/19/2015] [Accepted: 10/20/2015] [Indexed: 01/24/2023] Open
Abstract
Locally advanced rectal cancer (LARC) is treated with chemoradiation prior to surgical excision, leaving residual tumors altered or completely absent. Integrating layers of genomic profiling might identify regulatory pathways relevant to rectal tumorigenesis and inform therapeutic decisions and further research. We utilized formalin-fixed, paraffin-embedded pre-treatment LARC biopsies (n=138) and compared copy number, mRNA, and miRNA expression with matched normal rectal mucosa. An integrative model was used to predict regulatory interactions to explain gene expression changes. These predictions were evaluated in vitro using multiple colorectal cancer cell lines. The Cancer Genome Atlas (TCGA) was also used as an external cohort to validate our genomic profiling and predictions. We found differentially expressed mRNAs and miRNAs that characterize LARC. Our integrative model predicted the upregulation of miR-92a, miR-182, and miR-221 expression to be associated with downregulation of their target genes after adjusting for the effect of copy number alterations. Cell line studies using miR-92a mimics and inhibitors demonstrate that miR-92a expression regulates IQGAP2 expression. We show that endogenous miR-92a expression is inversely associated with endogenous KLF4 expression in multiple cell lines, and that this relationship is also present in rectal cancers of TCGA. Our integrative model predicted regulators of gene expression change in LARC using pre-treatment FFPE tissues. Our methodology implicated multiple regulatory interactions, some of which are corroborated by independent lines of study, while others indicate new opportunities for investigation.
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Affiliation(s)
- Raphael Pelossof
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Oliver S Chow
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lauren Fairchild
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - J Joshua Smith
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manu Setty
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chin-Tung Chen
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Fumiko Egawa
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Karin Avila
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christina S Leslie
- Computational Biology Program, Memorial 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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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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Verma A, Jiang Y, Du W, Fairchild L, Melnick A, Elemento O. Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma. Genome Med 2015; 7:110. [PMID: 26521025 PMCID: PMC4628784 DOI: 10.1186/s13073-015-0230-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [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: 05/08/2015] [Accepted: 10/08/2015] [Indexed: 12/14/2022] Open
Abstract
Background Gene profiling of diffuse large B cell lymphoma (DLBCL) has revealed broad gene expression deregulation compared to normal B cells. While many studies have interrogated well known and annotated genes in DLBCL, none have yet performed a systematic analysis to uncover novel unannotated long non-coding RNAs (lncRNA) in DLBCL. In this study we sought to uncover these lncRNAs by examining RNA-seq data from primary DLBCL tumors and performed supporting analysis to identify potential role of these lncRNAs in DLBCL. Methods We performed a systematic analysis of novel lncRNAs from the poly-adenylated transcriptome of 116 primary DLBCL samples. RNA-seq data were processed using de novo transcript assembly pipeline to discover novel lncRNAs in DLBCL. Systematic functional, mutational, cross-species, and co-expression analyses using numerous bioinformatics tools and statistical analysis were performed to characterize these novel lncRNAs. Results We identified 2,632 novel, multi-exonic lncRNAs expressed in more than one tumor, two-thirds of which are not expressed in normal B cells. Long read single molecule sequencing supports the splicing structure of many of these lncRNAs. More than one-third of novel lncRNAs are differentially expressed between the two major DLBCL subtypes, ABC and GCB. Novel lncRNAs are enriched at DLBCL super-enhancers, with a fraction of them conserved between human and dog lymphomas. We see transposable elements (TE) overlap in the exonic regions; particularly significant in the last exon of the novel lncRNAs suggest potential usage of cryptic TE polyadenylation signals. We identified highly co-expressed protein coding genes for at least 88 % of the novel lncRNAs. Functional enrichment analysis of co-expressed genes predicts a potential function for about half of novel lncRNAs. Finally, systematic structural analysis of candidate point mutations (SNVs) suggests that such mutations frequently stabilize lncRNA structures instead of destabilizing them. Conclusions Discovery of these 2,632 novel lncRNAs in DLBCL significantly expands the lymphoma transcriptome and our analysis identifies potential roles of these lncRNAs in lymphomagenesis and/or tumor maintenance. For further studies, these novel lncRNAs also provide an abundant source of new targets for antisense oligonucleotide pharmacology, including shared targets between human and dog lymphomas. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0230-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Akanksha Verma
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA.,Institute for Precision Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Yanwen Jiang
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA.,Institute for Precision Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.,Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Wei Du
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA.,Institute for Precision Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Lauren Fairchild
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA.,Institute for Precision Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Ari Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA. .,Institute for Precision Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA. .,Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.
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Pelossof R, Elkabets M, Chow OS, Fairchild L, Chen CT, Setty M, Smith JJ, Dow LE, O'Rourke KP, Lowe SW, Leslie CS, Garcia-Aguilar J. KRAS mutation in colorectal cancer and its association with a stromal-derived gene signature. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.3_suppl.628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
628 Background: KRAS mutation in colorectal cancer (CRC) is characterized by an altered transcriptional profile when compared to wild-type KRAS tumors. The list of differentially expressed genes overlaps significantly with a stromal fibroblast activation (SFA) signature present across multiple carcinomas. We have reported low expression of SFA genes in KRAS mutant CRC compared to KRAS wild type tumors. Here we sought to confirm the variation of the SFA signature with KRAS mutation and infer its origin in the stromal component of the tumor using experimental models. Methods: The SFA signature was assessed in an inducible-KRAS murine CRC model using RNA-sequencing, and in a CRC cell line with and without a transduced KRAS mutant vector by microarray analysis. Finally, RNA-sequencing of CRC patient-derived xenografts (PDXs) was used to determine whether the SFA signature was being expressed in the tumor epithelium or the surrounding stroma by leveraging the ability to align sequenced reads to the mouse and human genomes separately. Results: The SFA signature was identified in the inducible-KRAS mouse model, matching human cohort observations of decreased SFA gene expression in KRAS mutant CRC. On the other hand, KRAS transduction did not recapitulate the SFA signature in a CRC cell line, suggesting that the presence of stroma may be required for the expression of the SFA signature. Finally, RNA-seq reads for SFA signature genes in CRC PDXs immediately after implantation aligned primarily to the human genome but in later passages of the same PDXs aligned only to the mouse genome. These data suggest that the SFA transcriptional program is associated with the stroma rather than the epithelial tumor cells. Conclusions: KRAS mutation in CRC is associated with a gene expression signature derived from the tumor stroma. These findings suggest that KRAS mutation in the epithelial tumor cells may impact the tumor microenvironment in CRC.
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Affiliation(s)
| | | | - Oliver S Chow
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Manu Setty
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Lukas E. Dow
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Scott W. Lowe
- Memorial Sloan Kettering Cancer Center, New York, NY
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Pelossof R, Chow OS, Fairchild L, Setty M, Smith JJ, Chen CT, Chen Z, Egawa F, Leslie CS, Garcia-Aguilar J. Integrating Multiple Layers of Genomic Data to Identify Regulatory Programs of Gene Expression in KRAS Mutant Rectal Cancers. J Am Coll Surg 2014. [DOI: 10.1016/j.jamcollsurg.2014.07.039] [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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21
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Fairchild L. Death and dying on the southern Great Plains around 1900. Panhand-Plains Hist Rev 2001; 59:34-53. [PMID: 11617902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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22
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Abstract
The AccuLevel phenobarbital test is based on enzyme channeling and immunochromatography. AccuLevel is a noninstrumented test for the quantitative determination of phenobarbital concentration in whole blood. Within-run precision data, with 20 replicates at each of five concentrations, has coefficients of variation (CVs) of 4.7-9.2%. Between-run precision (n = 40) results in a CV of 5.9%. The AccuLevel phenobarbital test is very specific and is unaffected by endogenous substances and blood collection tube anticoagulants. Compared to the Emit method, this test has excellent linear correlation for the quantitation of 104 phenobarbital positive patient samples. Reagents stored at 4-8 degrees C are stable for 15 months with no effect on the assay quantitation. This accurate, precise, and specific test is easily performed in 20 min.
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Affiliation(s)
- L Fairchild
- Syntex Medical Diagnostics, Division of Syva Company, Palo Alto, California
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23
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Guyot GW, Fairchild L, Nickens J. Death concerns of runners and nonrunners. J Sports Med Phys Fitness 1984; 24:139-43. [PMID: 6503269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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24
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Fairchild L. Response
: Thermoregulation and Mate-Selection in Fowler's Toads? Science 1983; 219:519. [PMID: 17742830 DOI: 10.1126/science.219.4584.519] [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: 11/02/2022]
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Abstract
Male Fowler's toads produce mating calls that are affected by the body size and temperature of the caller. Females are able to discriminate between variations in these calls and select the largest available males. By thermoregulation, males are able to alter their calls to make them more attractive to females.
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Abstract
The relationship between physical fitness and field independence was assessed by measuring embedded-figures test performance in the following four groups of children in Grades 4 through 6: (1) 93 boys high in physical fitness, (2) 92 girls high in physical fitness, (3) 67 boys low in physical fitness, and (4) 77 girls low in physical fitness. The group of girls low in physical fitness was significantly more field dependent than the other three groups. No significant differences were found among the other three groups. It appears that skill in physical activities may be related to the embedded-figures test performance of girls, but not boys. In fact, girls skilled in physical activities may be as field independent as boys.
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27
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Fairchild L. "...As thyself". J Relig Health 1978; 17:210-214. [PMID: 24318385 DOI: 10.1007/bf01597273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- L Fairchild
- Department of Psychology at West Texas State University in Canyon, Texas
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28
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Fairchild L. Some retrospective impressions of psychiatric programs for treating children. Hosp Community Psychiatry 1977; 28:772-3. [PMID: 903087 DOI: 10.1176/ps.28.10.772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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