1
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Westin J, Davis RE, Feng L, Hagemeister F, Steiner R, Lee HJ, Fayad L, Nastoupil L, Ahmed S, Rodriguez A, Fanale M, Samaniego F, Iyer SP, Nair R, Oki Y, Fowler N, Wang M, Ma MCJ, Vega F, McDonnell T, Pinnix C, Griffith D, Lu Y, Tewari S, Sun R, Scott DW, Flowers CR, Neelapu S, Green MR. Smart Start: Rituximab, Lenalidomide, and Ibrutinib in Patients With Newly Diagnosed Large B-Cell Lymphoma. J Clin Oncol 2023; 41:745-755. [PMID: 35952327 PMCID: PMC10489211 DOI: 10.1200/jco.22.00597] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/11/2022] [Revised: 06/03/2022] [Accepted: 06/29/2022] [Indexed: 02/01/2023] Open
Abstract
PURPOSE Chemoimmunotherapy for patients with newly diagnosed diffuse large B-cell lymphoma (DLBCL) is largely unchanged for decades. Both preclinical models and clinical data suggest the combination of lenalidomide and ibrutinib may have synergy in DLBCL, particularly in the non-germinal center B-cell-like subset. METHODS We enrolled 60 patients with newly diagnosed non-germinal center B-cell-like DLBCL in this investigator-initiated, single-arm phase II trial of rituximab, lenalidomide, and ibrutinib (RLI) with the sequential addition of chemotherapy (ClinicalTrials.gov identifier: NCT02636322). Patients were treated with rituximab 375 mg/m2 intravenous once on day 1, lenalidomide 25 mg once per day on days 1-10, and ibrutinib 560 mg once daily continuously of each 21-day cycle (RLI). After two cycles, standard chemotherapy was added to RLI for six additional cycles. The primary end points were overall response rate (ORR) after two cycles of RLI alone and complete response rate after completion of RLI with chemotherapy. In evaluable samples, circulating tumor DNA and DLBCL90 assays were performed. RESULTS The median age was 63.5 years (range, 29-83 years) with 28% age 70 years or older. The revised international prognostic index identified 42% as high risk, and 62% were double expressor of MYC and BCL2 protein. The ORR after two cycles of RLI was 86.2%, and the complete response rate at the end of RLI-chemotherapy was 94.5%. With a median follow-up of 31 months, the progression-free survival and overall survival were at 91.3% and 96.6% at 2 years, respectively. CONCLUSION Smart Start is the first study, to our knowledge, to treat newly diagnosed DLBCL with a targeted therapy combination before chemotherapy. RLI produced a high ORR, and RLI with chemotherapy resulted in durable responses. This establishes the potential for developing biologically driven and noncytotoxic first-line therapies for DLBCL.
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Affiliation(s)
- Jason Westin
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - R. Eric Davis
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lei Feng
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Fredrick Hagemeister
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Raphael Steiner
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hun Ju Lee
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luis Fayad
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Loretta Nastoupil
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sairah Ahmed
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alma Rodriguez
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michelle Fanale
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
- Seagen, Bothell, WA
| | - Felipe Samaniego
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Swaminathan P. Iyer
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ranjit Nair
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yasuhiro Oki
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nathan Fowler
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael Wang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Man Chun John Ma
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Francisco Vega
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Timothy McDonnell
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chelsea Pinnix
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Donna Griffith
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yang Lu
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sanjit Tewari
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David W. Scott
- British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Christopher R. Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sattva Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael R. Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
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2
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Henderson J, Havranek O, Ma MCJ, Herman V, Kupcova K, Chrbolkova T, Pacheco-Blanco M, Wang Z, Comer JM, Zal T, Davis RE. Detecting Förster resonance energy transfer in living cells by conventional and spectral flow cytometry. Cytometry A 2022; 101:818-834. [PMID: 34128311 DOI: 10.1002/cyto.a.24472] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 12/21/2020] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 01/27/2023]
Abstract
Assays based on Förster resonance energy transfer (FRET) can be used to study many processes in cell biology. Although this is most often done with microscopy for fluorescence detection, we report two ways to measure FRET in living cells by flow cytometry. Using a conventional flow cytometer and the "3-cube method" for intensity-based calculation of FRET efficiency, we measured the enzymatic activity of specific kinases in cells expressing a genetically-encoded reporter. For both AKT and protein kinase A, the method measured kinase activity in time-course, dose-response, and kinetic assays. Using the Cytek Aurora spectral flow cytometer, which applies linear unmixing to emission measured in multiple wavelength ranges, FRET from the same reporters was measured with greater single-cell precision, in real time and in the presence of other fluorophores. Results from gene-knockout studies suggested that spectral flow cytometry might enable the sorting of cells on the basis of FRET. The methods we present provide convenient and flexible options for using FRET with flow cytometry in studies of cell biology.
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Affiliation(s)
- Jared Henderson
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Ondrej Havranek
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA.,BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic.,Department of Hematology, Charles University and General University Hospital, Prague, Czech Republic
| | - Man Chun John Ma
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Vaclav Herman
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic.,Department of Hematology, Charles University and General University Hospital, Prague, Czech Republic
| | - Kristyna Kupcova
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Tereza Chrbolkova
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | | | - Zhiqiang Wang
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Justin M Comer
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Tomasz Zal
- Department of Leukemia, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
| | - Richard Eric Davis
- Department of Lymphoma and Myeloma, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA.,Department of Translational Molecular Pathology, The University of Texas-MD Anderson Cancer Center, Houston, Texas, USA
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3
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Han G, Deng Q, Marques-Piubelli ML, Dai E, Dang M, Ma MCJ, Li X, Yang H, Henderson J, Kudryashova O, Meerson M, Isaev S, Kotlov N, Nomie KJ, Bagaev A, Parra ER, Solis Soto LM, Parmar S, Hagemeister FB, Ahmed S, Iyer SP, Samaniego F, Steiner R, Fayad L, Lee H, Fowler NH, Flowers CR, Strati P, Westin JR, Neelapu SS, Nastoupil LJ, Vega F, Wang L, Green MR. Follicular Lymphoma Microenvironment Characteristics Associated with Tumor Cell Mutations and MHC Class II Expression. Blood Cancer Discov 2022; 3:428-443. [PMID: 35687817 PMCID: PMC9894575 DOI: 10.1158/2643-3230.bcd-21-0075] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/02/2021] [Accepted: 06/03/2022] [Indexed: 01/01/2023] Open
Abstract
Follicular lymphoma (FL) is a B-cell malignancy with a complex tumor microenvironment that is rich in nonmalignant immune cells. We applied single-cell RNA sequencing to characterize the diverse tumor and immune cell populations of FL and identified major phenotypic subsets of FL T cells, including a cytotoxic CD4 T-cell population. We characterized four major FL subtypes with differential representation or relative depletion of distinct T-cell subsets. By integrating exome sequencing, we observed that somatic mutations are associated with, but not definitive for, reduced MHC expression on FL cells. In turn, expression of MHCII genes by FL cells was associated with significant differences in the proportions and targetable immunophenotypic characteristics of T cells. This provides a classification framework of the FL microenvironment in association with FL genotypes and MHC expression, and informs different potential immunotherapeutic strategies based upon tumor cell MHCII expression. SIGNIFICANCE We have characterized the FL-infiltrating T cells, identified cytotoxic CD4 T cells as an important component that is associated with tumor cell-intrinsic characteristics, and identified sets of targetable immune checkpoints on T cells that differed from FLs with normal versus low MHC expression. See related commentary by Melnick, p. 374. This article is highlighted in the In This Issue feature, p. 369.
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Affiliation(s)
- Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qing Deng
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Enyu Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Man Chun John Ma
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xubin Li
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Haopeng Yang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jared Henderson
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | | | | | | | - Edwin R. Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa M. Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Simrit Parmar
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Fredrick B. Hagemeister
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sairah Ahmed
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Swaminathan P. Iyer
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Felipe Samaniego
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Raphael Steiner
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luis Fayad
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hun Lee
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nathan H. Fowler
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
- BostonGene Corporation, Waltham, Massachusetts
| | - Christopher R. Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paolo Strati
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason R. Westin
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sattva S. Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Loretta J. Nastoupil
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Francisco Vega
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael R. Green
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
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4
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Nishida Y, Zhao R, Heese LE, Akiyama H, Patel S, Jaeger AM, Jacamo RO, Kojima K, Ma MCJ, Ruvolo VR, Chachad D, Devine W, Lindquist S, Davis RE, Porco JA, Whitesell L, Andreeff M, Ishizawa J. Inhibition of translation initiation factor eIF4a inactivates heat shock factor 1 (HSF1) and exerts anti-leukemia activity in AML. Leukemia 2021; 35:2469-2481. [PMID: 34127794 PMCID: PMC8764661 DOI: 10.1038/s41375-021-01308-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 04/01/2021] [Accepted: 05/21/2021] [Indexed: 01/31/2023]
Abstract
Eukaryotic initiation factor 4A (eIF4A), the enzymatic core of the eIF4F complex essential for translation initiation, plays a key role in the oncogenic reprogramming of protein synthesis, and thus is a putative therapeutic target in cancer. As important component of its anticancer activity, inhibition of translation initiation can alleviate oncogenic activation of HSF1, a stress-inducible transcription factor that enables cancer cell growth and survival. Here, we show that primary acute myeloid leukemia (AML) cells exhibit the highest transcript levels of eIF4A1 compared to other cancer types. eIF4A inhibition by the potent and specific compound rohinitib (RHT) inactivated HSF1 in these cells, and exerted pronounced in vitro and in vivo anti-leukemia effects against progenitor and leukemia-initiating cells, especially those with FLT3-internal tandem duplication (ITD). In addition to its own anti-leukemic activity, genetic knockdown of HSF1 also sensitized FLT3-mutant AML cells to clinical FLT3 inhibitors, and this synergy was conserved in FLT3 double-mutant cells carrying both ITD and tyrosine kinase domain mutations. Consistently, the combination of RHT and FLT3 inhibitors was highly synergistic in primary FLT3-mutated AML cells. Our results provide a novel therapeutic rationale for co-targeting eIF4A and FLT3 to address the clinical challenge of treating FLT3-mutant AML.
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Affiliation(s)
- Yuki Nishida
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ran Zhao
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren E. Heese
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hiroki Akiyama
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shreya Patel
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alex M. Jaeger
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Rodrigo O. Jacamo
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kensuke Kojima
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA,Department of Hematology, Kochi Medical School, Kochi University, Nankoku, Kochi, Japan
| | - Man Chun John Ma
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivian R. Ruvolo
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dhruv Chachad
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William Devine
- Department of Chemistry, Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - R. Eric Davis
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John A. Porco
- Department of Chemistry, Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - Luke Whitesell
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA,Present address: Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael Andreeff
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jo Ishizawa
- Department of Leukemia, Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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5
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Ma MCJ, Tadros S, Bouska A, Heavican T, Yang H, Deng Q, Moore D, Akhter A, Hartert K, Jain N, Showell J, Ghosh S, Street L, Davidson M, Carey C, Tobin J, Perumal D, Vose JM, Lunning MA, Sohani AR, Chen BJ, Buckley S, Nastoupil LJ, Davis RE, Westin JR, Fowler NH, Parekh S, Gandhi M, Neelapu S, Stewart D, Bhalla K, Iqbal J, Greiner T, Rodig SJ, Mansoor A, Green MR. Subtype-specific and co-occurring genetic alterations in B-cell non-Hodgkin lymphoma. Haematologica 2021; 107:690-701. [PMID: 33792219 PMCID: PMC8883549 DOI: 10.3324/haematol.2020.274258] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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: 10/16/2020] [Indexed: 11/09/2022] Open
Abstract
B-cell non-Hodgkin's lymphoma (B-NHL) encompasses multiple clinically and phenotypically distinct subtypes of malignancy with unique molecular etiologies. Common subtypes of B-NHL such as diffuse large B-cell lymphoma (DLBCL) have been comprehensively interrogated at the genomic level. But rarer subtypes such as mantle cell lymphoma (MCL) remain sparsely characterized. Furthermore, multiple B-NHL subtypes have thus far not been comprehensively compared using the same methodology to identify conserved or subtype-specific patterns of genomic alterations. Here, we employed a large targeted hybrid-capture sequencing approach encompassing 380 genes to interrogate the genomic landscapes of 685 B-NHL tumors at high depth; including DLBCL, MCL, follicular lymphoma (FL), and Burkitt lymphoma (BL). We identified conserved hallmarks of B-NHL that were deregulated in the majority of tumor from each subtype, including the frequent genetic deregulation of the ubiquitin proteasome system (UPS). In addition, we identified subtype-specific patterns of genetic alterations, including clusters of co-occurring mutations and DNA copy number alterations. The cumulative burden of mutations within a single cluster were more discriminatory of B-NHL subtypes than individual mutations, implicating likely patterns of genetic cooperation that contribute to disease etiology. We therefore provide the first cross-sectional analysis of mutations and DNA copy number alterations across major B-NHL subtypes and a framework of co-occurring genetic alterations that deregulate genetic hallmarks and likely cooperate in lymphomagenesis.
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Affiliation(s)
- Man Chun John Ma
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Saber Tadros
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alyssa Bouska
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Tayla Heavican
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Haopeng Yang
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Qing Deng
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dalia Moore
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE
| | - Ariz Akhter
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB
| | - Keenan Hartert
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE
| | - Neeraj Jain
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jordan Showell
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sreejoyee Ghosh
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lesley Street
- Section of Hematology, Department of Medicine, University of Calgary, Calgary, AB
| | - Marta Davidson
- Section of Hematology, Department of Medicine, University of Calgary, Calgary, AB
| | - Christopher Carey
- Northern Institute for Research, Newcastle University, Newcastle upon Tyne, England
| | - Joshua Tobin
- Diamantina Institute, University of Queensland, QLD
| | - Deepak Perumal
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Julie M Vose
- Department of Internal Medicine, Division of Hematology-Oncology, University of Nebraska Medical Center, Omaha, NE
| | - Matthew A Lunning
- Department of Internal Medicine, Division of Hematology-Oncology, University of Nebraska Medical Center, Omaha, NE
| | - Aliyah R Sohani
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Benjamin J Chen
- Department of Pathology, University of Massachusetts Medical School, UMass Memorial Medical Center, Worcester, MA
| | - Shannon Buckley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Loretta J Nastoupil
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - R Eric Davis
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jason R Westin
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nathan H Fowler
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Samir Parekh
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Maher Gandhi
- Diamantina Institute, University of Queensland, QLD
| | - Sattva Neelapu
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Douglas Stewart
- Section of Hematology, Department of Medicine, University of Calgary, Calgary, AB
| | - Kapil Bhalla
- Department of Pathology, Brigham and Womens Hospital, Boston, MA
| | - Javeed Iqbal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Timothy Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Scott J Rodig
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Adnan Mansoor
- Section of Hematology, Department of Medicine, University of Calgary, Calgary, AB
| | - Michael R Green
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX.
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6
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Jain N, Hartert K, Tadros S, Fiskus W, Havranek O, Ma MCJ, Bouska A, Heavican T, Kumar D, Deng Q, Moore D, Pak C, Liu CL, Gentles AJ, Hartmann E, Kridel R, Smedby KE, Juliusson G, Rosenquist R, Gascoyne RD, Rosenwald A, Giancotti F, Neelapu SS, Westin J, Vose JM, Lunning MA, Greiner T, Rodig S, Iqbal J, Alizadeh AA, Davis RE, Bhalla K, Green MR. Targetable genetic alterations of TCF4 ( E2-2) drive immunoglobulin expression in diffuse large B cell lymphoma. Sci Transl Med 2020; 11:11/497/eaav5599. [PMID: 31217338 DOI: 10.1126/scitranslmed.aav5599] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/31/2019] [Accepted: 05/15/2019] [Indexed: 12/12/2022]
Abstract
The activated B cell (ABC-like) subtype of diffuse large B cell lymphoma (DLBCL) is characterized by chronic activation of signaling initiated by immunoglobulin μ (IgM). By analyzing the DNA copy number profiles of 1000 DLBCL tumors, we identified gains of 18q21.2 as the most frequent genetic alteration in ABC-like DLBCL. Using integrative analysis of matched gene expression profiling data, we found that the TCF4 (E2-2) transcription factor gene was the target of these alterations. Overexpression of TCF4 in ABC-like DLBCL cell lines led to its occupancy on immunoglobulin (IGHM) and MYC gene enhancers and increased expression of these genes at the transcript and protein levels. Inhibition of TCF4 activity with dominant-negative constructs was synthetically lethal to ABC-like DLBCL cell lines harboring TCF4 DNA copy gains, highlighting these gains as an attractive potential therapeutic target. Furthermore, the TCF4 gene was one of the top BRD4-regulated genes in DLBCL cell lines. BET proteolysis-targeting chimera (PROTAC) ARV771 extinguished TCF4, MYC, and IgM expression and killed ABC-like DLBCL cells in vitro. In DLBCL xenograft models, ARV771 treatment reduced tumor growth and prolonged survival. This work highlights a genetic mechanism for promoting immunoglobulin signaling in ABC-like DLBCL and provides a functional rationale for the use of BET inhibitors in this disease.
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Affiliation(s)
- Neeraj Jain
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Keenan Hartert
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Saber Tadros
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Warren Fiskus
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ondrej Havranek
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Man Chun John Ma
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alyssa Bouska
- Department of Pathology and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Tayla Heavican
- Department of Pathology and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Dhiraj Kumar
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qing Deng
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dalia Moore
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Christine Pak
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Andrew J Gentles
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Elena Hartmann
- Institute of Pathology, University of Würzburg, Würzburg 97080, Germany.,Comprehensive Cancer Center Mainfranken, Wurzburg 97080, Germany
| | - Robert Kridel
- Princess Margaret Cancer Center, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Karin Ekstrom Smedby
- Department of Medicine, Solna, Clinical Epidemiology Unit, Karolinska Institutet, and Hematology Center, Karolinska University Hospital, Stockholm SE-171 76, Sweden
| | - Gunnar Juliusson
- Department of Laboratory Medicine, Stem Cell Center, Lund University, Lund SE-221 00, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Universitetssjukhuset, Stockholm SE-171 76, Sweden
| | - Randy D Gascoyne
- Center for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg 97080, Germany.,Comprehensive Cancer Center Mainfranken, Wurzburg 97080, Germany
| | - Filippo Giancotti
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sattva S Neelapu
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason Westin
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Julie M Vose
- Division of Hematology and Oncology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Matthew A Lunning
- Division of Hematology and Oncology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Timothy Greiner
- Department of Pathology and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Javeed Iqbal
- Department of Pathology and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - R Eric Davis
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kapil Bhalla
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael R Green
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. .,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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7
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Mondello P, Tadros S, Teater M, Fontan L, Chang AY, Jain N, Yang H, Singh S, Ying HY, Chu CS, Ma MCJ, Toska E, Alig S, Durant M, de Stanchina E, Ghosh S, Mottok A, Nastoupil L, Neelapu SS, Weigert O, Inghirami G, Baselga J, Younes A, Yee C, Dogan A, Scheinberg DA, Roeder RG, Melnick AM, Green MR. Selective Inhibition of HDAC3 Targets Synthetic Vulnerabilities and Activates Immune Surveillance in Lymphoma. Cancer Discov 2020; 10:440-459. [PMID: 31915197 PMCID: PMC7275250 DOI: 10.1158/2159-8290.cd-19-0116] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [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: 01/29/2019] [Revised: 11/11/2019] [Accepted: 01/03/2020] [Indexed: 11/16/2022]
Abstract
CREBBP mutations are highly recurrent in B-cell lymphomas and either inactivate its histone acetyltransferase (HAT) domain or truncate the protein. Herein, we show that these two classes of mutations yield different degrees of disruption of the epigenome, with HAT mutations being more severe and associated with inferior clinical outcome. Genes perturbed by CREBBP mutation are direct targets of the BCL6-HDAC3 onco-repressor complex. Accordingly, we show that HDAC3-selective inhibitors reverse CREBBP-mutant aberrant epigenetic programming, resulting in: (i) growth inhibition of lymphoma cells through induction of BCL6 target genes such as CDKN1A and (ii) restoration of immune surveillance due to induction of BCL6-repressed IFN pathway and antigen-presenting genes. By reactivating these genes, exposure to HDAC3 inhibitors restored the ability of tumor-infiltrating lymphocytes to kill DLBCL cells in an MHC class I and II-dependent manner, and synergized with PD-L1 blockade in a syngeneic model in vivo. Hence, HDAC3 inhibition represents a novel mechanism-based immune epigenetic therapy for CREBBP-mutant lymphomas. SIGNIFICANCE: We have leveraged the molecular characterization of different types of CREBBP mutations to define a rational approach for targeting these mutations through selective inhibition of HDAC3. This represents an attractive therapeutic avenue for targeting synthetic vulnerabilities in CREBBP-mutant cells in tandem with promoting antitumor immunity.This article is highlighted in the In This Issue feature, p. 327.
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Affiliation(s)
- Patrizia Mondello
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Saber Tadros
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Lorena Fontan
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Aaron Y Chang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neeraj Jain
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Haopeng Yang
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shailbala Singh
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hsia-Yuan Ying
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York
| | - Man Chun John Ma
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eneda Toska
- Department of Human Oncology and Pathogenesis, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stefan Alig
- Department of Internal Medicine III, University Hospital of the Ludwig-Maximilians-University Munich, Munich, Germany
| | - Matthew Durant
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sreejoyee Ghosh
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anja Mottok
- Institute of Pathology, University of Würzburg and Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Loretta Nastoupil
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sattva S Neelapu
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Oliver Weigert
- Department of Internal Medicine III, University Hospital of the Ludwig-Maximilians-University Munich, Munich, Germany
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - José Baselga
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York
| | - Anas Younes
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David A Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York.
| | - Michael R Green
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
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8
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Ishizawa J, Zarabi SF, Davis RE, Halgas O, Nii T, Jitkova Y, Zhao R, St-Germain J, Heese LE, Egan G, Ruvolo VR, Barghout SH, Nishida Y, Hurren R, Ma W, Gronda M, Link T, Wong K, Mabanglo M, Kojima K, Borthakur G, MacLean N, Ma MCJ, Leber AB, Minden MD, Houry W, Kantarjian H, Stogniew M, Raught B, Pai EF, Schimmer AD, Andreeff M. Mitochondrial ClpP-Mediated Proteolysis Induces Selective Cancer Cell Lethality. Cancer Cell 2019; 35:721-737.e9. [PMID: 31056398 PMCID: PMC6620028 DOI: 10.1016/j.ccell.2019.03.014] [Citation(s) in RCA: 194] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/13/2018] [Accepted: 03/29/2019] [Indexed: 12/20/2022]
Abstract
The mitochondrial caseinolytic protease P (ClpP) plays a central role in mitochondrial protein quality control by degrading misfolded proteins. Using genetic and chemical approaches, we showed that hyperactivation of the protease selectively kills cancer cells, independently of p53 status, by selective degradation of its respiratory chain protein substrates and disrupts mitochondrial structure and function, while it does not affect non-malignant cells. We identified imipridones as potent activators of ClpP. Through biochemical studies and crystallography, we show that imipridones bind ClpP non-covalently and induce proteolysis by diverse structural changes. Imipridones are presently in clinical trials. Our findings suggest a general concept of inducing cancer cell lethality through activation of mitochondrial proteolysis.
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MESH Headings
- Animals
- Cell Line, Tumor
- Cell Survival/drug effects
- Crystallography, X-Ray
- Drug Screening Assays, Antitumor
- Endopeptidase Clp/chemistry
- Endopeptidase Clp/genetics
- Endopeptidase Clp/metabolism
- Female
- HCT116 Cells
- HEK293 Cells
- Heterocyclic Compounds, 4 or More Rings/administration & dosage
- Heterocyclic Compounds, 4 or More Rings/chemistry
- Heterocyclic Compounds, 4 or More Rings/pharmacology
- Humans
- Imidazoles
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Mice
- Mitochondria/metabolism
- Models, Molecular
- Point Mutation
- Protein Conformation/drug effects
- Proteolysis
- Pyridines
- Pyrimidines
- Tumor Suppressor Protein p53/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Jo Ishizawa
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Sarah F Zarabi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - R Eric Davis
- The University of Texas MD Anderson Cancer Center; Department of Lymphoma and Myeloma, Houston, TX 77030, USA
| | - Ondrej Halgas
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Takenobu Nii
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Yulia Jitkova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ran Zhao
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Lauren E Heese
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Grace Egan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Vivian R Ruvolo
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Samir H Barghout
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Yuki Nishida
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Wencai Ma
- The University of Texas MD Anderson Cancer Center, Bioinformatics and Comp Biology, Houston, TX 77030, USA
| | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Todd Link
- The University of Texas MD Anderson Cancer Center, Genomic Medicine, Houston, TX 77030, USA
| | - Keith Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mark Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kensuke Kojima
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA; Saga University, Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Saga 849-8501, Japan
| | - Gautam Borthakur
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Neil MacLean
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Man Chun John Ma
- The University of Texas MD Anderson Cancer Center; Department of Lymphoma and Myeloma, Houston, TX 77030, USA
| | - Andrew B Leber
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Walid Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Hagop Kantarjian
- The University of Texas MD Anderson Cancer Center; Department of Leukemia, Houston, TX 77030, USA
| | | | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Emil F Pai
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Michael Andreeff
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center; Department of Leukemia, Houston, TX 77030, USA.
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9
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Ishizawa J, Nakamaru K, Seki T, Tazaki K, Kojima K, Chachad D, Zhao R, Heese L, Ma W, Ma MCJ, DiNardo C, Pierce S, Patel KP, Tse A, Davis RE, Rao A, Andreeff M. Predictive Gene Signatures Determine Tumor Sensitivity to MDM2 Inhibition. Cancer Res 2018; 78:2721-2731. [PMID: 29490944 DOI: 10.1158/0008-5472.can-17-0949] [Citation(s) in RCA: 36] [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] [Received: 04/03/2017] [Revised: 12/05/2017] [Accepted: 02/22/2018] [Indexed: 12/21/2022]
Abstract
Early clinical trials using murine double minute 2 (MDM2) inhibitors demonstrated proof-of-concept of p53-induced apoptosis by MDM2 inhibition in cancer cells; however, not all wild-type TP53 tumors are sensitive to MDM2 inhibition. Therefore, more potent inhibitors and biomarkers predictive of tumor sensitivity are needed. The novel MDM2 inhibitor DS-3032b is 10-fold more potent than the first-generation inhibitor nutlin-3a. TP53 mutations were predictive of resistance to DS-3032b, and allele frequencies of TP53 mutations were negatively correlated with sensitivity to DS-3032b. However, sensitivity to DS-3032b of TP53 wild-type tumors varied greatly. We thus used two methods to create predictive gene signatures. First, by comparing sensitivity to MDM2 inhibition with basal mRNA expression profiles in 240 cancer cell lines, a 175-gene signature was defined and validated in patient-derived tumor xenograft models and ex vivo human acute myeloid leukemia (AML) cells. Second, an AML-specific 1,532-gene signature was defined by performing random forest analysis with cross-validation using gene expression profiles of 41 primary AML samples. The combination of TP53 mutation status with the two gene signatures provided the best positive predictive values (81% and 82%, compared with 62% for TP53 mutation status alone). In addition, the top-ranked 50 genes selected from the AML-specific 1,532-gene signature conserved high predictive performance, suggesting that a more feasible size of gene signature can be generated through this method for clinical implementation. Our model is being tested in ongoing clinical trials of MDM2 inhibitors.Significance: This study demonstrates that gene expression profiling combined with TP53 mutational status predicts antitumor effects of MDM2 inhibitors in vitro and in vivoCancer Res; 78(10); 2721-31. ©2018 AACR.
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Affiliation(s)
- Jo Ishizawa
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kenji Nakamaru
- Daiichi Sankyo Co., Ltd., Hiromachi, Shinagawa-ku, Tokyo, Japan
| | - Takahiko Seki
- Daiichi Sankyo Co., Ltd., Hiromachi, Shinagawa-ku, Tokyo, Japan
| | - Koichi Tazaki
- Daiichi Sankyo Co., Ltd., Hiromachi, Shinagawa-ku, Tokyo, Japan
| | - Kensuke Kojima
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Hematology, Respiratory Medicine and Oncology, Department of Medicine, Saga University, Saga, Japan
| | - Dhruv Chachad
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ran Zhao
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lauren Heese
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wencai Ma
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Man Chun John Ma
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Courtney DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sherry Pierce
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Archie Tse
- Daiichi Sankyo, Inc., Edison, New Jersey
| | - R Eric Davis
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Arvind Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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10
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Martín-Gálvez D, Dunoyer de Segonzac D, Ma MCJ, Kwitek AE, Thybert D, Flicek P. Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat. BMC Genomics 2017; 18:986. [PMID: 29272997 PMCID: PMC5741965 DOI: 10.1186/s12864-017-4351-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 08/07/2017] [Accepted: 11/27/2017] [Indexed: 11/10/2022] Open
Abstract
Background The genomes of laboratory rat strains are characterised by a mosaic haplotype structure caused by their unique breeding history. These mosaic haplotypes have been recently mapped by extensive sequencing of key strains. Comparison of genomic variation between two closely related rat strains with different phenotypes has been proposed as an effective strategy for the discovery of candidate strain-specific regions involved in phenotypic differences. We developed a method to prioritise strain-specific haplotypes by integrating genomic variation and genomic regulatory data predicted to be involved in specific phenotypes. Specifically, we aimed to identify genomic regions associated with Metabolic Syndrome (MetS), a disorder of energy utilization and storage affecting several organ systems. Results We compared two Lyon rat strains, Lyon Hypertensive (LH) which is susceptible to MetS, and Lyon Low pressure (LL), which is susceptible to obesity as an intermediate MetS phenotype, with a third strain (Lyon Normotensive, LN) that is resistant to both MetS and obesity. Applying a novel metric, we ranked the identified strain-specific haplotypes using evolutionary conservation of the occupancy three liver-specific transcription factors (HNF4A, CEBPA, and FOXA1) in five rodents including rat. Consideration of regulatory information effectively identified regions with liver-associated genes and rat orthologues of human GWAS variants related to obesity and metabolic traits. We attempted to find possible causative variants and compared them with the candidate genes proposed by previous studies. In strain-specific regions with conserved regulation, we found a significant enrichment for published evidence to obesity—one of the metabolic symptoms shown by the Lyon strains—amongst the genes assigned to promoters with strain-specific variation. Conclusions Our results show that the use of functional regulatory conservation is a potentially effective approach to select strain-specific genomic regions associated with phenotypic differences among Lyon rats and could be extended to other systems. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4351-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Martín-Gálvez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Denis Dunoyer de Segonzac
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Man Chun John Ma
- Department of Pharmacology, University of Iowa, Iowa City, IA, USA.,Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA.,Present address: MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Anne E Kwitek
- Department of Pharmacology, University of Iowa, Iowa City, IA, USA.,Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | - David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. .,Present address: Earlham Institute, Norwich research Park, Norwich, NR4 7UH, UK.
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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11
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Ma MCJ, Pettus JM, Jakoubek JA, Traxler MG, Clark KC, Mennie AK, Kwitek AE. Contribution of independent and pleiotropic genetic effects in the metabolic syndrome in a hypertensive rat. PLoS One 2017; 12:e0182650. [PMID: 28792545 PMCID: PMC5549746 DOI: 10.1371/journal.pone.0182650] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 07/22/2017] [Indexed: 11/26/2022] Open
Abstract
Hypertension is a major risk factor for cardiovascular disease, Type 2 diabetes, and end organ failure, and is often found concomitant with disorders characteristic of the Metabolic Syndrome (MetS), including obesity, dyslipidemia, and insulin resistance. While the associated features often occur together, the pathway(s) or mechanism(s) linking hypertension in MetS are not well understood. Previous work determined that genetic variation on rat chromosome 17 (RNO17) contributes to several MetS-defining traits (including hypertension, obesity, and dyslipidemia) in the Lyon Hypertensive (LH) rat, a genetically determined MetS model. We hypothesized that at least some of the traits on RNO17 are controlled by a single gene with pleiotropic effects. To address this hypothesis, consomic and congenic strains were developed, whereby a defined fragment of RNO17 from the LH rat was substituted with the control Lyon Normotensive (LN) rat, and MetS phenotypes were measured in the resultant progeny. Compared to LH rats, LH-17LN consomic rats have significantly reduced body weight, blood pressure, and lipid profiles. A congenic strain (LH-17LNc), with a substituted fragment at the distal end of RNO17 (17q12.3; 74–97 Mb; rn4 assembly), showed differences from the LH rat in blood pressure and serum total cholesterol and triglycerides. Interestingly, there was no difference in body weight between the LH-17LNc and the parental LH rat. These data indicate that blood pressure and serum lipids are regulated by a gene(s) in the distal congenic interval, and could be due to pleiotropy. The data also indicate that body weight is not determined by the same gene(s) at this locus. Interestingly, only two small haplotypes spanning a total of approximately 0.5 Mb differ between the LH and LN genomes in the congenic interval. Genes in these haplotypes are strong candidate genes for causing dyslipidemia in the LH rat. Overall, MetS, even in a simplified genetic model such as the LH-17LN rat, is likely due to both independent and pleiotropic gene effects.
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Affiliation(s)
- Man Chun John Ma
- Department of Pharmacology, University of Iowa, Iowa City, Iowa, United States of America
| | - Janette M. Pettus
- Department of Pharmacology, University of Iowa, Iowa City, Iowa, United States of America
| | - Jessica A. Jakoubek
- Department of Pharmacology, University of Iowa, Iowa City, Iowa, United States of America
| | - Matthew G. Traxler
- Department of Pharmacology, University of Iowa, Iowa City, Iowa, United States of America
| | - Karen C. Clark
- Department of Pharmacology, University of Iowa, Iowa City, Iowa, United States of America
| | - Amanda K. Mennie
- Department of Pharmacology, University of Iowa, Iowa City, Iowa, United States of America
| | - Anne E. Kwitek
- Department of Pharmacology, University of Iowa, Iowa City, Iowa, United States of America
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Nastoupil LJ, Westin JR, Fowler NH, Fanale MA, Samaniego F, Oki Y, Obi C, Cao J, Cheng X, Ma MCJ, Wang Z, Chu F, Feng L, Zhou S, Davis RE, Neelapu SS. Response rates with pembrolizumab in combination with rituximab in patients with relapsed follicular lymphoma: Interim results of an on open-label, phase II study. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.7519] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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
7519 Background: Follicular lymphoma (FL) tumors are infiltrated with antitumor T cells, however, their function is impaired by immune checkpoints such as PD-1/PD-ligand pathway. Blocking PD-1 enhances the function of antitumor T cells in FL. In addition, blocking PD-1 on NK cells has been shown to enhance the ADCC effect of NK cells. We reasoned that the combination of pembrolizumab (P), an anti-PD-1 antibody (ab), and rituximab (R), an anti-CD20 ab that induces ADCC, is likely to be synergistic through activation of both the innate and adaptive immune systems and result in enhanced clinical activity in FL. Methods: We evaluated P and R in an open-label, non-randomized, single institution, phase II trial (N=30). Key inclusion criteria included adult (age ≥ 18 years), FL grade 1-3a, ECOG 0-1, in relapse after ≥1 prior therapy (tx) and R sensitive disease, defined as a complete (CR) or partial response lasting at least 6 months (mos) after most recent R-containing therapy. Pts received R (375 mg/m2 IV) on days 1, 8, 15, and 22 of cycle 1 and P (200mg IV) q 3 weeks for up to 16 cycles starting on day 2 of cycle 1. Primary endpoint was overall response rate (ORR). Results: 27 pts have initiated therapy, median age 65 (range 42-79), 52% male, 76% had intermediate or high risk FLIPI, 56% met GELF criteria. Median prior tx =1 (range 1-4). Adverse events (AE) regardless of causality were mild, most grade 1-2. Grade 3 AE’s included nausea (N=2), infusion reaction (N=2), aseptic meningitis (N=1), pneumonia (N=1). Immune-related AEs included grade 2 diarrhea (N=2), grade 2 pneumonitis (N=1), grade 2 skin rash (N=1). At the pre-planned interim analysis (N=15), ORR was 80%, CR rate was 60%. With a median follow up of 7 mos (range 0.5-17), median DOR, PFS, and OS has not been reached. PD-L1 expression was tested in 8 baseline tumor samples using PD-L1 22C3 IHC pharmDx and was detected in histiocytes in all 8 tumors, present in only 1-8% of tumor cells in 5 tumors. Additional biomarker analyses are ongoing. Conclusions: The combination of P and R is well tolerated in relapsed FL and is associated with high overall and CR rate. These interim results warrant further investigation of this combination in FL. Clinical trial information: NCT02446457.
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Affiliation(s)
| | - Jason R. Westin
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Yasuhiro Oki
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chizobam Obi
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - JingJing Cao
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xiaoyun Cheng
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Zhiqiang Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Fuliang Chu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lei Feng
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shouhao Zhou
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Wang J, Ma MCJ, Mennie AK, Pettus JM, Xu Y, Lin L, Traxler MG, Jakoubek J, Atanur SS, Aitman TJ, Xing Y, Kwitek AE. Systems biology with high-throughput sequencing reveals genetic mechanisms underlying the metabolic syndrome in the Lyon hypertensive rat. ACTA ACUST UNITED AC 2015; 8:316-26. [PMID: 25573024 DOI: 10.1161/circgenetics.114.000520] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 11/25/2014] [Indexed: 11/16/2022]
Abstract
BACKGROUND The metabolic syndrome (MetS) is a collection of co-occurring complex disorders including obesity, hypertension, dyslipidemia, and insulin resistance. The Lyon hypertensive and Lyon normotensive rats are models of MetS sensitivity and resistance, respectively. To identify genetic determinants and mechanisms underlying MetS, an F2 intercross between Lyon hypertensive and Lyon normotensive was comprehensively studied. METHODS AND RESULTS Multidimensional data were obtained including genotypes of 1536 single-nucleotide polymorphisms, 23 physiological traits, and >150 billion nucleotides of RNA-seq reads from the livers of F2 intercross offspring and parental rats. Phenotypic and expression quantitative trait loci (eQTL) were mapped. Application of systems biology methods identified 17 candidate MetS genes. Several putative causal cis-eQTL were identified corresponding with phenotypic QTL loci. We found an eQTL hotspot on rat chromosome 17 that is causally associated with multiple MetS-related traits and found RGD1562963, a gene regulated in cis by this eQTL hotspot, as the most likely eQTL driver gene directly affected by genetic variation between Lyon hypertensive and Lyon normotensive rats. CONCLUSIONS Our study sheds light on the intricate pathogenesis of MetS and demonstrates that systems biology with high-throughput sequencing is a powerful method to study the pathogenesis of complex genetic diseases.
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Affiliation(s)
- Jinkai Wang
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.)
| | - Man Chun John Ma
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.)
| | - Amanda K Mennie
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.)
| | - Janette M Pettus
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.)
| | - Yang Xu
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.)
| | - Lan Lin
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.)
| | - Matthew G Traxler
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.)
| | - Jessica Jakoubek
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.)
| | - Santosh S Atanur
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.)
| | - Timothy J Aitman
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.)
| | - Yi Xing
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.).
| | - Anne E Kwitek
- From the Department of Internal Medicine (J.W., A.K.M., J.M.P., Y. Xu, L.L., Y. Xing, A.E.K.), Department of Pharmacology (M.C.J.M., A.K.M., J.M.P., Y. Xu, M.G.T., J.J., A.E.K.), and Iowa Institute of Human Genetics (A.E.K.), University of Iowa, Iowa City; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (J.W., L.L., Y. Xing); and Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom (S.S.A., T.J.A.).
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Ma MCJ, Atanur SS, Aitman TJ, Kwitek AE. Genomic structure of nucleotide diversity among Lyon rat models of metabolic syndrome. BMC Genomics 2014; 15:197. [PMID: 24628878 PMCID: PMC4003853 DOI: 10.1186/1471-2164-15-197] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 08/25/2013] [Accepted: 03/01/2014] [Indexed: 12/29/2022] Open
Abstract
Background The metabolic syndrome (MetS), a complex disorder involving hypertension, obesity, dyslipidemia and insulin resistance, is a major risk factor for heart disease, stroke, and diabetes. The Lyon Hypertensive (LH), Lyon Normotensive (LN) and Lyon Low-pressure (LL) rats are inbred strains simultaneously derived from a common outbred Sprague Dawley colony by selection for high, normal, and low blood pressure, respectively. Further studies found that LH is a MetS susceptible strain, while LN is resistant and LL has an intermediate phenotype. Whole genome sequencing determined that, while the strains are phenotypically divergent, they are nearly 98% similar at the nucleotide level. Using the sequence of the three strains, we applied an approach that harnesses the distribution of Observed Strain Differences (OSD), or nucleotide diversity, to distinguish genomic regions of identity-by-descent (IBD) from those with divergent ancestry between the three strains. This information was then used to fine-map QTL identified in a cross between LH and LN rats in order to identify candidate genes causing the phenotypes. Results We identified haplotypes that, in total, contain at least 95% of the identifiable polymorphisms between the Lyon strains that are likely of differing ancestral origin. By intersecting the identified haplotype blocks with Quantitative Trait Loci (QTL) previously identified in a cross between LH and LN strains, the candidate QTL regions have been narrowed by 78%. Because the genome sequence has been determined, we were further able to identify putative functional variants in genes that are candidates for causing the QTL. Conclusions Whole genome sequence analysis between the LH, LN, and LL strains identified the haplotype structure of these three strains and identified candidate genes with sequence variants predicted to affect gene function. This approach, merged with additional integrative genetics approaches, will likely lead to novel mechanisms underlying complex disease and provide new drug targets and therapies. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-197) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Anne E Kwitek
- Department of Pharmacology, University of Iowa, Iowa City, IA, USA.
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Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, Ma MCJ, Keane TM, Hummel O, Saar K, Chen W, Guryev V, Gopalakrishnan K, Garrett MR, Joe B, Citterio L, Bianchi G, McBride M, Dominiczak A, Adams DJ, Serikawa T, Flicek P, Cuppen E, Hubner N, Petretto E, Gauguier D, Kwitek A, Jacob H, Aitman TJ. Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell 2013; 154:691-703. [PMID: 23890820 PMCID: PMC3732391 DOI: 10.1016/j.cell.2013.06.040] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/30/2013] [Accepted: 06/21/2013] [Indexed: 12/24/2022]
Abstract
Large numbers of inbred laboratory rat strains have been developed for a range of complex disease phenotypes. To gain insights into the evolutionary pressures underlying selection for these phenotypes, we sequenced the genomes of 27 rat strains, including 11 models of hypertension, diabetes, and insulin resistance, along with their respective control strains. Altogether, we identified more than 13 million single-nucleotide variants, indels, and structural variants across these rat strains. Analysis of strain-specific selective sweeps and gene clusters implicated genes and pathways involved in cation transport, angiotensin production, and regulators of oxidative stress in the development of cardiovascular disease phenotypes in rats. Many of the rat loci that we identified overlap with previously mapped loci for related traits in humans, indicating the presence of shared pathways underlying these phenotypes in rats and humans. These data represent a step change in resources available for evolutionary analysis of complex traits in disease models. PaperClip
Genomes of 27 rat strains were sequenced; >13 million sequence variants identified Selective sweeps and coevolved gene clusters were detected in 11 disease models Previously identified and new disease genes and pathways were identified This is first evolutionary analysis of artificial selection for disease phenotypes
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Affiliation(s)
- Santosh S Atanur
- Physiological Genomic and Medicine Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
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