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He T, Xiao L, Qiao Y, Klingbeil O, Young E, Wu XS, Mannan R, Mahapatra S, Redin E, Cho H, Bao Y, Kandarpa M, Ching-Yi Tien J, Wang X, Eyunni S, Zheng Y, Kim N, Zheng H, Hou S, Su F, Miner SJ, Mehra R, Cao X, Abbineni C, Samajdar S, Ramachandra M, Dhanasekaran SM, Talpaz M, Parolia A, Rudin CM, Vakoc CR, Chinnaiyan AM. Targeting the mSWI/SNF complex in POU2F-POU2AF transcription factor-driven malignancies. Cancer Cell 2024; 42:1336-1351.e9. [PMID: 39029462 DOI: 10.1016/j.ccell.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/19/2024] [Accepted: 06/11/2024] [Indexed: 07/21/2024]
Abstract
The POU2F3-POU2AF2/3 transcription factor complex is the master regulator of the tuft cell lineage and tuft cell-like small cell lung cancer (SCLC). Here, we identify a specific dependence of the POU2F3 molecular subtype of SCLC (SCLC-P) on the activity of the mammalian switch/sucrose non-fermentable (mSWI/SNF) chromatin remodeling complex. Treatment of SCLC-P cells with a proteolysis targeting chimera (PROTAC) degrader of mSWI/SNF ATPases evicts POU2F3 and its coactivators from chromatin and attenuates downstream signaling. B cell malignancies which are dependent on the POU2F1/2 cofactor, POU2AF1, are also sensitive to mSWI/SNF ATPase degraders, with treatment leading to chromatin eviction of POU2AF1 and IRF4 and decreased IRF4 signaling in multiple myeloma cells. An orally bioavailable mSWI/SNF ATPase degrader significantly inhibits tumor growth in preclinical models of SCLC-P and multiple myeloma without signs of toxicity. This study suggests that POU2F-POU2AF-driven malignancies have an intrinsic dependence on the mSWI/SNF complex, representing a therapeutic vulnerability.
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Affiliation(s)
- Tongchen He
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Eleanor Young
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Somnath Mahapatra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Esther Redin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hanbyul Cho
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yi Bao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Malathi Kandarpa
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jean Ching-Yi Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - NamHoon Kim
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Heng Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Siyu Hou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephanie J Miner
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Moshe Talpaz
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medicine Graduate School of Medicine Sciences, New York, NY 10065, USA
| | | | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA.
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2
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Roessner PM, Seufert I, Chapaprieta V, Jayabalan R, Briesch H, Massoni-Badosa R, Boskovic P, Benckendorff J, Roider T, Arseni L, Coelho M, Chakraborty S, Vaca AM, Sivina M, Muckenhuber M, Rodriguez-Rodriguez S, Bonato A, Herbst SA, Zapatka M, Sun C, Kretzmer H, Naake T, Bruch PM, Czernilofsky F, ten Hacken E, Schneider M, Helm D, Yosifov DY, Kauer J, Danilov AV, Bewarder M, Heyne K, Schneider C, Stilgenbauer S, Wiestner A, Mallm JP, Burger JA, Efremov DG, Lichter P, Dietrich S, Martin-Subero JI, Rippe K, Seiffert M. T-bet suppresses proliferation of malignant B cells in chronic lymphocytic leukemia. Blood 2024; 144:510-524. [PMID: 38684038 PMCID: PMC11307267 DOI: 10.1182/blood.2023021990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/28/2024] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
ABSTRACT The T-box transcription factor T-bet is known as a master regulator of the T-cell response but its role in malignant B cells has not been sufficiently explored. Here, we conducted single-cell resolved multi-omics analyses of malignant B cells from patients with chronic lymphocytic leukemia (CLL) and studied a CLL mouse model with a genetic knockout of Tbx21. We found that T-bet acts as a tumor suppressor in malignant B cells by decreasing their proliferation rate. NF-κB activity, induced by inflammatory signals provided by the microenvironment, triggered T-bet expression, which affected promoter-proximal and distal chromatin coaccessibility and controlled a specific gene signature by mainly suppressing transcription. Gene set enrichment analysis identified a positive regulation of interferon signaling and negative control of proliferation by T-bet. In line, we showed that T-bet represses cell cycling and is associated with longer overall survival of patients with CLL. Our study uncovered a novel tumor suppressive role of T-bet in malignant B cells via its regulation of inflammatory processes and cell cycling, which has implications for the stratification and therapy of patients with CLL. Linking T-bet activity to inflammation explains the good prognostic role of genetic alterations in the inflammatory signaling pathways in CLL.
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MESH Headings
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
- Animals
- Humans
- Cell Proliferation
- Mice
- B-Lymphocytes/pathology
- B-Lymphocytes/metabolism
- B-Lymphocytes/immunology
- Mice, Knockout
- Gene Expression Regulation, Leukemic
- NF-kappa B/metabolism
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Affiliation(s)
- Philipp M. Roessner
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Isabelle Seufert
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | | | - Ruparoshni Jayabalan
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Hannah Briesch
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Ramon Massoni-Badosa
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
- Single Cell Genomics, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Pavle Boskovic
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | | | - Tobias Roider
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Lavinia Arseni
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Mariana Coelho
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Supriya Chakraborty
- Molecular Hematology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Alicia M. Vaca
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mariela Sivina
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Markus Muckenhuber
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | | | - Alice Bonato
- Molecular Hematology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Sophie A. Herbst
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Clare Sun
- Laboratory of Lymphoid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thomas Naake
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peter-Martin Bruch
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Felix Czernilofsky
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | | | - Martin Schneider
- Proteomics Core Facility, German Cancer Research Center, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, German Cancer Research Center, Heidelberg, Germany
| | - Deyan Y. Yosifov
- Division of Chronic Lymphocytic Leukemia, Department of Internal Medicine III, Ulm University, Ulm, Germany
- Cooperation Unit Mechanisms of Leukemogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Joseph Kauer
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Alexey V. Danilov
- Department of Hematology, City of Hope National Medical Center, Duarte, CA
| | - Moritz Bewarder
- José Carreras Center for Immuno- and Gene Therapy and Internal Medicine I, Saarland University Medical School, Homburg/Saar, Germany
| | - Kristina Heyne
- José Carreras Center for Immuno- and Gene Therapy and Internal Medicine I, Saarland University Medical School, Homburg/Saar, Germany
| | - Christof Schneider
- Division of Chronic Lymphocytic Leukemia, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Stephan Stilgenbauer
- Division of Chronic Lymphocytic Leukemia, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Adrian Wiestner
- Laboratory of Lymphoid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Jan-Philipp Mallm
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Jan A. Burger
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dimitar G. Efremov
- Molecular Hematology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - José I. Martin-Subero
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center and BioQuant, Heidelberg, Germany
| | - Martina Seiffert
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
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SoRelle ED, Haynes LE, Willard KA, Chang B, Ch’ng J, Christofk H, Luftig MA. Epstein-Barr virus reactivation induces divergent abortive, reprogrammed, and host shutoff states by lytic progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598975. [PMID: 38915538 PMCID: PMC11195279 DOI: 10.1101/2024.06.14.598975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Viral infection leads to heterogeneous cellular outcomes ranging from refractory to abortive and fully productive states. Single cell transcriptomics enables a high resolution view of these distinct post-infection states. Here, we have interrogated the host-pathogen dynamics following reactivation of Epstein-Barr virus (EBV). While benign in most people, EBV is responsible for infectious mononucleosis, up to 2% of human cancers, and is a trigger for the development of multiple sclerosis. Following latency establishment in B cells, EBV reactivates and is shed in saliva to enable infection of new hosts. Beyond its importance for transmission, the lytic cycle is also implicated in EBV-associated oncogenesis. Conversely, induction of lytic reactivation in latent EBV-positive tumors presents a novel therapeutic opportunity. Therefore, defining the dynamics and heterogeneity of EBV lytic reactivation is a high priority to better understand pathogenesis and therapeutic potential. In this study, we applied single-cell techniques to analyze diverse fate trajectories during lytic reactivation in two B cell models. Consistent with prior work, we find that cell cycle and MYC expression correlate with cells refractory to lytic reactivation. We further found that lytic induction yields a continuum from abortive to complete reactivation. Abortive lytic cells upregulate NFκB and IRF3 pathway target genes, while cells that proceed through the full lytic cycle exhibit unexpected expression of genes associated with cellular reprogramming. Distinct subpopulations of lytic cells further displayed variable profiles for transcripts known to escape virus-mediated host shutoff. These data reveal previously unknown and promiscuous outcomes of lytic reactivation with broad implications for viral replication and EBV-associated oncogenesis.
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Affiliation(s)
- Elliott D. SoRelle
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Virology, Durham, NC 27710, USA
| | - Lauren E. Haynes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Virology, Durham, NC 27710, USA
| | - Katherine A. Willard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Virology, Durham, NC 27710, USA
| | - Beth Chang
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - James Ch’ng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Heather Christofk
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Virology, Durham, NC 27710, USA
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He T, Xiao L, Qiao Y, Klingbeil O, Young E, Wu XS, Mannan R, Mahapatra S, Eyunni S, Ching-Yi Tien J, Wang X, Zheng Y, Kim N, Zheng H, Hou S, Su F, Miner SJ, Mehra R, Cao X, Abbineni C, Samajdar S, Ramachandra M, Parolia A, Vakoc CR, Chinnaiyan AM. Targeting the mSWI/SNF Complex in POU2F-POU2AF Transcription Factor-Driven Malignancies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576669. [PMID: 38328238 PMCID: PMC10849552 DOI: 10.1101/2024.01.22.576669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The POU2F3-POU2AF2/3 (OCA-T1/2) transcription factor complex is the master regulator of the tuft cell lineage and tuft cell-like small cell lung cancer (SCLC). Here, we found that the POU2F3 molecular subtype of SCLC (SCLC-P) exhibits an exquisite dependence on the activity of the mammalian switch/sucrose non-fermentable (mSWI/SNF) chromatin remodeling complex. SCLC-P cell lines were sensitive to nanomolar levels of a mSWI/SNF ATPase proteolysis targeting chimera (PROTAC) degrader when compared to other molecular subtypes of SCLC. POU2F3 and its cofactors were found to interact with components of the mSWI/SNF complex. The POU2F3 transcription factor complex was evicted from chromatin upon mSWI/SNF ATPase degradation, leading to attenuation of downstream oncogenic signaling in SCLC-P cells. A novel, orally bioavailable mSWI/SNF ATPase PROTAC degrader, AU-24118, demonstrated preferential efficacy in the SCLC-P relative to the SCLC-A subtype and significantly decreased tumor growth in preclinical models. AU-24118 did not alter normal tuft cell numbers in lung or colon, nor did it exhibit toxicity in mice. B cell malignancies which displayed a dependency on the POU2F1/2 cofactor, POU2AF1 (OCA-B), were also remarkably sensitive to mSWI/SNF ATPase degradation. Mechanistically, mSWI/SNF ATPase degrader treatment in multiple myeloma cells compacted chromatin, dislodged POU2AF1 and IRF4, and decreased IRF4 signaling. In a POU2AF1-dependent, disseminated murine model of multiple myeloma, AU-24118 enhanced survival compared to pomalidomide, an approved treatment for multiple myeloma. Taken together, our studies suggest that POU2F-POU2AF-driven malignancies have an intrinsic dependence on the mSWI/SNF complex, representing a therapeutic vulnerability.
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Affiliation(s)
- Tongchen He
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- These authors contributed equally
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Eleanor Young
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoli S. Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Somnath Mahapatra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jean Ching-Yi Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - NamHoon Kim
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Heng Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Siyu Hou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie J. Miner
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | | | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
- Lead contact
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5
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Raab N, Zeh N, Kretz R, Weiß L, Stadermann A, Lindner B, Fischer S, Stoll D, Otte K. Nature as blueprint: Global phenotype engineering of CHO production cells based on a multi-omics comparison with plasma cells. Metab Eng 2024; 83:110-122. [PMID: 38561148 DOI: 10.1016/j.ymben.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/17/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Especially for the production of artificial, difficult to express molecules a further development of the CHO production cell line is required to keep pace with the continuously increasing demands. However, the identification of novel targets for cell line engineering to improve CHO cells is a time and cost intensive process. Since plasma cells are evolutionary optimized for a high antibody expression in mammals, we performed a comprehensive multi-omics comparison between CHO and plasma cells to exploit optimized cellular production traits. Comparing the transcriptome, proteome, miRNome, surfaceome and secretome of both cell lines identified key differences including 392 potential overexpression targets for CHO cell engineering categorized in 15 functional classes like transcription factors, protein processing or secretory pathway. In addition, 3 protein classes including 209 potential knock-down/out targets for CHO engineering were determined likely to affect aggregation or proteolysis. For production phenotype engineering, several of these novel targets were successfully applied to transient and transposase mediated overexpression or knock-down strategies to efficiently improve productivity of CHO cells. Thus, substantial improvement of CHO productivity was achieved by taking nature as a blueprint for cell line engineering.
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Affiliation(s)
- Nadja Raab
- Biberach University of Applied Sciences, Germany.
| | - Nikolas Zeh
- Biberach University of Applied Sciences, Germany; Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Robin Kretz
- Hochschule Albstadt Sigmaringen, Germany; NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Linus Weiß
- Biberach University of Applied Sciences, Germany
| | - Anna Stadermann
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Benjamin Lindner
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Simon Fischer
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Dieter Stoll
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Kerstin Otte
- Biberach University of Applied Sciences, Germany
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6
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Wright NE, Kennedy DE, Ai J, Veselits ML, Attaway M, Yoon YM, Durkee MS, Veselits J, Maienschein-Cline M, Mandal M, Clark MR. BRWD1 establishes epigenetic states for germinal center initiation, maintenance, and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591154. [PMID: 38712068 PMCID: PMC11071454 DOI: 10.1101/2024.04.25.591154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Germinal center (GC) B cells segregate into three subsets that compartmentalize the antagonistic molecular programs of selection, proliferation, and somatic hypermutation. In bone marrow, the epigenetic reader BRWD1 orchestrates and insulates the sequential stages of cell proliferation and Igk recombination. We hypothesized BRWD1 might play similar insulative roles in the periphery. In Brwd1 -/- follicular B cells, GC initiation and class switch recombination following immunization were inhibited. In contrast, in Brwd1 -/- GC B cells there was admixing of chromatin accessibility across GC subsets and transcriptional dysregulation including induction of inflammatory pathways. This global molecular GC dysregulation was associated with specific defects in proliferation, affinity maturation, and tolerance. These data suggest that GC subset identity is required for some but not all GC-attributed functions. Furthermore, these data demonstrate a central role for BRWD1 in orchestrating epigenetic transitions at multiple steps along B cell developmental and activation pathways.
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7
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Layden HM, Ellis JD, Bomber ML, Bartlett LN, Hiebert SW, Stengel KR. Mutant FOXO1 controls an oncogenic network via enhancer accessibility. CELL GENOMICS 2024; 4:100537. [PMID: 38604128 PMCID: PMC11019358 DOI: 10.1016/j.xgen.2024.100537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/21/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
Transcriptional dysregulation is a hallmark of diffuse large B cell lymphoma (DLBCL), as transcriptional regulators are frequently mutated. However, our mechanistic understanding of how normal transcriptional programs are co-opted in DLBCL has been hindered by a lack of methodologies that provide the temporal resolution required to separate direct and indirect effects on transcriptional control. We applied a chemical-genetic approach to engineer the inducible degradation of the transcription factor FOXO1, which is recurrently mutated (mFOXO1) in DLBCL. The combination of rapid degradation of mFOXO1, nascent transcript detection, and assessment of chromatin accessibility allowed us to identify the direct targets of mFOXO1. mFOXO1 was required to maintain accessibility at specific enhancers associated with multiple oncogenes, and mFOXO1 degradation impaired RNA polymerase pause-release at some targets. Wild-type FOXO1 appeared to weakly regulate many of the same targets as mFOXO1 and was able to complement the degradation of mFOXO1 in the context of AKT inhibition.
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Affiliation(s)
- Hillary M Layden
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jacob D Ellis
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Monica L Bomber
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Luke N Bartlett
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA.
| | - Kristy R Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA; Montefiore Einstein Cancer Center, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY, USA.
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8
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Alpsoy A, Wu XS, Pal S, Klingbeil O, Kumar P, El Demerdash O, Nalbant B, Vakoc CR. IκBζ is a dual-use coactivator of NF-κB and POU transcription factors. Mol Cell 2024; 84:1149-1157.e7. [PMID: 38309274 PMCID: PMC10960667 DOI: 10.1016/j.molcel.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
OCA-B, OCA-T1, and OCA-T2 belong to a family of coactivators that bind to POU transcription factors (TFs) to regulate gene expression in immune cells. Here, we identify IκBζ (encoded by the NFKBIZ gene) as an additional coactivator of POU TFs. Although originally discovered as an inducible regulator of NF-κB, we show here that IκBζ shares a microhomology with OCA proteins and uses this segment to bind to POU TFs and octamer-motif-containing DNA. Our functional experiments suggest that IκBζ requires its interaction with POU TFs to coactivate immune-related genes. This finding is reinforced by epigenomic analysis of MYD88L265P-mutant lymphoma cells, which revealed colocalization of IκBζ with the POU TF OCT2 and NF-κB:p50 at hundreds of DNA elements harboring octamer and κB motifs. These results suggest that IκBζ is a transcriptional coactivator that can amplify and integrate the output of NF-κB and POU TFs at inducible genes in immune cells.
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Affiliation(s)
- Aktan Alpsoy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sujay Pal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Pramod Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Benan Nalbant
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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9
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Rudzanová B, Thon V, Vespalcová H, Martyniuk CJ, Piler P, Zvonař M, Klánová J, Bláha L, Adamovsky O. Altered Transcriptome Response in PBMCs of Czech Adults Linked to Multiple PFAS Exposure: B Cell Development as a Target of PFAS Immunotoxicity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:90-98. [PMID: 38112183 PMCID: PMC10785749 DOI: 10.1021/acs.est.3c05109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
While the immunomodulation effects of per- and polyfluoroalkyl substances (PFASs) are described on the level of clinical signs in epidemiological studies (e.g., suppressed antibody response after vaccination), the underlying mechanism has still not been fully elucidated. To reveal mechanisms of PFAS exposure on immunity, we investigated the genome-wide transcriptomic changes of peripheral blood mononuclear cells (PBMCs) responding to PFAS exposure (specifically, exposure to PFPA, PFOA, PFNA, PFDA, PFUnDA, PFHxS, and PFOS). Blood samples and the chemical load in the blood were analyzed under the cross-sectional CELSPAC: Young Adults study. The overall aim of the study was to identify sensitive gene sets and cellular pathways conserved for multiple PFAS chemicals. Transcriptome networks related to adaptive immunity were perturbed by multiple PFAS exposure (i.e., blood levels of at least four PFASs). Specifically, processes tightly connected with late B cell development, such as B cell receptor signaling, germinal center reactions, and plasma cell development, were shown to be affected. Our comprehensive transcriptome analysis identified the disruption of B cell development, specifically the impact on the maturation of antibody-secreting cells, as a potential mechanism underlying PFAS immunotoxicity.
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Affiliation(s)
- Barbora Rudzanová
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic
| | - Vojtěch Thon
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic
| | - Hana Vespalcová
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic
| | - Christopher J. Martyniuk
- Department
of Physiological Sciences and Center for Environmental and Human Toxicology,
UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32611, United States
| | - Pavel Piler
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic
| | - Martin Zvonař
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic
- Department
of Kinesiology, Faculty of Sports Studies, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jana Klánová
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic
| | - Luděk Bláha
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic
| | - Ondrej Adamovsky
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 602 00 Brno, Czech Republic
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10
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Wang X, Duan M, Li J, Ma A, Xin G, Xu D, Li Z, Liu B, Ma Q. MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer. Nat Commun 2024; 15:338. [PMID: 38184630 PMCID: PMC10771517 DOI: 10.1038/s41467-023-44570-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/14/2023] [Indexed: 01/08/2024] Open
Abstract
Rare cell populations are key in neoplastic progression and therapeutic response, offering potential intervention targets. However, their computational identification and analysis often lag behind major cell types. To fill this gap, we introduce MarsGT: Multi-omics Analysis for Rare population inference using a Single-cell Graph Transformer. It identifies rare cell populations using a probability-based heterogeneous graph transformer on single-cell multi-omics data. MarsGT outperforms existing tools in identifying rare cells across 550 simulated and four real human datasets. In mouse retina data, it reveals unique subpopulations of rare bipolar cells and a Müller glia cell subpopulation. In human lymph node data, MarsGT detects an intermediate B cell population potentially acting as lymphoma precursors. In human melanoma data, it identifies a rare MAIT-like population impacted by a high IFN-I response and reveals the mechanism of immunotherapy. Hence, MarsGT offers biological insights and suggests potential strategies for early detection and therapeutic intervention of disease.
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Affiliation(s)
- Xiaoying Wang
- School of Mathematics, Shandong University, Jinan, Shandong, 250100, China
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Maoteng Duan
- School of Mathematics, Shandong University, Jinan, Shandong, 250100, China
| | - Jingxian Li
- School of Mathematics, Shandong University, Jinan, Shandong, 250100, China
| | - Anjun Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Gang Xin
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, Shandong, 250100, China.
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
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11
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Betzler AC, Brunner C. The Role of the Transcriptional Coactivator BOB.1/OBF.1 in Adaptive Immunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:53-77. [PMID: 39017839 DOI: 10.1007/978-3-031-62731-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
BOB.1/OBF.1 is a transcriptional coactivator involved in octamer-dependent transcription. Thereby, BOB.1/OBF.1 is involved in the transcriptional regulation of genes important for lymphocyte physiology. BOB.1/OBF.1-deficient mice reveal multiple B- and T-cell developmental defects. The most prominent defect of these mice is the complete absence of germinal centers (GCs) resulting in severely impaired T-cell-dependent immune responses. In humans, BOB.1/OBF.1 is associated with several autoimmune and inflammatory diseases but also linked to liquid and solid tumors. Although its role for B-cell development is relatively well understood, its exact role for the GC reaction and T-cell biology has long been unclear. Here, the contribution of BOB.1/OBF.1 for B-cell maturation is summarized, and recent findings regarding its function in GC B- as well as in various T-cell populations are discussed. Finally, a detailed perspective on how BOB.1/OBF.1 contributes to different pathologies is provided.
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Affiliation(s)
- Annika C Betzler
- Department of Oto-Rhino-Larnygology, Ulm University Medical Center, Ulm, Germany
- Core Facility Immune Monitoring, Ulm University, Ulm, Germany
| | - Cornelia Brunner
- Department of Oto-Rhino-Larnygology, Ulm University Medical Center, Ulm, Germany.
- Core Facility Immune Monitoring, Ulm University, Ulm, Germany.
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12
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García-Caballero D, Hart JR, Vogt PK. Long Non-Coding RNAs as "MYC Facilitators". PATHOPHYSIOLOGY 2023; 30:389-399. [PMID: 37755396 PMCID: PMC10534484 DOI: 10.3390/pathophysiology30030030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
In this article, we discuss a class of MYC-interacting lncRNAs (long non-coding RNAs) that share the following criteria: They are direct transcriptional targets of MYC. Their expression is coordinated with the expression of MYC. They are required for sustained MYC-driven cell proliferation, and they are not essential for cell survival. We refer to these lncRNAs as "MYC facilitators" and discuss two representative members of this class of lncRNAs, SNHG17 (small nuclear RNA host gene) and LNROP (long non-coding regulator of POU2F2). We also present a general hypothesis on the role of lncRNAs in MYC-mediated transcriptional regulation.
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Affiliation(s)
| | | | - Peter K. Vogt
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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13
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Bravo González-Blas C, De Winter S, Hulselmans G, Hecker N, Matetovici I, Christiaens V, Poovathingal S, Wouters J, Aibar S, Aerts S. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. Nat Methods 2023; 20:1355-1367. [PMID: 37443338 PMCID: PMC10482700 DOI: 10.1038/s41592-023-01938-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 06/06/2023] [Indexed: 07/15/2023]
Abstract
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inference of enhancer-driven GRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TFs) and links these enhancers to candidate target genes. To improve both recall and precision of TF identification, we curated and clustered a motif collection with more than 30,000 motifs. We benchmarked SCENIC+ on diverse datasets from different species, including human peripheral blood mononuclear cells, ENCODE cell lines, melanoma cell states and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers and GRNs between human and mouse cell types in the cerebral cortex. Finally, we use SCENIC+ to study the dynamics of gene regulation along differentiation trajectories and the effect of TF perturbations on cell state. SCENIC+ is available at scenicplus.readthedocs.io .
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seppe De Winter
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikolai Hecker
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Jasper Wouters
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
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14
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Zhou M, Zhang H, Bai Z, Mann-Krzisnik D, Wang F, Li Y. Single-cell multi-omics topic embedding reveals cell-type-specific and COVID-19 severity-related immune signatures. CELL REPORTS METHODS 2023; 3:100563. [PMID: 37671028 PMCID: PMC10475851 DOI: 10.1016/j.crmeth.2023.100563] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 03/31/2023] [Accepted: 07/28/2023] [Indexed: 09/07/2023]
Abstract
The advent of single-cell multi-omics sequencing technology makes it possible for researchers to leverage multiple modalities for individual cells and explore cell heterogeneity. However, the high-dimensional, discrete, and sparse nature of the data make the downstream analysis particularly challenging. Here, we propose an interpretable deep learning method called moETM to perform integrative analysis of high-dimensional single-cell multimodal data. moETM integrates multiple omics data via a product-of-experts in the encoder and employs multiple linear decoders to learn the multi-omics signatures. moETM demonstrates superior performance compared with six state-of-the-art methods on seven publicly available datasets. By applying moETM to the scRNA + scATAC data, we identified sequence motifs corresponding to the transcription factors regulating immune gene signatures. Applying moETM to CITE-seq data from the COVID-19 patients revealed not only known immune cell-type-specific signatures but also composite multi-omics biomarkers of critical conditions due to COVID-19, thus providing insights from both biological and clinical perspectives.
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Affiliation(s)
- Manqi Zhou
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine, New York, NY 10021, USA
| | - Hao Zhang
- Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10021, USA
| | - Zilong Bai
- Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine, New York, NY 10021, USA
- Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Fei Wang
- Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine, New York, NY 10021, USA
- Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10021, USA
| | - Yue Li
- Quantitative Life Science, McGill University, Montréal, QC H3A 0G4, Canada
- School of Computer Science, McGill University, Montréal, QC H3A 0G4, Canada
- Mila – Quebec AI Institute, Montréal, QC H2S 3H1, Canada
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15
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Wang X, Duan M, Li J, Ma A, Xu D, Li Z, Liu B, Ma Q. MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553454. [PMID: 37645917 PMCID: PMC10462017 DOI: 10.1101/2023.08.15.553454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Rare cell populations are key in neoplastic progression and therapeutic response, offering potential intervention targets. However, their computational identification and analysis often lag behind major cell types. To fill this gap, we introduced MarsGT: Multi-omics Analysis for Rare population inference using Single-cell Graph Transformer. It identifies rare cell populations using a probability-based heterogeneous graph transformer on single-cell multi-omics data. MarsGT outperformed existing tools in identifying rare cells across 400 simulated and four real human datasets. In mouse retina data, it revealed unique subpopulations of rare bipolar cells and a Müller glia cell subpopulation. In human lymph node data, MarsGT detected an intermediate B cell population potentially acting as lymphoma precursors. In human melanoma data, it identified a rare MAIT-like population impacted by a high IFN-I response and revealed the mechanism of immunotherapy. Hence, MarsGT offers biological insights and suggests potential strategies for early detection and therapeutic intervention of disease.
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Affiliation(s)
- Xiaoying Wang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Maoteng Duan
- School of Mathematics, Shandong University, Jinan, Shandong, 250100, China
| | - Jingxian Li
- School of Mathematics, Shandong University, Jinan, Shandong, 250100, China
| | - Anjun Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, Shandong, 250100, China
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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16
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Xiong Y, Zhang Y, Liu N, Li Y, Liu H, Yang Q, Chen Y, Xia Z, Chen X, Wanggou S, Li X. Integration of single-cell regulon atlas and multi-omics data for prognostic stratification and personalized treatment prediction in human lung adenocarcinoma. J Transl Med 2023; 21:499. [PMID: 37491302 PMCID: PMC10369768 DOI: 10.1186/s12967-023-04331-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/07/2023] [Indexed: 07/27/2023] Open
Abstract
Transcriptional programs are often dysregulated in cancers. A comprehensive investigation of potential regulons is critical to the understanding of tumorigeneses. We first constructed the regulatory networks from single-cell RNA sequencing data in human lung adenocarcinoma (LUAD). We next introduce LPRI (Lung Cancer Prognostic Regulon Index), a precision oncology framework to identify new biomarkers associated with prognosis by leveraging the single cell regulon atlas and bulk RNA sequencing or microarray datasets. We confirmed that LPRI could be a robust biomarker to guide prognosis stratification across lung adenocarcinoma cohorts. Finally, a multi-omics data analysis to characterize molecular alterations associated with LPRI was performed from The Cancer Genome Atlas (TCGA) dataset. Our study provides a comprehensive chart of regulons in LUAD. Additionally, LPRI will be used to help prognostic prediction and developing personalized treatment for future studies.
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Affiliation(s)
- Yi Xiong
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Yihao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Na Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Postdoctoral Research Workstation, Xiangya Hospital, Central South University, Hunan, 410078, China
| | - Yueshuo Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Postdoctoral Research Workstation, Xiangya Hospital, Central South University, Hunan, 410078, China
| | - Hongwei Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qi Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yu Chen
- Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Zhizhi Xia
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Xin Chen
- Songjiang Research Institute, Shanghai Songjiang District Central Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 201600, China.
| | - Siyi Wanggou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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17
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Fang WQ, Wu YL, Hwang MJ. A Noise-Tolerating Gene Association Network Uncovering an Oncogenic Regulatory Motif in Lymphoma Transcriptomics. Life (Basel) 2023; 13:1331. [PMID: 37374114 DOI: 10.3390/life13061331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
In cancer genomics research, gene expressions provide clues to gene regulations implicating patients' risk of survival. Gene expressions, however, fluctuate due to noises arising internally and externally, making their use to infer gene associations, hence regulation mechanisms, problematic. Here, we develop a new regression approach to model gene association networks while considering uncertain biological noises. In a series of simulation experiments accounting for varying levels of biological noises, the new method was shown to be robust and perform better than conventional regression methods, as judged by a number of statistical measures on unbiasedness, consistency and accuracy. Application to infer gene associations in germinal-center B cells led to the discovery of a three-by-two regulatory motif gene expression and a three-gene prognostic signature for diffuse large B-cell lymphoma.
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Affiliation(s)
- Wei-Quan Fang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Division of New Drug, Center for Drug Evaluation, Taipei 115, Taiwan
| | - Yu-Le Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Ming-Jing Hwang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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18
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Zhou M, Zhang H, Baii Z, Mann-Krzisnik D, Wang F, Li Y. Single-cell multi-omic topic embedding reveals cell-type-specific and COVID-19 severity-related immune signatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526312. [PMID: 36778483 PMCID: PMC9915637 DOI: 10.1101/2023.01.31.526312] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The advent of single-cell multi-omics sequencing technology makes it possible for re-searchers to leverage multiple modalities for individual cells and explore cell heterogeneity. However, the high dimensional, discrete, and sparse nature of the data make the downstream analysis particularly challenging. Most of the existing computational methods for single-cell data analysis are either limited to single modality or lack flexibility and interpretability. In this study, we propose an interpretable deep learning method called multi-omic embedded topic model (moETM) to effectively perform integrative analysis of high-dimensional single-cell multimodal data. moETM integrates multiple omics data via a product-of-experts in the encoder for efficient variational inference and then employs multiple linear decoders to learn the multi-omic signatures of the gene regulatory programs. Through comprehensive experiments on public single-cell transcriptome and chromatin accessibility data (i.e., scRNA+scATAC), as well as scRNA and proteomic data (i.e., CITE-seq), moETM demonstrates superior performance compared with six state-of-the-art single-cell data analysis methods on seven publicly available datasets. By applying moETM to the scRNA+scATAC data in human bone marrow mononuclear cells (BMMCs), we identified sequence motifs corresponding to the transcription factors that regulate immune gene signatures. Applying moETM analysis to CITE-seq data from the COVID-19 patients revealed not only known immune cell-type-specific signatures but also composite multi-omic biomarkers of critical conditions due to COVID-19, thus providing insights from both biological and clinical perspectives.
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Affiliation(s)
- Manqi Zhou
- Department of Computational Biology, Cornell University
- Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine
| | - Hao Zhang
- Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine
| | - Zilong Baii
- Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine
- Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine
| | | | - Fei Wang
- Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine
- Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine
| | - Yue Li
- Quantitative Life Science, McGill University
- School of Computer Science, McGill University
- Mila - Quebec AI Institute
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19
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Martínez-Zamudio RI, Stefa A, Nabuco Leva Ferreira Freitas JA, Vasilopoulos T, Simpson M, Doré G, Roux PF, Galan MA, Chokshi RJ, Bischof O, Herbig U. Escape from oncogene-induced senescence is controlled by POU2F2 and memorized by chromatin scars. CELL GENOMICS 2023; 3:100293. [PMID: 37082139 PMCID: PMC10112333 DOI: 10.1016/j.xgen.2023.100293] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 01/13/2023] [Accepted: 03/02/2023] [Indexed: 04/22/2023]
Abstract
Although oncogene-induced senescence (OIS) is a potent tumor-suppressor mechanism, recent studies revealed that cells could escape from OIS with features of transformed cells. However, the mechanisms that promote OIS escape remain unclear, and evidence of post-senescent cells in human cancers is missing. Here, we unravel the regulatory mechanisms underlying OIS escape using dynamic multidimensional profiling. We demonstrate a critical role for AP1 and POU2F2 transcription factors in escape from OIS and identify senescence-associated chromatin scars (SACSs) as an epigenetic memory of OIS detectable during colorectal cancer progression. POU2F2 levels are already elevated in precancerous lesions and as cells escape from OIS, and its expression and binding activity to cis-regulatory elements are associated with decreased patient survival. Our results support a model in which POU2F2 exploits a precoded enhancer landscape necessary for senescence escape and reveal POU2F2 and SACS gene signatures as valuable biomarkers with diagnostic and prognostic potential.
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Affiliation(s)
- Ricardo Iván Martínez-Zamudio
- Center for Cell Signaling, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Alketa Stefa
- Center for Cell Signaling, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Graduate School of Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103 USA
| | - José Américo Nabuco Leva Ferreira Freitas
- Sorbonne Université, UMR 8256, Biological Adaptation and Ageing – IBPS, 75005 Paris, France
- INSERM U1164, 75005 Paris, France
- IMRB, Mondor Institute for Biomedical Research, INSERM U955 – Université Paris Est Créteil, UPEC, Faculté de Médecine de Créteil 8, rue du Général Sarrail, 94010 Créteil, France
| | - Themistoklis Vasilopoulos
- Center for Cell Signaling, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Graduate School of Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103 USA
| | - Mark Simpson
- Center for Cell Signaling, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Gregory Doré
- Institut Pasteur, Plasmodium RNA Biology Unit, 25 Rue du Docteur Roux, 75724 Cedex 15 Paris, France
| | - Pierre-François Roux
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Mark A. Galan
- Department of Pathology and Laboratory Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Ravi J. Chokshi
- Department of Surgery, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Oliver Bischof
- IMRB, Mondor Institute for Biomedical Research, INSERM U955 – Université Paris Est Créteil, UPEC, Faculté de Médecine de Créteil 8, rue du Général Sarrail, 94010 Créteil, France
| | - Utz Herbig
- Center for Cell Signaling, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
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20
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García-Caballero D, Hart JR, Vogt PK. The MYC-regulated lncRNA LNROP (ENSG00000254887) enables MYC-driven cell proliferation by controlling the expression of OCT2. Cell Death Dis 2023; 14:168. [PMID: 36849510 PMCID: PMC9971199 DOI: 10.1038/s41419-023-05683-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 03/01/2023]
Abstract
MYC controls most of the non-coding genome. Several long noncoding transcripts were originally identified in the human B cell line P496-3 and then shown to be required for MYC-driven proliferation of Burkitt lymphoma-derived RAMOS cells. In this study, we used RAMOS cells exclusively as a representative of the human B cell lineage. One of the MYC-controlled lncRNAs required for RAMOS cell proliferation is ENSG00000254887 which we will term LNROP (long non-coding regulator of POU2F2). In the genome, LNROP is located in close proximity of POU2F2, the gene encoding OCT2. OCT2 is a transcription factor with important roles in sustaining the proliferation of human B cells. Here we show that LNROP is a nuclear RNA and a direct target of MYC. Downregulation of LNROP attenuates the expression of OCT2. This effect of LNROP on the expression of OCT2 is unidirectional as downregulation of OCT2 does not alter the expression of LNROP. Our data suggest that LNROP is a cis-acting regulator of OCT2. To illustrate the downstream reach of LNROP, we chose a prominent target of OCT2, the tyrosine phosphatase SHP-1. Downregulation of OCT2 elevates the expression of SHP-1. Our data suggest the following path of interactions: LNROP enables the proliferation of B cells by positively and unidirectionally regulating the growth-stimulatory transcription factor OCT2. In actively proliferating B cells, OCT2 attenuates the expression and anti-proliferative activity of SHP-1.
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Affiliation(s)
- Daniel García-Caballero
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Jonathan R Hart
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter K Vogt
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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21
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Betzler AC, Ushmorov A, Brunner C. The transcriptional program during germinal center reaction - a close view at GC B cells, Tfh cells and Tfr cells. Front Immunol 2023; 14:1125503. [PMID: 36817488 PMCID: PMC9936310 DOI: 10.3389/fimmu.2023.1125503] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
The germinal center (GC) reaction is a key process during an adaptive immune response to T cell specific antigens. GCs are specialized structures within secondary lymphoid organs, in which B cell proliferation, somatic hypermutation and antibody affinity maturation occur. As a result, high affinity antibody secreting plasma cells and memory B cells are generated. An effective GC response needs interaction between multiple cell types. Besides reticular cells and follicular dendritic cells, particularly B cells, T follicular helper (Tfh) cells as well as T follicular regulatory (Tfr) cells are a key player during the GC reaction. Whereas Tfh cells provide help to GC B cells in selection processes, Tfr cells, a specialized subset of regulatory T cells (Tregs), are able to suppress the GC reaction maintaining the balance between immune activation and tolerance. The formation and function of GCs is regulated by a complex network of signals and molecules at multiple levels. In this review, we highlight recent developments in GC biology by focusing on the transcriptional program regulating the GC reaction. This review focuses on the transcriptional co-activator BOB.1/OBF.1, whose important role for GC B, Tfh and Tfr cell differentiation became increasingly clear in recent years. Moreover, we outline how deregulation of the GC transcriptional program can drive lymphomagenesis.
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Affiliation(s)
- Annika C. Betzler
- Department of Oto-Rhino-Laryngology, Ulm University Medical Center, Ulm, Germany
| | - Alexey Ushmorov
- Ulm University, Institute of Physiological Chemistry, Ulm, Germany
| | - Cornelia Brunner
- Department of Oto-Rhino-Laryngology, Ulm University Medical Center, Ulm, Germany,*Correspondence: Cornelia Brunner,
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22
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Yang J, Guo Q, Wang L, Yu S. POU Domain Class 2 Transcription Factor 2 Inhibits Ferroptosis in Cerebral Ischemia Reperfusion Injury by Activating Sestrin2. Neurochem Res 2023; 48:658-670. [PMID: 36306010 DOI: 10.1007/s11064-022-03791-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/12/2022] [Accepted: 10/12/2022] [Indexed: 02/07/2023]
Abstract
Cerebral ischemia reperfusion injury (CIRI) is the commonest cause of brain dysfunction. Up-regulation of POU domain class 2 transcription factor 2 (POU2F2) has been reported in patients with cerebral ischemia, while the role of POU2F2 in CIRI remains elusive. Middle cerebral artery occlusion/reperfusion (MCAO/R) in mice and oxygen and glucose deprivation/reperfusion (OGD/R) in mouse primary cortical neurons were used as models of CIRI injury in vivo and in vitro. Lentivirus-mediated POU2F2 knockdown further impaired CIRI induced by MCAO/R in mice, which was accompanied by increased-neurological deficits, cerebral infarct volume and neuronal loss. Our evidence suggested that POU2F2 deficiency deteriorated oxidative stress and ferroptosis according to the phenomenon such as the abatement of SOD, GSH, glutathione peroxidase 4 (GPX4) activity and accumulation of ROS, lipid ROS, 4-hydroxynonenal (4-HNE) and MDA. In vivo, primary cortical neurons with POU2F2 knockdown also showed worse neuronal damage, oxidative stress and ferroptosis. Sestrin2 (Sesn2) was reported as a neuroprotection gene and involved in ferroptosis mechanism. Up-regulation of Sesn2 was observed in the ischemic penumbra and OGD/R-induced neuronal cells. Further, we proved that POU2F2, as a transcription factor, could bind to Sesn2 promoter and positively regulate its expression. Sesn2 overexpression relieved oxidative stress and ferroptosis induced by POU2F2 knockdown in OGD/R-treated neurons. This research demonstrated that CIRI induced a compensatory increase of POU2F2 and Sesn2. Down-regulated POU2F2 exacerbated CIRI through the acceleration of oxidative stress and ferroptosis possibly by decreasing Sesn2 expression, which offers new sights into therapeutic mechanisms for CIRI.
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Affiliation(s)
- Jinghui Yang
- Department of Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin Province, China
| | - Qian Guo
- Department of Neurology, China-Japan Union Hospital of Jilin University, No. 126, Xiantai Street, Changchun, Jilin Province, China
| | - Lu Wang
- Department of Neurology, China-Japan Union Hospital of Jilin University, No. 126, Xiantai Street, Changchun, Jilin Province, China
| | - Shan Yu
- Department of Neurology, China-Japan Union Hospital of Jilin University, No. 126, Xiantai Street, Changchun, Jilin Province, China.
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23
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Zhang W, Liu L, Xiao X, Zhou H, Peng Z, Wang W, Huang L, Xie Y, Xu H, Tao L, Nie W, Yuan X, Liu F, Yuan Q. Identification of common molecular signatures of SARS-CoV-2 infection and its influence on acute kidney injury and chronic kidney disease. Front Immunol 2023; 14:961642. [PMID: 37026010 PMCID: PMC10070855 DOI: 10.3389/fimmu.2023.961642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the main cause of COVID-19, causing hundreds of millions of confirmed cases and more than 18.2 million deaths worldwide. Acute kidney injury (AKI) is a common complication of COVID-19 that leads to an increase in mortality, especially in intensive care unit (ICU) settings, and chronic kidney disease (CKD) is a high risk factor for COVID-19 and its related mortality. However, the underlying molecular mechanisms among AKI, CKD, and COVID-19 are unclear. Therefore, transcriptome analysis was performed to examine common pathways and molecular biomarkers for AKI, CKD, and COVID-19 in an attempt to understand the association of SARS-CoV-2 infection with AKI and CKD. Three RNA-seq datasets (GSE147507, GSE1563, and GSE66494) from the GEO database were used to detect differentially expressed genes (DEGs) for COVID-19 with AKI and CKD to search for shared pathways and candidate targets. A total of 17 common DEGs were confirmed, and their biological functions and signaling pathways were characterized by enrichment analysis. MAPK signaling, the structural pathway of interleukin 1 (IL-1), and the Toll-like receptor pathway appear to be involved in the occurrence of these diseases. Hub genes identified from the protein-protein interaction (PPI) network, including DUSP6, BHLHE40, RASGRP1, and TAB2, are potential therapeutic targets in COVID-19 with AKI and CKD. Common genes and pathways may play pathogenic roles in these three diseases mainly through the activation of immune inflammation. Networks of transcription factor (TF)-gene, miRNA-gene, and gene-disease interactions from the datasets were also constructed, and key gene regulators influencing the progression of these three diseases were further identified among the DEGs. Moreover, new drug targets were predicted based on these common DEGs, and molecular docking and molecular dynamics (MD) simulations were performed. Finally, a diagnostic model of COVID-19 was established based on these common DEGs. Taken together, the molecular and signaling pathways identified in this study may be related to the mechanisms by which SARS-CoV-2 infection affects renal function. These findings are significant for the effective treatment of COVID-19 in patients with kidney diseases.
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Affiliation(s)
- Weiwei Zhang
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Leping Liu
- Department of Pediatrics, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiangcheng Xiao
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Hongshan Zhou
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Zhangzhe Peng
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Wei Wang
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Ling Huang
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Yanyun Xie
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Hui Xu
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Lijian Tao
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Wannian Nie
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Xiangning Yuan
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Fang Liu
- Health Management Center, Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Fang Liu, ; Qiongjing Yuan,
| | - Qiongjing Yuan
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
- National Clinical Medical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, China
- Research Center for Medical Metabolomics, Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Fang Liu, ; Qiongjing Yuan,
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24
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Deutsch N, Pajkos M, Erdős G, Dosztányi Z. DisCanVis: Visualizing integrated structural and functional annotations to better understand the effect of cancer mutations located within disordered proteins. Protein Sci 2023; 32:e4522. [PMID: 36452990 PMCID: PMC9793970 DOI: 10.1002/pro.4522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
Intrinsically disordered proteins (IDPs) play important roles in a wide range of biological processes and have been associated with various diseases, including cancer. In the last few years, cancer genome projects have systematically collected genetic variations underlying multiple cancer types. In parallel, the number and different types of disordered proteins characterized by experimental methods have also significantly increased. Nevertheless, the role of IDPs in various types of cancer is still not well understood. In this work, we present DisCanVis, a novel visualization tool for cancer mutations with a special focus on IDPs. In order to aid the interpretation of observed mutations, genome level information is combined with information about the structural and functional properties of proteins. The web server enables users to inspect individual proteins, collect examples with existing annotations of protein disorder and associated function or to discover currently uncharacterized examples with likely disease relevance. Through a REST API interface and precompiled tables the analysis can be extended to a group of proteins.
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Affiliation(s)
- Norbert Deutsch
- Department of BiochemistryInstitute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
| | - Mátyás Pajkos
- Department of BiochemistryInstitute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
| | - Gábor Erdős
- Department of BiochemistryInstitute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
| | - Zsuzsanna Dosztányi
- Department of BiochemistryInstitute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
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25
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Wang Y, Du J, Gao Z, Sun H, Mei M, Wang Y, Ren Y, Zhou X. Evolving landscape of PD-L2: bring new light to checkpoint immunotherapy. Br J Cancer 2022; 128:1196-1207. [PMID: 36522474 PMCID: PMC10050415 DOI: 10.1038/s41416-022-02084-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
AbstractImmune checkpoint blockade therapy targeting programmed cell death protein 1 (PD-1) has revolutionized the landscape of multiple human cancer types, including head and neck squamous carcinoma (HNSCC). Programmed death ligand-2 (PD-L2), a PD-1 ligand, mediates cancer cell immune escape (or tolerance independent of PD-L1) and predicts poor prognosis of patients with HNSCC. Therefore, an in-depth understanding of the regulatory process of PD-L2 expression may stratify patients with HNSCC to benefit from anti-PD-1 immunotherapy. In this review, we summarised the PD-L2 expression and its immune-dependent and independent functions in HNSCC and other solid tumours. We focused on recent findings on the mechanisms that regulate PD-L2 at the genomic, transcriptional, post-transcriptional, translational, and post-translational levels, also in intercellular communication of tumour microenvironment (TME). We also discussed the prospects of using small molecular agents indirectly targeting PD-L2 in cancer therapy. These findings may provide a notable avenue in developing novel and effective PD-L2-targeted therapeutic strategies for immune combination therapy and uncovering biomarkers that improve the clinical efficacy of anti-PD-1 therapies.
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26
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Taylor CA, Watson RA, Tong O, Ye W, Nassiri I, Gilchrist JJ, de Los Aires AV, Sharma PK, Koturan S, Cooper RA, Woodcock VK, Jungkurth E, Shine B, Coupe N, Payne MJ, Church DN, Naranbhai V, Groha S, Emery P, Mankia K, Freedman ML, Choueiri TK, Middleton MR, Gusev A, Fairfax BP. IL7 genetic variation and toxicity to immune checkpoint blockade in patients with melanoma. Nat Med 2022; 28:2592-2600. [PMID: 36526722 PMCID: PMC9800275 DOI: 10.1038/s41591-022-02095-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/18/2022] [Indexed: 12/23/2022]
Abstract
Treatment with immune checkpoint blockade (ICB) frequently triggers immune-related adverse events (irAEs), causing considerable morbidity. In 214 patients receiving ICB for melanoma, we observed increased severe irAE risk in minor allele carriers of rs16906115, intronic to IL7. We found that rs16906115 forms a B cell-specific expression quantitative trait locus (eQTL) to IL7 in patients. Patients carrying the risk allele demonstrate increased pre-treatment B cell IL7 expression, which independently associates with irAE risk, divergent immunoglobulin expression and more B cell receptor mutations. Consistent with the role of IL-7 in T cell development, risk allele carriers have distinct ICB-induced CD8+ T cell subset responses, skewing of T cell clonality and greater proportional repertoire occupancy by large clones. Finally, analysis of TCGA data suggests that risk allele carriers independently have improved melanoma survival. These observations highlight key roles for B cells and IL-7 in both ICB response and toxicity and clinical outcomes in melanoma.
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Affiliation(s)
- Chelsea A Taylor
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Robert A Watson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Orion Tong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Weiyu Ye
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Isar Nassiri
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - James J Gilchrist
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alba Verge de Los Aires
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Piyush Kumar Sharma
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Surya Koturan
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Rosalin A Cooper
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Victoria K Woodcock
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Elsita Jungkurth
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Brian Shine
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Nicholas Coupe
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Miranda J Payne
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - David N Church
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Vivek Naranbhai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Stefan Groha
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- National Institute for Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Kulveer Mankia
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- National Institute for Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mark R Middleton
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alexander Gusev
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin P Fairfax
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Department of Oncology, University of Oxford, Oxford, UK.
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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27
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Liu L, Khan A, Sanchez-Rodriguez E, Zanoni F, Li Y, Steers N, Balderes O, Zhang J, Krithivasan P, LeDesma RA, Fischman C, Hebbring SJ, Harley JB, Moncrieffe H, Kottyan LC, Namjou-Khales B, Walunas TL, Knevel R, Raychaudhuri S, Karlson EW, Denny JC, Stanaway IB, Crosslin D, Rauen T, Floege J, Eitner F, Moldoveanu Z, Reily C, Knoppova B, Hall S, Sheff JT, Julian BA, Wyatt RJ, Suzuki H, Xie J, Chen N, Zhou X, Zhang H, Hammarström L, Viktorin A, Magnusson PKE, Shang N, Hripcsak G, Weng C, Rundek T, Elkind MSV, Oelsner EC, Barr RG, Ionita-Laza I, Novak J, Gharavi AG, Kiryluk K. Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits. Nat Commun 2022; 13:6859. [PMID: 36369178 PMCID: PMC9651905 DOI: 10.1038/s41467-022-34456-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulin A (IgA) mediates mucosal responses to food antigens and the intestinal microbiome and is involved in susceptibility to mucosal pathogens, celiac disease, inflammatory bowel disease, and IgA nephropathy. We performed a genome-wide association study of serum IgA levels in 41,263 individuals of diverse ancestries and identified 20 genome-wide significant loci, including 9 known and 11 novel loci. Co-localization analyses with expression QTLs prioritized candidate genes for 14 of 20 significant loci. Most loci encoded genes that produced immune defects and IgA abnormalities when genetically manipulated in mice. We also observed positive genetic correlations of serum IgA levels with IgA nephropathy, type 2 diabetes, and body mass index, and negative correlations with celiac disease, inflammatory bowel disease, and several infections. Mendelian randomization supported elevated serum IgA as a causal factor in IgA nephropathy. African ancestry was consistently associated with higher serum IgA levels and greater frequency of IgA-increasing alleles compared to other ancestries. Our findings provide novel insights into the genetic regulation of IgA levels and its potential role in human disease.
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Affiliation(s)
- Lili Liu
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Elena Sanchez-Rodriguez
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Yifu Li
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Nicholas Steers
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Olivia Balderes
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Junying Zhang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Robert A LeDesma
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Clara Fischman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott J Hebbring
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - John B Harley
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Halima Moncrieffe
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Leah C Kottyan
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Bahram Namjou-Khales
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Theresa L Walunas
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rachel Knevel
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth W Karlson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joshua C Denny
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ian B Stanaway
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - David Crosslin
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA, USA
| | - Thomas Rauen
- Department of Nephrology, RWTH University of Aachen, Aachen, Germany
| | - Jürgen Floege
- Department of Nephrology, RWTH University of Aachen, Aachen, Germany
| | - Frank Eitner
- Department of Nephrology, RWTH University of Aachen, Aachen, Germany
- Kidney Diseases Research, Bayer Pharma AG, Wuppertal, Germany
| | - Zina Moldoveanu
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Colin Reily
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Barbora Knoppova
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stacy Hall
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Justin T Sheff
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bruce A Julian
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert J Wyatt
- Division of Pediatric Nephrology, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Hitoshi Suzuki
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Jingyuan Xie
- Department of Nephrology, Institute of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nan Chen
- Department of Nephrology, Institute of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xujie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Viktorin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ning Shang
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Tatjana Rundek
- Department of Neurology, University of Miami, Miami, FL, USA
- Evelyn F. McKnight Brain Institute, University of Miami, Miami, FL, USA
| | - Mitchell S V Elkind
- Department of Neurology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Elizabeth C Oelsner
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - R Graham Barr
- Division of General Medicine, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Jan Novak
- Department of Microbiology and Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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28
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Wu S, Yin Y, Wang X. The epigenetic regulation of the germinal center response. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194828. [PMID: 35643396 DOI: 10.1016/j.bbagrm.2022.194828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
In response to T-cell-dependent antigens, antigen-experienced B cells migrate to the center of the B-cell follicle to seed the germinal center (GC) response after cognate interactions with CD4+ T cells. These GC B cells eventually mature into memory and long-lived antibody-secreting plasma cells, thus generating long-lived humoral immunity. Within GC, B cells undergo somatic hypermutation of their B cell receptors (BCR) and positive selection for the emergence of high-affinity antigen-specific B-cell clones. However, this process may be dangerous, as the accumulation of aberrant mutations could result in malignant transformation of GC B cells or give rise to autoreactive B cell clones that can cause autoimmunity. Because of this, better understanding of GC development provides diagnostic and therapeutic clues to the underlying pathologic process. A productive GC response is orchestrated by multiple mechanisms. An emerging important regulator of GC reaction is epigenetic modulation, which has key transcriptional regulatory properties. In this review, we summarize the current knowledge on the biology of epigenetic mechanisms in the regulation of GC reaction and outline its importance in identification of immunotherapy decision making.
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Affiliation(s)
- Shusheng Wu
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuye Yin
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoming Wang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China.
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29
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Gladbach YS, Sklarz LM, Roolf C, Beck J, Schütz E, Fuellen G, Junghanss C, Murua Escobar H, Hamed M. Molecular Characterization of the Response to Conventional Chemotherapeutics in Pro-B-ALL Cell Lines in Terms of Tumor Relapse. Genes (Basel) 2022; 13:genes13071240. [PMID: 35886023 PMCID: PMC9316692 DOI: 10.3390/genes13071240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 11/29/2022] Open
Abstract
Little is known about optimally applying chemotherapeutic agents in a specific temporal sequence to rapidly reduce the tumor load and to improve therapeutic efficacy. The clinical optimization of drug efficacy while reducing side effects is still restricted due to an incomplete understanding of the mode of action and related tumor relapse mechanisms on the molecular level. The molecular characterization of transcriptomic drug signatures can help to identify the affected pathways, downstream regulated genes and regulatory interactions related to tumor relapse in response to drug application. We tried to outline the dynamic regulatory reprogramming leading to tumor relapse in relapsed MLL-rearranged pro-B-cell acute lymphoblastic leukemia (B-ALL) cells in response to two first-line treatments: dexamethasone (Dexa) and cytarabine (AraC). We performed an integrative molecular analysis of whole transcriptome profiles of each treatment, specifically considering public knowledge of miRNA regulation via a network-based approach to unravel key driver genes and miRNAs that may control the relapse mechanisms accompanying each treatment. Our results gave hints to the crucial regulatory roles of genes leading to Dexa-resistance and related miRNAs linked to chemosensitivity. These genes and miRNAs should be further investigated in preclinical models to obtain more hints about relapse processes.
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Affiliation(s)
- Yvonne Saara Gladbach
- Institute for Biostatistics and Informatics in Medicine and Ageing Research (IBIMA), Rostock University Medical Center, 18057 Rostock, Germany; (Y.S.G.); (G.F.)
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lisa-Madeleine Sklarz
- Clinic III—Hematology, Oncology, Palliative Medicine, Center for Internal Medicine, Rostock University Medical Center, 18057 Rostock, Germany; (L.-M.S.); (C.R.); (C.J.); (H.M.E.)
| | - Catrin Roolf
- Clinic III—Hematology, Oncology, Palliative Medicine, Center for Internal Medicine, Rostock University Medical Center, 18057 Rostock, Germany; (L.-M.S.); (C.R.); (C.J.); (H.M.E.)
| | - Julia Beck
- Chronix Biomedical GmbH, 37073 Göttingen, Germany; (J.B.); (E.S.)
| | - Ekkehard Schütz
- Chronix Biomedical GmbH, 37073 Göttingen, Germany; (J.B.); (E.S.)
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research (IBIMA), Rostock University Medical Center, 18057 Rostock, Germany; (Y.S.G.); (G.F.)
| | - Christian Junghanss
- Clinic III—Hematology, Oncology, Palliative Medicine, Center for Internal Medicine, Rostock University Medical Center, 18057 Rostock, Germany; (L.-M.S.); (C.R.); (C.J.); (H.M.E.)
| | - Hugo Murua Escobar
- Clinic III—Hematology, Oncology, Palliative Medicine, Center for Internal Medicine, Rostock University Medical Center, 18057 Rostock, Germany; (L.-M.S.); (C.R.); (C.J.); (H.M.E.)
- Comprehensive Cancer Center Mecklenburg-Vorpommern (CCC-MV), Campus Rostock, Rostock University Medical Center, 18057 Rostock, Germany
| | - Mohamed Hamed
- Institute for Biostatistics and Informatics in Medicine and Ageing Research (IBIMA), Rostock University Medical Center, 18057 Rostock, Germany; (Y.S.G.); (G.F.)
- Correspondence:
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30
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Qu J, Yang F, Zhu T, Wang Y, Fang W, Ding Y, Zhao X, Qi X, Xie Q, Chen M, Xu Q, Xie Y, Sun Y, Chen D. A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys. Nat Commun 2022; 13:4069. [PMID: 35831300 PMCID: PMC9279386 DOI: 10.1038/s41467-022-31770-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/01/2022] [Indexed: 12/24/2022] Open
Abstract
Non-human primates are attractive laboratory animal models that accurately reflect both developmental and pathological features of humans. Here we present a compendium of cell types across multiple organs in cynomolgus monkeys (Macaca fascicularis) using both single-cell chromatin accessibility and RNA sequencing data. The integrated cell map enables in-depth dissection and comparison of molecular dynamics, cell-type compositions and cellular heterogeneity across multiple tissues and organs. Using single-cell transcriptomic data, we infer pseudotime cell trajectories and cell-cell communications to uncover key molecular signatures underlying their cellular processes. Furthermore, we identify various cell-specific cis-regulatory elements and construct organ-specific gene regulatory networks at the single-cell level. Finally, we perform comparative analyses of single-cell landscapes among mouse, monkey and human. We show that cynomolgus monkey has strikingly higher degree of similarities in terms of immune-associated gene expression patterns and cellular communications to human than mouse. Taken together, our study provides a valuable resource for non-human primate cell biology. Non-human primates are attractive laboratory animal models that can accurately reflect some developmental and pathological features of humans. Here the authors chart a reference cell map of cynomolgus monkeys using both scATAC-seq and scRNA-seq data across multiple organs, providing insights into the molecular dynamics and cellular heterogeneity of this organism.
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Affiliation(s)
- Jiao Qu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Fa Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yingshuo Wang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China
| | - Wen Fang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yan Ding
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Xue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Xianjia Qi
- Shanghai XuRan Biotechnology Co., Ltd., 1088 Zhongchun Road, 201109, Shanghai, China
| | - Qiangmin Xie
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China
| | - Yicheng Xie
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310052, Hangzhou, China.
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China. .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China.
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023, Nanjing, China.
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31
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Tang XJ, Xiao QH, Wang XL, He Y, Tian YN, Xia BT, Guo Y, Huang JL, Duan P, Tan Y. Single-Cell Transcriptomics-Based Study of Transcriptional Regulatory Features in the Non-Obstructive Azoospermia Testis. Front Genet 2022; 13:875762. [PMID: 35669193 PMCID: PMC9163961 DOI: 10.3389/fgene.2022.875762] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/04/2022] [Indexed: 11/18/2022] Open
Abstract
Non-obstructive azoospermia (NOA) is one of the most important causes of male infertility. Although many congenital factors have been identified, the aetiology in the majority of idiopathic NOA (iNOA) cases remains unknown. Herein, using single-cell RNA-Seq data sets (GSE149512) from the Gene Expression Omnibus (GEO) database, we constructed transcriptional regulatory networks (TRNs) to explain the mutual regulatory relationship and the causal relationship between transcription factors (TFs). We defined 10 testicular cell types by their marker genes and found that the proportion of Leydig cells (LCs) and macrophages (tMΦ) was significantly increased in iNOA testis. We identified specific TFs including LHX9, KLF8, KLF4, ARID5B and RXRG in iNOA LCs. In addition, we found specific TFs in iNOA tMΦ such as POU2F2, SPIB IRF5, CEBPA, ELK4 and KLF6. All these identified TFs are strongly engaged in cellular fate, function and homeostasis of the microenvironment. Changes in the activity of the above-mentioned TFs might affect the function of LCs and tMΦ and ultimately cause spermatogenesis failure. This study illustrate that these TFs play important regulatory roles in the occurrence and development of NOA.
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Affiliation(s)
- Xiao-juan Tang
- Department of Andrology, Renmin Hospital, Hubei University of Medicine, Shiyan, China
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Xiangyang City, Department of Obstetrics and Gynaecology, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Qiao-hong Xiao
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Xiangyang City, Department of Obstetrics and Gynaecology, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Xue-lin Wang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Xiangyang City, Department of Obstetrics and Gynaecology, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Yan He
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Xiangyang City, Department of Obstetrics and Gynaecology, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
- Postgraduate Training Basement of Jinzhou Medicical University, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Ya-nan Tian
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Xiangyang City, Department of Obstetrics and Gynaecology, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
- Postgraduate Training Basement of Jinzhou Medicical University, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Bin-tong Xia
- Department of Urology Surgery, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Yang Guo
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Xiangyang City, Department of Obstetrics and Gynaecology, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Jiao-long Huang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Xiangyang City, Department of Obstetrics and Gynaecology, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Peng Duan
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Xiangyang City, Department of Obstetrics and Gynaecology, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Yan Tan
- Department of Andrology, Renmin Hospital, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
- Biomedical Engineering College, Hubei University of Medicine, Shiyan, China
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32
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Chen C, Yu W, Alikarami F, Qiu Q, Chen CH, Flournoy J, Gao P, Uzun Y, Fang L, Davenport JW, Hu Y, Zhu Q, Wang K, Libbrecht C, Felmeister A, Rozich I, Ding YY, Hunger SP, Felix CA, Wu H, Brown PA, Guest EM, Barrett DM, Bernt KM, Tan K. Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell-like blasts in KMT2A-rearranged leukemia. Blood 2022; 139:2198-2211. [PMID: 34864916 PMCID: PMC8990373 DOI: 10.1182/blood.2021013442] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/30/2021] [Indexed: 11/20/2022] Open
Abstract
KMT2A-rearranged (KMT2A-r) infant acute lymphoblastic leukemia (ALL) is a devastating malignancy with a dismal outcome, and younger age at diagnosis is associated with increased risk of relapse. To discover age-specific differences and critical drivers that mediate poor outcome in KMT2A-r ALL, we subjected KMT2A-r leukemias and normal hematopoietic cells from patients of different ages to single-cell multiomics analyses. We uncovered the following critical new insights: leukemia cells from patients <6 months have significantly increased lineage plasticity. Steroid response pathways are downregulated in the most immature blasts from younger patients. We identify a hematopoietic stem and progenitor-like (HSPC-like) population in the blood of younger patients that contains leukemic blasts and form an immunosuppressive signaling circuit with cytotoxic lymphocytes. These observations offer a compelling explanation for the ability of leukemias in young patients to evade chemotherapy and immune-mediated control. Our analysis also revealed preexisting lymphomyeloid primed progenitors and myeloid blasts at initial diagnosis of B-ALL. Tracking of leukemic clones in 2 patients whose leukemia underwent a lineage switch documented the evolution of such clones into frank acute myeloid leukemia (AML). These findings provide critical insights into KMT2A-r ALL and have clinical implications for molecularly targeted and immunotherapy approaches. Beyond infant ALL, our study demonstrates the power of single-cell multiomics to detect tumor intrinsic and extrinsic factors affecting rare but critical subpopulations within a malignant population that ultimately determines patient outcome.
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Affiliation(s)
- Changya Chen
- Division of Oncology and Center for Childhood Cancer Research and
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Wenbao Yu
- Division of Oncology and Center for Childhood Cancer Research and
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine
| | | | - Qi Qiu
- Department of Genetics, Perelman School of Medicine
- Penn Epigenetics Institute, and
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA
| | - Chia-Hui Chen
- Division of Oncology and Center for Childhood Cancer Research and
| | - Jennifer Flournoy
- Department of Genetics, Perelman School of Medicine
- Penn Epigenetics Institute, and
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA
| | - Peng Gao
- Division of Oncology and Center for Childhood Cancer Research and
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Yasin Uzun
- Division of Oncology and Center for Childhood Cancer Research and
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Yuxuan Hu
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Qin Zhu
- Graduate Group in Genomics and Computational Biology
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, and
| | - Clara Libbrecht
- Division of Oncology and Center for Childhood Cancer Research and
| | - Alex Felmeister
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Isaiah Rozich
- Graduate Group in Immunology, University of Pennsylvania, Philadelphia, PA
| | - Yang-Yang Ding
- Division of Oncology and Center for Childhood Cancer Research and
- Department of Pediatrics, Perelman School of Medicine
| | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research and
- Department of Pediatrics, Perelman School of Medicine
| | - Carolyn A Felix
- Division of Oncology and Center for Childhood Cancer Research and
- Department of Pediatrics, Perelman School of Medicine
| | - Hao Wu
- Department of Genetics, Perelman School of Medicine
- Penn Epigenetics Institute, and
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA
| | - Patrick A Brown
- Division of Pediatric Oncology, Johns Hopkins University, Baltimore, MD; and
| | - Erin M Guest
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO
| | - David M Barrett
- Division of Oncology and Center for Childhood Cancer Research and
- Department of Pediatrics, Perelman School of Medicine
| | - Kathrin M Bernt
- Division of Oncology and Center for Childhood Cancer Research and
- Department of Pediatrics, Perelman School of Medicine
| | - Kai Tan
- Division of Oncology and Center for Childhood Cancer Research and
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine
- Department of Genetics, Perelman School of Medicine
- Penn Epigenetics Institute, and
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA
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Zhuang Y, Che J, Wu M, Guo Y, Xu Y, Dong X, Yang H. Altered pathways and targeted therapy in double hit lymphoma. J Hematol Oncol 2022; 15:26. [PMID: 35303910 PMCID: PMC8932183 DOI: 10.1186/s13045-022-01249-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/07/2022] [Indexed: 12/20/2022] Open
Abstract
High-grade B-cell lymphoma with translocations involving MYC and BCL2 or BCL6, usually referred to as double hit lymphoma (DHL), is an aggressive hematological malignance with distinct genetic features and poor clinical prognosis. Current standard chemoimmunotherapy fails to confer satisfying outcomes and few targeted therapeutics are available for the treatment against DHL. Recently, the delineating of the genetic landscape in tumors has provided insight into both biology and targeted therapies. Therefore, it is essential to understand the altered signaling pathways of DHL to develop treatment strategies with better clinical benefits. Herein, we summarized the genetic alterations in the two DHL subtypes (DHL-BCL2 and DHL-BCL6). We further elucidate their implications on cellular processes, including anti-apoptosis, epigenetic regulations, B-cell receptor signaling, and immune escape. Ongoing and potential therapeutic strategies and targeted drugs steered by these alterations were reviewed accordingly. Based on these findings, we also discuss the therapeutic vulnerabilities that coincide with these genetic changes. We believe that the understanding of the DHL studies will provide insight into this disease and capacitate the finding of more effective treatment strategies.
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Affiliation(s)
- Yuxin Zhuang
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
| | - Meijuan Wu
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
| | - Yu Guo
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
| | - Yongjin Xu
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People’s Republic of China
| | - Haiyan Yang
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
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Tompkins VS, Rouse WB, O’Leary CA, Andrews RJ, Moss WN. Analyses of human cancer driver genes uncovers evolutionarily conserved RNA structural elements involved in posttranscriptional control. PLoS One 2022; 17:e0264025. [PMID: 35213597 PMCID: PMC8880891 DOI: 10.1371/journal.pone.0264025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/01/2022] [Indexed: 12/02/2022] Open
Abstract
Experimental breakthroughs have provided unprecedented insights into the genes involved in cancer. The identification of such cancer driver genes is a major step in gaining a fuller understanding of oncogenesis and provides novel lists of potential therapeutic targets. A key area that requires additional study is the posttranscriptional control mechanisms at work in cancer driver genes. This is important not only for basic insights into the biology of cancer, but also to advance new therapeutic modalities that target RNA—an emerging field with great promise toward the treatment of various cancers. In the current study we performed an in silico analysis on the transcripts associated with 800 cancer driver genes (10,390 unique transcripts) that identified 179,190 secondary structural motifs with evidence of evolutionarily ordered structures with unusual thermodynamic stability. Narrowing to one transcript per gene, 35,426 predicted structures were subjected to phylogenetic comparisons of sequence and structural conservation. This identified 7,001 RNA secondary structures embedded in transcripts with evidence of covariation between paired sites, supporting structure models and suggesting functional significance. A select set of seven structures were tested in vitro for their ability to regulate gene expression; all were found to have significant effects. These results indicate potentially widespread roles for RNA structure in posttranscriptional control of human cancer driver genes.
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Affiliation(s)
- Van S. Tompkins
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Warren B. Rouse
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Collin A. O’Leary
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Ryan J. Andrews
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Walter N. Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
- * E-mail:
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Meeuwsen MH, Wouters AK, Jahn L, Hagedoorn RS, Kester MG, Remst DF, Morton LT, van der Steen DM, Kweekel C, de Ru AH, Griffioen M, van Veelen PA, Falkenburg JF, Heemskerk MH. A broad and systematic approach to identify B cell malignancy-targeting TCRs for multi-antigen-based T cell therapy. Mol Ther 2022; 30:564-578. [PMID: 34371177 PMCID: PMC8821929 DOI: 10.1016/j.ymthe.2021.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/01/2021] [Accepted: 07/20/2021] [Indexed: 02/04/2023] Open
Abstract
CAR T cell therapy has shown great promise for the treatment of B cell malignancies. However, antigen-negative escape variants often cause disease relapse, necessitating the development of multi-antigen-targeting approaches. We propose that a T cell receptor (TCR)-based strategy would increase the number of potential antigenic targets, as peptides from both intracellular and extracellular proteins can be recognized. Here, we aimed to isolate a broad range of promising TCRs targeting multiple antigens for treatment of B cell malignancies. As a first step, 28 target genes for B cell malignancies were selected based on gene expression profiles. Twenty target peptides presented in human leukocyte antigen (HLA)-A∗01:01, -A∗24:02, -B∗08:01, or -B∗35:01 were identified from the immunopeptidome of B cell malignancies and used to form peptide-HLA (pHLA)-tetramers for T cell isolation. Target-peptide-specific CD8 T cells were isolated from HLA-mismatched healthy donors and subjected to a stringent stepwise selection procedure to ensure potency and eliminate cross-reactivity. In total, five T cell clones specific for FCRL5 in HLA-A∗01:01, VPREB3 in HLA-A∗24:02, and BOB1 in HLA-B∗35:01 recognized B cell malignancies. For all three specificities, TCR gene transfer into CD8 T cells resulted in cytokine production and efficient killing of multiple B cell malignancies. In conclusion, using this systematic approach we successfully identified three promising TCRs for T cell therapy against B cell malignancies.
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Affiliation(s)
- Miranda H. Meeuwsen
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands,Corresponding author: Miranda H. Meeuwsen, Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
| | - Anne K. Wouters
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Lorenz Jahn
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands,Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Renate S. Hagedoorn
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Michel G.D. Kester
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Dennis F.G. Remst
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Laura T. Morton
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Dirk M. van der Steen
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Christiaan Kweekel
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | | | - Mirjam H.M. Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands,Corresponding author: Mirjam H.M. Heemskerk, Department of Hematology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
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36
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Penter L, Gohil SH, Lareau C, Ludwig LS, Parry EM, Huang T, Li S, Zhang W, Livitz D, Leshchiner I, Parida L, Getz G, Rassenti LZ, Kipps TJ, Brown JR, Davids MS, Neuberg DS, Livak KJ, Sankaran VG, Wu CJ. Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History. Cancer Discov 2021; 11:3048-3063. [PMID: 34112698 PMCID: PMC8660953 DOI: 10.1158/2159-8290.cd-21-0276] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/04/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022]
Abstract
While cancers evolve during disease progression and in response to therapy, temporal dynamics remain difficult to study in humans due to the lack of consistent barcodes marking individual clones in vivo. We employ mitochondrial single-cell assay for transposase-accessible chromatin with sequencing to profile 163,279 cells from 9 patients with chronic lymphocytic leukemia (CLL) collected across disease course and utilize mitochondrial DNA (mtDNA) mutations as natural genetic markers of cancer clones. We observe stable propagation of mtDNA mutations over years in the absence of strong selective pressure, indicating clonal persistence, but dramatic changes following tight bottlenecks, including disease transformation and relapse posttherapy, paralleled by acquisition of copy-number variants and changes in chromatin accessibility and gene expression. Furthermore, we link CLL subclones to distinct chromatin states, providing insight into nongenetic sources of relapse. mtDNA mutations thus mirror disease history and provide naturally occurring genetic barcodes to enable patient-specific study of cancer subclonal dynamics. SIGNIFICANCE Single-cell multi-omic profiling of CLL reveals the utility of somatic mtDNA mutations as in vivo barcodes, which mark subclones that can evolve over time along with changes in accessible chromatin and gene expression profiles to capture dynamics of disease evolution. See related commentary by Hilton and Scott, p. 2965. This article is highlighted in the In This Issue feature, p. 2945.
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Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Hematology, Oncology, and Tumor Immunology, Charité – Universitätsmedizin Berlin (CVK), Berlin, Germany
| | - Satyen H. Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Academic Haematology, University College London Cancer Institute, London, United Kingdom
- Department of Haematology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Caleb Lareau
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Leif S. Ludwig
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Berlin Institute of Health at Charité — Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany
| | - Erin M. Parry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Teddy Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Dimitri Livitz
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Ignaty Leshchiner
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Laxmi Parida
- IBM TJ Watson Research Center, Yorktown Heights, New York, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Laura Z. Rassenti
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Thomas J. Kipps
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Donna S. Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kenneth J. Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Vijay G. Sankaran
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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37
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Shaffer AL, Phelan JD, Wang JQ, Huang D, Wright GW, Kasbekar M, Choi J, Young RM, Webster DE, Yang Y, Zhao H, Yu X, Xu W, Roulland S, Ceribelli M, Zhang X, Wilson KM, Chen L, McKnight C, Klumpp-Thomas C, Thomas CJ, Häupl B, Oellerich T, Rae Z, Kelly MC, Ahn IE, Sun C, Gaglione EM, Wilson WH, Wiestner A, Staudt LM. Overcoming Acquired Epigenetic Resistance to BTK Inhibitors. Blood Cancer Discov 2021; 2:630-647. [PMID: 34778802 DOI: 10.1158/2643-3230.bcd-21-0063] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/17/2021] [Accepted: 08/31/2021] [Indexed: 12/14/2022] Open
Abstract
The use of Bruton tyrosine kinase (BTK) inhibitors to block B-cell receptor (BCR)-dependent NF-κB activation in lymphoid malignancies has been a major clinical advance, yet acquired therapeutic resistance is a recurring problem. We modeled the development of resistance to the BTK inhibitor ibrutinib in the activated B-cell (ABC) subtype of diffuse large B-cell lymphoma, which relies on chronic active BCR signaling for survival. The primary mode of resistance was epigenetic, driven in part by the transcription factor TCF4. The resultant phenotypic shift altered BCR signaling such that the GTPase RAC2 substituted for BTK in the activation of phospholipase Cγ2, thereby sustaining NF-κB activity. The interaction of RAC2 with phospholipase Cγ2 was also increased in chronic lymphocytic leukemia cells from patients with persistent or progressive disease on BTK inhibitor treatment. We identified clinically available drugs that can treat epigenetic ibrutinib resistance, suggesting combination therapeutic strategies. Significance In diffuse large B-cell lymphoma, we show that primary resistance to BTK inhibitors is due to epigenetic rather than genetic changes that circumvent the BTK blockade. We also observed this resistance mechanism in chronic lymphocytic leukemia, suggesting that epigenetic alterations may contribute more to BTK inhibitor resistance than currently thought.See related commentary by Pasqualucci, p. 555. This article is highlighted in the In This Issue feature, p. 549.
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Affiliation(s)
- Arthur L Shaffer
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - James D Phelan
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - James Q Wang
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - DaWei Huang
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - George W Wright
- Biometric Research Program, Division of Cancer Diagnosis and Treatment, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Monica Kasbekar
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jaewoo Choi
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ryan M Young
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Daniel E Webster
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yandan Yang
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Hong Zhao
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Xin Yu
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Weihong Xu
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sandrine Roulland
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Michele Ceribelli
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Xiaohu Zhang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Kelli M Wilson
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Lu Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Crystal McKnight
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Carleen Klumpp-Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Craig J Thomas
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Björn Häupl
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt; German Cancer Consortium/German Cancer Research Center, Heidelberg; and Department of Molecular Diagnostics and Translational Proteomics, Frankfurt Cancer Institute, Frankfurt, Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt; German Cancer Consortium/German Cancer Research Center, Heidelberg; and Department of Molecular Diagnostics and Translational Proteomics, Frankfurt Cancer Institute, Frankfurt, Germany
| | - Zachary Rae
- Cancer Research Technology Program, Single-Cell Analysis Facility, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Michael C Kelly
- Cancer Research Technology Program, Single-Cell Analysis Facility, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Inhye E Ahn
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Clare Sun
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Erika M Gaglione
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Louis M Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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38
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Hay M, Kumar V, Ricaño-Ponce I. The role of the X chromosome in infectious diseases. Brief Funct Genomics 2021; 21:143-158. [PMID: 34651167 DOI: 10.1093/bfgp/elab039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023] Open
Abstract
Many infectious diseases in humans present with a sex bias. This bias arises from a combination of environmental factors, hormones and genetics. In this study, we review the contribution of the X chromosome to the genetic factor associated with infectious diseases. First, we give an overview of the X-linked genes that have been described in the context of infectious diseases and group them in four main pathways that seem to be dysregulated in infectious diseases: nuclear factor kappa-B, interleukin 2 and interferon γ cascade, toll-like receptors and programmed death ligand 1. Then, we review the infectious disease associations in existing genome-wide association studies (GWAS) from the GWAS Catalog and the Pan-UK Biobank, describing the main associations and their possible implications for the disease. Finally, we highlight the importance of including the X chromosome in GWAS analysis and the importance of sex-specific analysis.
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39
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OCT2 pre-positioning facilitates cell fate transition and chromatin architecture changes in humoral immunity. Nat Immunol 2021; 22:1327-1340. [PMID: 34556886 PMCID: PMC9829245 DOI: 10.1038/s41590-021-01025-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 08/05/2021] [Indexed: 01/12/2023]
Abstract
During the germinal center (GC) reaction, B cells undergo profound transcriptional, epigenetic and genomic architectural changes. How such changes are established remains unknown. Mapping chromatin accessibility during the humoral immune response, we show that OCT2 was the dominant transcription factor linked to differential accessibility of GC regulatory elements. Silent chromatin regions destined to become GC-specific super-enhancers (SEs) contained pre-positioned OCT2-binding sites in naive B cells (NBs). These preloaded SE 'seeds' featured spatial clustering of regulatory elements enriched in OCT2 DNA-binding motifs that became heavily loaded with OCT2 and its GC-specific coactivator OCAB in GC B cells (GCBs). SEs with high abundance of pre-positioned OCT2 binding preferentially formed long-range chromatin contacts in GCs, to support expression of GC-specifying factors. Gain in accessibility and architectural interactivity of these regions were dependent on recruitment of OCAB. Pre-positioning key regulators at SEs may represent a broadly used strategy for facilitating rapid cell fate transitions.
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40
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Loss of synergistic transcriptional feedback loops drives diverse B-cell cancers. EBioMedicine 2021; 71:103559. [PMID: 34461601 PMCID: PMC8403728 DOI: 10.1016/j.ebiom.2021.103559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/30/2022] Open
Abstract
Background The most common B-cell cancers, chronic lymphocytic leukemia/lymphoma (CLL), follicular and diffuse large B-cell (FL, DLBCL) lymphomas, have distinct clinical courses, yet overlapping “cell-of-origin”. Dynamic changes to the epigenome are essential regulators of B-cell differentiation. Therefore, we reasoned that these distinct cancers may be driven by shared mechanisms of disruption in transcriptional circuitry. Methods We compared purified malignant B-cells from 52 patients with normal B-cell subsets (germinal center centrocytes and centroblasts, naïve and memory B-cells) from 36 donor tonsils using >325 high-resolution molecular profiling assays for histone modifications, open chromatin (ChIP-, FAIRE-seq), transcriptome (RNA-seq), transcription factor (TF) binding, and genome copy number (microarrays). Findings From the resulting data, we identified gains in active chromatin in enhancers/super-enhancers that likely promote unchecked B-cell receptor signaling, including one we validated near the immunoglobulin superfamily receptors FCMR and PIGR. More striking and pervasive was the profound loss of key B-cell identity TFs, tumor suppressors and their super-enhancers, including EBF1, OCT2(POU2F2), and RUNX3. Using a novel approach to identify transcriptional feedback, we showed that these core transcriptional circuitries are self-regulating. Their selective gain and loss form a complex, iterative, and interactive process that likely curbs B-cell maturation and spurs proliferation. Interpretation Our study is the first to map the transcriptional circuitry of the most common blood cancers. We demonstrate that a critical subset of B-cell TFs and their cognate enhancers form self-regulatory transcriptional feedback loops whose disruption is a shared mechanism underlying these diverse subtypes of B-cell lymphoma. Funding National Institute of Health, Siteman Cancer Center, Barnes-Jewish Hospital Foundation, Doris Duke Foundation.
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Biological importance of OCT transcription factors in reprogramming and development. Exp Mol Med 2021; 53:1018-1028. [PMID: 34117345 PMCID: PMC8257633 DOI: 10.1038/s12276-021-00637-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
Ectopic expression of Oct4, Sox2, Klf4 and c-Myc can reprogram somatic cells into induced pluripotent stem cells (iPSCs). Attempts to identify genes or chemicals that can functionally replace each of these four reprogramming factors have revealed that exogenous Oct4 is not necessary for reprogramming under certain conditions or in the presence of alternative factors that can regulate endogenous Oct4 expression. For example, polycistronic expression of Sox2, Klf4 and c-Myc can elicit reprogramming by activating endogenous Oct4 expression indirectly. Experiments in which the reprogramming competence of all other Oct family members tested and also in different species have led to the decisive conclusion that Oct proteins display different reprogramming competences and species-dependent reprogramming activity despite their profound sequence conservation. We discuss the roles of the structural components of Oct proteins in reprogramming and how donor cell epigenomes endow Oct proteins with different reprogramming competences. Cells can be reprogrammed into induced pluripotent stem cells (iPSCs), embryonic-like stem cells that can turn into any cell type and have extensive potential medical uses, without adding the transcription factor OCT4. Although other nearly identical OCT family members had been tried, only OCT4 could induce reprogramming and was previously thought to be indispensable. However, it now appears that the reprogramming can be induced by multiple pathways, as detailed in a review by Hans Schöler, Max Planck Institute for Biomolecular Medicine, Münster, and Johnny Kim, Max Planck Institute for Heart and Lung Research, Bad Nauheim, in Germany. They report that any factors that trigger cells to activate endogeous OCT4 can produce iPSCs without exogeously admistration of OCT4. The mechanisms for producing iPSCs can differ between species. These results illuminate the complex mechanisms of reprogramming.
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OBF1 and Oct factors control the germinal center transcriptional program. Blood 2021; 137:2920-2934. [PMID: 33512466 DOI: 10.1182/blood.2020010175] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022] Open
Abstract
OBF1 is a specific coactivator of the POU family transcription factors OCT1 and OCT2. OBF1 and OCT2 are B cell-specific and indispensable for germinal center (GC) formation, but their mechanism of action is unclear. Here, we show by chromatin immunoprecipitation-sequencing that OBF1 extensively colocalizes with OCT1 and OCT2. We found that these factors also often colocalize with transcription factors of the ETS family. Furthermore, we showed that OBF1, OCT2, and OCT1 bind widely to the promoters or enhancers of genes involved in GC formation in mouse and human GC B cells. Short hairpin RNA knockdown experiments demonstrated that OCT1, OCT2, and OBF1 regulate each other and are essential for proliferation of GC-derived lymphoma cell lines. OBF1 downregulation disrupts the GC transcriptional program: genes involved in GC maintenance, such as BCL6, are downregulated, whereas genes related to exit from the GC program, such as IRF4, are upregulated. Ectopic expression of BCL6 does not restore the proliferation of GC-derived lymphoma cells depleted of OBF1 unless IRF4 is also depleted, indicating that OBF1 controls an essential regulatory node in GC differentiation.
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Klintman J, Appleby N, Stamatopoulos B, Ridout K, Eyre TA, Robbe P, Pascua LL, Knight SJL, Dreau H, Cabes M, Popitsch N, Ehinger M, Martín-Subero JI, Campo E, Månsson R, Rossi D, Taylor JC, Vavoulis DV, Schuh A. Genomic and transcriptomic correlates of Richter transformation in chronic lymphocytic leukemia. Blood 2021; 137:2800-2816. [PMID: 33206936 PMCID: PMC8163497 DOI: 10.1182/blood.2020005650] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
The transformation of chronic lymphocytic leukemia (CLL) to high-grade B-cell lymphoma is known as Richter syndrome (RS), a rare event with dismal prognosis. In this study, we conducted whole-genome sequencing (WGS) of paired circulating CLL (PB-CLL) and RS biopsies (tissue-RS) from 17 patients recruited into a clinical trial (CHOP-O). We found that tissue-RS was enriched for mutations in poor-risk CLL drivers and genes in the DNA damage response (DDR) pathway. In addition, we identified genomic aberrations not previously implicated in RS, including the protein tyrosine phosphatase receptor (PTPRD) and tumor necrosis factor receptor-associated factor 3 (TRAF3). In the noncoding genome, we discovered activation-induced cytidine deaminase-related and unrelated kataegis in tissue-RS affecting regulatory regions of key immune-regulatory genes. These include BTG2, CXCR4, NFATC1, PAX5, NOTCH-1, SLC44A5, FCRL3, SELL, TNIP2, and TRIM13. Furthermore, differences between the global mutation signatures of pairs of PB-CLL and tissue-RS samples implicate DDR as the dominant mechanism driving transformation. Pathway-based clonal deconvolution analysis showed that genes in the MAPK and DDR pathways demonstrate high clonal-expansion probability. Direct comparison of nodal-CLL and tissue-RS pairs from an independent cohort confirmed differential expression of the same pathways by RNA expression profiling. Our integrated analysis of WGS and RNA expression data significantly extends previous targeted approaches, which were limited by the lack of germline samples, and it facilitates the identification of novel genomic correlates implicated in RS transformation, which could be targeted therapeutically. Our results inform the future selection of investigative agents for a UK clinical platform study. This trial was registered at www.clinicaltrials.gov as #NCT03899337.
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MESH Headings
- Aged
- Aged, 80 and over
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Base Sequence
- Clonal Evolution/genetics
- Clone Cells/pathology
- Combined Modality Therapy
- Cyclophosphamide/administration & dosage
- DNA Repair
- Disease Progression
- Doxorubicin/administration & dosage
- Female
- Gene Expression Regulation, Neoplastic/genetics
- Gene Regulatory Networks
- Genes, Neoplasm
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Mutation
- Neoplasm Proteins/genetics
- Prednisone/administration & dosage
- Prospective Studies
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- Syndrome
- Transcriptome
- Vincristine/administration & dosage
- Whole Genome Sequencing
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Affiliation(s)
- Jenny Klintman
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Translational Medicine, Skåne University Hospital, Lund University, Lund, Sweden
| | - Niamh Appleby
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
| | - Basile Stamatopoulos
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Katie Ridout
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Toby A Eyre
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
| | - Pauline Robbe
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Laura Lopez Pascua
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Samantha J L Knight
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Helene Dreau
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Maite Cabes
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
| | - Niko Popitsch
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- The Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Mats Ehinger
- Pathology, Department of Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden
| | - Jose I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm, Sweden; and
| | - Davide Rossi
- Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | - Jenny C Taylor
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dimitrios V Vavoulis
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anna Schuh
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
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Induction of OCT2 contributes to regulate the gene expression program in human neutrophils activated via TLR8. Cell Rep 2021; 35:109143. [PMID: 34010659 DOI: 10.1016/j.celrep.2021.109143] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/27/2021] [Accepted: 04/26/2021] [Indexed: 12/23/2022] Open
Abstract
The transcription factors (TFs) that regulate inducible genes in activated neutrophils are not yet completely characterized. Herein, we show that the genomic distribution of the histone modification H3K27Ac, as well as PU.1 and C/EBPβ, two myeloid-lineage-determining TFs (LDTFs), significantly changes in human neutrophils treated with R848, a ligand of Toll-like receptor 8 (TLR8). Interestingly, differentially acetylated and LDTF-marked regions reveal an over-representation of OCT-binding motifs that are selectively bound by OCT2/POU2F2. Analysis of OCT2 genomic distribution in primary neutrophils and of OCT2-depletion in HL-60-differentiated neutrophils proves the requirement for OCT2 in contributing to promote, along with nuclear factor κB (NF-κB) and activator protein 1 (AP-1), the TLR8-induced gene expression program in neutrophils. Altogether, our data demonstrate that neutrophils, upon activation via TLR8, profoundly reprogram their chromatin status, ultimately displaying cell-specific, prolonged transcriptome changes. Data also show an unexpected role for OCT2 in amplifying the transcriptional response to TLR8-mediated activation.
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Yang R, Wang M, Zhang G, Li Y, Wang L, Cui H. POU2F2 regulates glycolytic reprogramming and glioblastoma progression via PDPK1-dependent activation of PI3K/AKT/mTOR pathway. Cell Death Dis 2021; 12:433. [PMID: 33931589 PMCID: PMC8087798 DOI: 10.1038/s41419-021-03719-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 01/08/2023]
Abstract
The POU Class Homeobox 2 (POU2F2) is a member of POU transcription factors family, which involves in cell immune response by regulating B cell proliferation and differentiation genes. Recent studies have shown that POU2F2 acts as tumor-promoting roles in some cancers, but the underlying mechanism remains little known. Here, we identified that the highly expressed POU2F2 significantly correlated with poor prognosis of glioblastoma (GBM) patients. POU2F2 promoted cell proliferation and regulated glycolytic reprogramming. Mechanistically, the AKT/mTOR signaling pathway played important roles in the regulation of POU2F2-mediated aerobic glycolysis and cell growth. Furthermore, we demonstrated that POU2F2 activated the transcription of PDPK1 by directly binding to its promoter. Reconstituted the expression of PDPK1 in POU2F2-knockdown GBM cells reactivated AKT/mTOR pathway and recovered cell glycolysis and proliferation, whereas this effect was abolished by the PDPK1/AKT interaction inhibitor. In addition, we showed that POU2F2-PDPK1 axis promoted tumorigenesis by regulating glycolysis in vivo. In conclusion, our findings indicate that POU2F2 leads a metabolic shift towards aerobic glycolysis and promotes GBM progression in PDPK1-dependent activation of PI3K/AKT/mTOR pathway.
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Affiliation(s)
- Rui Yang
- Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, Jining, China. .,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.
| | - Mei Wang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Guanghui Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.,Cancer center, Medical Research Institute, Southwest University, Chongqing, China
| | - Yanping Li
- Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, Jining, China
| | - Lulin Wang
- Key Laboratory of Molecular Pharmacology, Liaocheng People's Hospital, Liaocheng, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China. .,Cancer center, Medical Research Institute, Southwest University, Chongqing, China.
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Kennedy DE, Clark MR. Compartments and Connections Within the Germinal Center. Front Immunol 2021; 12:659151. [PMID: 33868306 PMCID: PMC8045557 DOI: 10.3389/fimmu.2021.659151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Protective high affinity antibody responses emerge through an orchestrated developmental process that occurs in germinal centers (GCs). While GCs have been appreciated since 1930, a wealth of recent progress provides new insights into the molecular and cellular dynamics governing humoral immunity. In this review, we highlight advances that demonstrate that fundamental GC B cell function, selection, proliferation and SHM occur within distinct cell states. The resulting new model provides new opportunities to understand the evolution of immunity in infectious, autoimmune and neoplastic diseases.
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Affiliation(s)
| | - Marcus R. Clark
- Gwen Knapp Center for Lupus and Immunology Research, Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL, United States
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Gaikwad AS, Hu J, Chapple DG, O'Bryan MK. The functions of CAP superfamily proteins in mammalian fertility and disease. Hum Reprod Update 2020; 26:689-723. [PMID: 32378701 DOI: 10.1093/humupd/dmaa016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/11/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Members of the cysteine-rich secretory proteins (CRISPS), antigen 5 (Ag5) and pathogenesis-related 1 (Pr-1) (CAP) superfamily of proteins are found across the bacterial, fungal, plant and animal kingdoms. Although many CAP superfamily proteins remain poorly characterized, over the past decade evidence has accumulated, which provides insights into the functional roles of these proteins in various processes, including fertilization, immune defence and subversion, pathogen virulence, venom toxicology and cancer biology. OBJECTIVE AND RATIONALE The aim of this article is to summarize the current state of knowledge on CAP superfamily proteins in mammalian fertility, organismal homeostasis and disease pathogenesis. SEARCH METHODS The scientific literature search was undertaken via PubMed database on all articles published prior to November 2019. Search terms were based on following keywords: 'CAP superfamily', 'CRISP', 'Cysteine-rich secretory proteins', 'Antigen 5', 'Pathogenesis-related 1', 'male fertility', 'CAP and CTL domain containing', 'CRISPLD1', 'CRISPLD2', 'bacterial SCP', 'ion channel regulator', 'CatSper', 'PI15', 'PI16', 'CLEC', 'PRY proteins', 'ASP proteins', 'spermatogenesis', 'epididymal maturation', 'capacitation' and 'snake CRISP'. In addition to that, reference lists of primary and review article were reviewed for additional relevant publications. OUTCOMES In this review, we discuss the breadth of knowledge on CAP superfamily proteins with regards to their protein structure, biological functions and emerging significance in reproduction, health and disease. We discuss the evolution of CAP superfamily proteins from their otherwise unembellished prokaryotic predecessors into the multi-domain and neofunctionalized members found in eukaryotic organisms today. At least in part because of the rapid evolution of these proteins, many inconsistencies in nomenclature exist within the literature. As such, and in part through the use of a maximum likelihood phylogenetic analysis of the vertebrate CRISP subfamily, we have attempted to clarify this confusion, thus allowing for a comparison of orthologous protein function between species. This framework also allows the prediction of functional relevance between species based on sequence and structural conservation. WIDER IMPLICATIONS This review generates a picture of critical roles for CAP proteins in ion channel regulation, sterol and lipid binding and protease inhibition, and as ligands involved in the induction of multiple cellular processes.
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Affiliation(s)
- Avinash S Gaikwad
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Jinghua Hu
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - David G Chapple
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Moira K O'Bryan
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
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Chu CS, Hellmuth JC, Singh R, Ying HY, Skrabanek L, Teater MR, Doane AS, Elemento O, Melnick AM, Roeder RG. Unique Immune Cell Coactivators Specify Locus Control Region Function and Cell Stage. Mol Cell 2020; 80:845-861.e10. [PMID: 33232656 DOI: 10.1016/j.molcel.2020.10.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/09/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022]
Abstract
Locus control region (LCR) functions define cellular identity and have critical roles in diseases such as cancer, although the hierarchy of structural components and associated factors that drive functionality are incompletely understood. Here we show that OCA-B, a B cell-specific coactivator essential for germinal center (GC) formation, forms a ternary complex with the lymphoid-enriched OCT2 and GC-specific MEF2B transcription factors and that this complex occupies and activates an LCR that regulates the BCL6 proto-oncogene and is uniquely required by normal and malignant GC B cells. Mechanistically, through OCA-B-MED1 interactions, this complex is required for Mediator association with the BCL6 promoter. Densely tiled CRISPRi screening indicates that only LCR segments heavily bound by this ternary complex are essential for its function. Our results demonstrate how an intimately linked complex of lineage- and stage-specific factors converges on specific and highly essential enhancer elements to drive the function of a cell-type-defining LCR.
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Affiliation(s)
- Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Johannes C Hellmuth
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rajat Singh
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hsia-Yuan Ying
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lucy Skrabanek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY 10065, USA
| | - Matthew R Teater
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ashley S Doane
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ari M Melnick
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
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Novel specialized cell state and spatial compartments within the germinal center. Nat Immunol 2020; 21:660-670. [PMID: 32341509 PMCID: PMC7255947 DOI: 10.1038/s41590-020-0660-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 03/11/2020] [Indexed: 01/08/2023]
Abstract
Within germinal centers (GCs), complex and highly orchestrated molecular programs must balance proliferation, somatic hypermutation (SHM) and selection to both provide effective humoral immunity and to protect against genomic instability and neoplastic transformation. In contrast to this complexity, GC B cells are canonically divided into two principal populations, dark zone (DZ) and light zone (LZ) cells. We now demonstrate that following selection in the LZ, B cells migrated to specialized sites within the canonical DZ that contained tingible body macrophages (TBMs) and were sites of ongoing cell division. Proliferating DZ (DZp) cells then transited into the larger DZ to become differentiating DZ (DZd) cells before re-entering the LZ. Multidimensional analysis revealed distinct molecular programs in each population commensurate with observed compartmentization of non-compatable functions. These data provide a new three-cell population model that both orders critical GC functions and reveals essential molecular programs of humoral adaptive immunity.
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