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Madan V, Shyamsunder P, Dakle P, Woon TW, Han L, Cao Z, Nordin HBM, Jizhong S, Shuizhou Y, Hossain MZ, Koeffler HP. Dissecting the role of SWI/SNF component ARID1B in steady-state hematopoiesis. Blood Adv 2023; 7:6553-6566. [PMID: 37611161 PMCID: PMC10632677 DOI: 10.1182/bloodadvances.2023009946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
The adenosine triphosphate (ATP)-dependent chromatin remodeling complex, SWItch/Sucrose Non-Fermentable (SWI/SNF), has been implicated in normal hematopoiesis. The AT-rich interaction domain 1B (ARID1B) and its paralog, ARID1A, are mutually exclusive, DNA-interacting subunits of the BRG1/BRM-associated factor (BAF) subclass of SWI/SNF complex. Although the role of several SWI/SNF components in hematopoietic differentiation and stem cell maintenance has been reported, the function of ARID1B in hematopoietic development has not been defined. To this end, we generated a mouse model of Arid1b deficiency specifically in the hematopoietic compartment. Unlike the extensive phenotype observed in mice deficient in its paralog, ARID1A, Arid1b knockout (KO) mice exhibited a modest effect on steady-state hematopoiesis. Nonetheless, transplantation experiments showed that the reconstitution of myeloid cells in irradiated recipient mice was dependent on ARID1B. Furthermore, to assess the effect of the complete loss of ARID1 proteins in the BAF complex, we generated mice lacking both ARID1A and ARID1B in the hematopoietic compartment. The double-KO mice succumbed to acute bone marrow failure resulting from complete loss of BAF-mediated chromatin remodeling activity. Our Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) analyses revealed that >80% of loci regulated by ARID1B were distinct from those regulated by ARID1A; and ARID1B controlled expression of genes crucial in myelopoiesis. Overall, loss of ARID1B affected chromatin dynamics in murine hematopoietic stem and progenitor cells, albeit to a lesser extent than cells lacking ARID1A.
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Affiliation(s)
- Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Teoh Weoi Woon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Lin Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Zeya Cao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Shi Jizhong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yu Shuizhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Md Zakir Hossain
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - H. Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA
- Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Hospital, Singapore
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2
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Russ BE, Barugahare A, Dakle P, Tsyganov K, Quon S, Yu B, Li J, Lee JKC, Olshansky M, He Z, Harrison PF, See M, Nussing S, Morey AE, Udupa VA, Bennett TJ, Kallies A, Murre C, Collas P, Powell D, Goldrath AW, Turner SJ. Active maintenance of CD8 + T cell naivety through regulation of global genome architecture. Cell Rep 2023; 42:113301. [PMID: 37858463 PMCID: PMC10679840 DOI: 10.1016/j.celrep.2023.113301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/07/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
The differentiation of naive CD8+ T lymphocytes into cytotoxic effector and memory CTL results in large-scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organization underpin these transcriptional programs. We use Hi-C to map changes in the spatial organization of long-range genome contacts within naive, effector, and memory virus-specific CD8+ T cells. We observe that the architecture of the naive CD8+ T cell genome is distinct from effector and memory genome configurations, with extensive changes within discrete functional chromatin domains associated with effector/memory differentiation. Deletion of BACH2, or to a lesser extent, reducing SATB1 DNA binding, within naive CD8+ T cells results in a chromatin architecture more reminiscent of effector/memory states. This suggests that key transcription factors within naive CD8+ T cells act to restrain T cell differentiation by actively enforcing a unique naive chromatin state.
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Affiliation(s)
- Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Adele Barugahare
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pushkar Dakle
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Kirril Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sara Quon
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Bingfei Yu
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Jasmine Li
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Jason K C Lee
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Moshe Olshansky
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Zhaohren He
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Paul F Harrison
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michael See
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Simone Nussing
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Alison E Morey
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Vibha A Udupa
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Taylah J Bennett
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Phillipe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - David Powell
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ananda W Goldrath
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
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3
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Kusuma FK, Prabhu A, Tieo G, Ahmed SM, Dakle P, Yong WK, Pathak E, Madan V, Jiang YY, Tam WL, Kappei D, Dröge P, Koeffler HP, Jeitany M. Signalling inhibition by ponatinib disrupts productive alternative lengthening of telomeres (ALT). Nat Commun 2023; 14:1919. [PMID: 37024489 PMCID: PMC10079688 DOI: 10.1038/s41467-023-37633-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) supports telomere maintenance in 10-15% of cancers, thus representing a compelling target for therapy. By performing anti-cancer compound library screen on isogenic cell lines and using extrachromosomal telomeric C-circles, as a bona fide marker of ALT activity, we identify a receptor tyrosine kinase inhibitor ponatinib that deregulates ALT mechanisms, induces telomeric dysfunction, reduced ALT-associated telomere synthesis, and targets, in vivo, ALT-positive cells. Using RNA-sequencing and quantitative phosphoproteomic analyses, combined with C-circle level assessment, we find an ABL1-JNK-JUN signalling circuit to be inhibited by ponatinib and to have a role in suppressing telomeric C-circles. Furthermore, transcriptome and interactome analyses suggest a role of JUN in DNA damage repair. These results are corroborated by synergistic drug interactions between ponatinib and either DNA synthesis or repair inhibitors, such as triciribine. Taken together, we describe here a signalling pathway impacting ALT which can be targeted by a clinically approved drug.
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Affiliation(s)
- Frances Karla Kusuma
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Aishvaryaa Prabhu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Galen Tieo
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Syed Moiz Ahmed
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wai Khang Yong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Elina Pathak
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yan Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P. R. China
| | - Wai Leong Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, CA, USA
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Hospital, Singapore, Singapore
| | - Maya Jeitany
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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Ran XB, Ding LW, Sun QY, Yang H, Said JW, Zhentang L, Madan V, Dakle P, Xiao JF, Loh X, Li Y, Xu L, Xiang XQ, Wang LZ, Goh BC, Lin DC, Chng WJ, Tan SY, Jha S, Koeffler HP. Targeting RNA Exonuclease XRN1 Potentiates Efficacy of Cancer Immunotherapy. Cancer Res 2023; 83:922-938. [PMID: 36638333 DOI: 10.1158/0008-5472.can-21-3052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 06/29/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Despite the remarkable clinical responses achieved with immune checkpoint blockade therapy, the response rate is relatively low and only a subset of patients can benefit from the treatment. Aberrant RNA accumulation can mediate IFN signaling and stimulate an immune response, suggesting that targeting RNA decay machinery might sensitize tumor cells to immunotherapy. With this in mind, we identified an RNA exoribonuclease, XRN1, as a potential therapeutic target to suppress RNA decay and stimulate antitumor immunity. Silencing of XRN1 suppressed tumor growth in syngeneic immunocompetent mice and potentiated immunotherapy efficacy, while silencing of XRN1 alone did not affect tumor growth in immunodeficient mice. Mechanistically, XRN1 depletion activated IFN signaling and the viral defense pathway; both pathways play determinant roles in regulating immune evasion. Aberrant RNA-sensing signaling proteins (RIG-I/MAVS) mediated the expression of IFN genes, as depletion of each of them blunted the elevation of antiviral/IFN signaling in XRN1-silenced cells. Analysis of pan-cancer CRISPR-screening data indicated that IFN signaling triggered by XRN1 silencing is a common phenomenon, suggesting that the effect of XRN1 silencing may be extended to multiple types of cancers. Overall, XRN1 depletion triggers aberrant RNA-mediated IFN signaling, highlighting the importance of the aberrant RNA-sensing pathway in regulating immune responses. These findings provide the molecular rationale for developing XRN1 inhibitors and exploring their potential clinical application in combination with cancer immunotherapy. SIGNIFICANCE Targeting XRN1 activates an intracellular innate immune response mediated by RNA-sensing signaling and potentiates cancer immunotherapy efficacy, suggesting inhibition of RNA decay machinery as a novel strategy for cancer treatment.
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Affiliation(s)
- Xue-Bin Ran
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Qiao-Yang Sun
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jonathan W Said
- Santa Monica-University of California, Los Angeles Medical Center, California, Los Angeles
| | - Lao Zhentang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
| | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
| | - Xinyi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ying Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- College of life Science, Zhejiang University, Hangzhou, China
| | - Xiao-Qiang Xiang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai, China
| | - Ling-Zhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - De-Chen Lin
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Soo-Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University, Singapore, Singapore
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
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5
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Kanojia D, Kirtonia A, Srujana NSV, Jeevanandan SP, Shyamsunder P, Sampath SS, Dakle P, Mayakonda A, Kaur H, Yanyi J, Koeffler HP, Garg M. Transcriptome analysis identifies TODL as a novel lncRNA associated with proliferation, differentiation, and tumorigenesis in liposarcoma through FOXM1 Running Title: TODL lncRNA as a potential therapeutic target for liposarcoma. Pharmacol Res 2022; 185:106462. [PMID: 36167276 DOI: 10.1016/j.phrs.2022.106462] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 11/15/2022]
Abstract
Liposarcoma, the most common soft tissue sarcoma, is a group of fat cell mesenchymal tumors with different histological subtypes. The dysregulation of long non-coding RNAs (lncRNAs) has been observed in human cancers including a few studies in sarcoma. However, the global transcriptome analysis and potential role of lncRNAs remain unexplored in liposarcoma. The present investigation uncovers the transcriptomic profile of liposarcoma by RNA sequencing to gain insight into the global transcriptional changes in liposarcoma. Our RNA sequencing analysis has identified that many oncogenic lncRNAs are differentially expressed in different subtypes of liposarcoma including MALAT1, PVT1, SNHG15, LINC00152, and MIR210HG. Importantly, we identified a highly overexpressed, unannotated, and novel lncRNA in dedifferentiated liposarcomas. We have named it TODL, transcript overexpressed in dedifferentiated liposarcoma. TODL lncRNA displayed significantly higher expression in dedifferentiated liposarcoma cell lines and patient samples. Interestingly, functional studies revealed that TODL lncRNA has an oncogenic function in liposarcoma cells by regulating proliferation, cell cycle, apoptosis, differentiation, and tumorigenesis in the murine model. Silencing of TODL lncRNA highlighted the enrichment of several key oncogenic signaling pathways including cell cycle, transcriptional misregulation, FOXM1 network, p53 signaling, PLK1 signaling, FoxO, and signaling Aurora signaling pathways. RNA pull-down assay revealed the binding of TODL lncRNA with FOXM1, an oncogenic transcription factor, and the key regulator of the cell cycle. Silencing of TODL lncRNA also induces adipogenesis in dedifferentiated liposarcomas. Altogether, our finding indicates that TODL could be utilized as a novel, specific diagnostic biomarker, and a pharmacological target for therapeutic development in controlling aggressive and metastatic dedifferentiated liposarcomas.
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Affiliation(s)
- Deepika Kanojia
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.
| | - Anuradha Kirtonia
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University, Sector-125, Noida, Uttar Pradesh, 201313, India
| | | | | | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | | | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Harvinder Kaur
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Jiang Yanyi
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, School of Medicine, Los Angeles, California, 90048, USA
| | - Manoj Garg
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University, Sector-125, Noida, Uttar Pradesh, 201313, India.
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6
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Abbas T, Chaturvedi G, Prakrithi P, Pathak AK, Kutum R, Dakle P, Narang A, Manchanda V, Patil R, Aggarwal D, Girase B, Srivastava A, Kapoor M, Gupta I, Pandey R, Juvekar S, Dash D, Mukerji M, Prasher B. Whole Exome Sequencing in Healthy Individuals of Extreme Constitution Types Reveals Differential Disease Risk: A Novel Approach towards Predictive Medicine. J Pers Med 2022; 12:jpm12030489. [PMID: 35330488 PMCID: PMC8952204 DOI: 10.3390/jpm12030489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/10/2022] Open
Abstract
Precision medicine aims to move from traditional reactive medicine to a system where risk groups can be identified before the disease occurs. However, phenotypic heterogeneity amongst the diseased and healthy poses a major challenge for identification markers for risk stratification and early actionable interventions. In Ayurveda, individuals are phenotypically stratified into seven constitution types based on multisystem phenotypes termed “Prakriti”. It enables the prediction of health and disease trajectories and the selection of health interventions. We hypothesize that exome sequencing in healthy individuals of phenotypically homogeneous Prakriti types might enable the identification of functional variations associated with the constitution types. Exomes of 144 healthy Prakriti stratified individuals and controls from two genetically homogeneous cohorts (north and western India) revealed differential risk for diseases/traits like metabolic disorders, liver diseases, and body and hematological measurements amongst healthy individuals. These SNPs differ significantly from the Indo-European background control as well. Amongst these we highlight novel SNPs rs304447 (IFIT5) and rs941590 (SERPINA10) that could explain differential trajectories for immune response, bleeding or thrombosis. Our method demonstrates the requirement of a relatively smaller sample size for a well powered study. This study highlights the potential of integrating a unique phenotyping approach for the identification of predictive markers and the at-risk population amongst the healthy.
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Affiliation(s)
- Tahseen Abbas
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Gaura Chaturvedi
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - P. Prakrithi
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - Ankit Kumar Pathak
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - Rintu Kutum
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Pushkar Dakle
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
| | - Ankita Narang
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
| | - Vijeta Manchanda
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
| | - Rutuja Patil
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Dhiraj Aggarwal
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Bhushan Girase
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Ankita Srivastava
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA;
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India;
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India;
| | - Sanjay Juvekar
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Debasis Dash
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Correspondence: (D.D.); (M.M.); (B.P.)
| | - Mitali Mukerji
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Jodhpur 342037, India
- Correspondence: (D.D.); (M.M.); (B.P.)
| | - Bhavana Prasher
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
- Correspondence: (D.D.); (M.M.); (B.P.)
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7
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Xu L, Chen Y, Huang Y, Sandanaraj E, Yu JS, Lin RYT, Dakle P, Ke XY, Chong YK, Koh L, Mayakonda A, Nacro K, Hill J, Huang ML, Gery S, Lim SW, Huang Z, Xu Y, Chen J, Bai L, Wang S, Wakimoto H, Yeo TT, Ang BT, Müschen M, Tang C, Tan TZ, Koeffler PH. Abstract 2123: Chromatin profiling of glioblastoma tissues identifies core oncogenic dependency and therapeutic opportunities. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Glioblastoma (GBM) is the most aggressive and therapy-refractory brain tumor in adults. Molecular profiling of GBM on the basis of gene expression, DNA methylation and genomic variations has advanced both cancer research and clinical diagnosis. However, the enhancer architectures and regulatory circuitries governing tumor-intrinsic transcriptional diversity and subtype identity are still elusive.
Methods: Chromatin immunoprecipitation followed by sequencing analysis was applied to examine H3K27ac deposition and to map the active regulatory landscapes across 95 GBM biopsies and 12 normal brain tissues. RNA-sequencing analysis was performed to measure transcriptome and to classify transcriptional subtypes. Super-enhancer associated genes and master transcriptional factors were identified. Function of novel cancer associated genes was explored using both patient-derived GBM propagating cells and orthotopic xenograft models.
Results: Analyses of differentially regulated enhancers and super-enhancers uncovered previously unrecognized layers of inter-tumor heterogeneity. Integrative analysis of variant enhancer loci and transcriptome identified topographies of transcriptional enhancers and core regulatory circuitries in four molecular subtypes of primary tumors: AC1-mesenchymal, AC1-classical, AC2-proneural and AC3-proneural. Subtype-specific enhancer domains contributed to transcriptional diversity and shaped subtype identity. Moreover, this study reveals novel oncogenic dependency of GBM on various super-enhancer-driven transcriptional factors and druggable targets (e.g., BRD4).
Conclusion: Through profiling of transcriptional enhancers, we provide clinically relevant insights into the molecular classification, pathogenesis and therapeutic intervention of GBM.
Citation Format: Liang Xu, Ye Chen, Yulun Huang, Edwin Sandanaraj, John S. Yu, Ruby Yu-Tong Lin, Pushkar Dakle, Xin-Yu Ke, Yuk Kien Chong, Lynnette Koh, Anand Mayakonda, Kassoum Nacro, Jeffrey Hill, Mo-Li Huang, Sigal Gery, See Wee Lim, Zhengyun Huang, Ying Xu, Jianxiang Chen, Longchuan Bai, Shaomeng Wang, Hiroaki Wakimoto, Tseng Tsai Yeo, Beng Ti Ang, Markus Müschen, Carol Tang, Tuan Zea Tan, Phillip H. Koeffler. Chromatin profiling of glioblastoma tissues identifies core oncogenic dependency and therapeutic opportunities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2123.
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Affiliation(s)
- Liang Xu
- 1Cancer Science Institute of Singapore, Singapore, Singapore
| | - Ye Chen
- 1Cancer Science Institute of Singapore, Singapore, Singapore
| | - Yulun Huang
- 2The First Affiliated Hospital of Soochow University, Suzhou, China
| | | | - John S. Yu
- 4Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Pushkar Dakle
- 1Cancer Science Institute of Singapore, Singapore, Singapore
| | - Xin-Yu Ke
- 1Cancer Science Institute of Singapore, Singapore, Singapore
| | | | - Lynnette Koh
- 3National Neuroscience Institute, Singapore, Singapore
| | - Anand Mayakonda
- 1Cancer Science Institute of Singapore, Singapore, Singapore
| | - Kassoum Nacro
- 5Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jeffrey Hill
- 6Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | | | - Sigal Gery
- 4Cedars-Sinai Medical Center, Los Angeles, CA
| | - See Wee Lim
- 3National Neuroscience Institute, Singapore, Singapore
| | | | - Ying Xu
- 7Soochow University, Suzhou, China
| | | | | | | | | | | | - Beng Ti Ang
- 3National Neuroscience Institute, Singapore, Singapore
| | - Markus Müschen
- 12City of Hope Comprehensive Cancer Center, Monrovia, CA
| | - Carol Tang
- 3National Neuroscience Institute, Singapore, Singapore
| | - Tuan Zea Tan
- 1Cancer Science Institute of Singapore, Singapore, Singapore
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8
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Xu L, Chen Y, Huang Y, Sandanaraj E, Yu JS, Lin RYT, Dakle P, Ke XY, Chong YK, Koh L, Mayakonda A, Nacro K, Hill J, Huang ML, Gery S, Lim SW, Huang Z, Xu Y, Chen J, Bai L, Wang S, Wakimoto H, Yeo TT, Ang BT, Müschen M, Tang C, Tan TZ, Koeffler HP. Topography of transcriptionally active chromatin in glioblastoma. Sci Adv 2021; 7:7/18/eabd4676. [PMID: 33931443 PMCID: PMC8087410 DOI: 10.1126/sciadv.abd4676] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 03/08/2021] [Indexed: 05/07/2023]
Abstract
Molecular profiling of the most aggressive brain tumor glioblastoma (GBM) on the basis of gene expression, DNA methylation, and genomic variations advances both cancer research and clinical diagnosis. The enhancer architectures and regulatory circuitries governing tumor-intrinsic transcriptional diversity and subtype identity are still elusive. Here, by mapping H3K27ac deposition, we analyze the active regulatory landscapes across 95 GBM biopsies, 12 normal brain tissues, and 38 cell line counterparts. Analyses of differentially regulated enhancers and super-enhancers uncovered previously unrecognized layers of intertumor heterogeneity. Integrative analysis of variant enhancer loci and transcriptome identified topographies of transcriptional enhancers and core regulatory circuitries in four molecular subtypes of primary tumors: AC1-mesenchymal, AC1-classical, AC2-proneural, and AC3-proneural. Moreover, this study reveals core oncogenic dependency on super-enhancer-driven transcriptional factors, long noncoding RNAs, and druggable targets in GBM. Through profiling of transcriptional enhancers, we provide clinically relevant insights into molecular classification, pathogenesis, and therapeutic intervention of GBM.
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Affiliation(s)
- Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ye Chen
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.
| | - Yulun Huang
- Department of Neurosurgery, Dushu Lake Hospital Affiliated of Soochow University, Suzhou, 215124, China
- Department of Neurosurgery, Medical Center of Soochow University, Suzhou, 215124, China
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Edwin Sandanaraj
- Department of Research, National Neuroscience Institute, 308433, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology, and Research, 117609, Singapore
| | - John S Yu
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ruby Yu-Tong Lin
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Xin-Yu Ke
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Yuk Kien Chong
- Department of Research, National Neuroscience Institute, 308433, Singapore
| | - Lynnette Koh
- Department of Research, National Neuroscience Institute, 308433, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Kassoum Nacro
- Experimental Drug Development Centre, Agency for Science, Technology and Research, 138670, Singapore
| | - Jeffrey Hill
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Mo-Li Huang
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Sigal Gery
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - See Wee Lim
- Department of Research, National Neuroscience Institute, 308433, Singapore
| | - Zhengyun Huang
- Cambridge-Suda Genomic Research Center, Soochow University, Suzhou, 215123, China
| | - Ying Xu
- Cambridge-Suda Genomic Research Center, Soochow University, Suzhou, 215123, China
| | - Jianxiang Chen
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, China
- Department of Hepatology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310015, China
| | - Longchuan Bai
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shaomeng Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tseng Tsai Yeo
- National University Cancer Institute, National University Hospital, 119074, Singapore
| | - Beng Ti Ang
- Department of Neurosurgery, National Neuroscience Institute, 308433, Singapore
- Duke-National University of Singapore Medical School, 169857, Singapore
| | - Markus Müschen
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA
- Department of Immunobiology, Yale University, New Haven, CT 06511, USA
| | - Carol Tang
- Department of Research, National Neuroscience Institute, 308433, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
- Cancer and Stem Cell Biology Program, Duke-National University of Singapore Medical School, 169857, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- National University Cancer Institute, National University Hospital, 119074, Singapore
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9
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Madan V, Cao Z, Teoh WW, Dakle P, Han L, Shyamsunder P, Jeitany M, Zhou S, Li J, Nordin HBM, Shi J, Yu S, Yang H, Hossain MZ, Chng WJ, Koeffler HP. ZRSR1 cooperates with ZRSR2 in regulating splicing of U12-type introns in murine hematopoietic cells. Haematologica 2021; 107:680-689. [PMID: 33691379 PMCID: PMC8883539 DOI: 10.3324/haematol.2020.260562] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Indexed: 12/03/2022] Open
Abstract
Recurrent loss-of-function mutations of spliceosome gene, ZRSR2, occur in myelodysplastic syndromes (MDS). Mutation/loss of ZRSR2 in human myeloid cells primarily causes impaired splicing of the U12-type introns. In order to further investigate the role of this splice factor in RNA splicing and hematopoietic development, we generated mice lacking ZRSR2. Unexpectedly, Zrsr2-deficient mice developed normal hematopoiesis with no abnormalities in myeloid differentiation evident in either young or ≥1-year old knockout mice. Repopulation ability of Zrsr2-deficient hematopoietic stem cells was also unaffected in both competitive and non-competitive reconstitution assays. Myeloid progenitors lacking ZRSR2 exhibited mis-splicing of U12-type introns, however, this phenotype was moderate compared to the ZRSR2-deficient human cells. Our investigations revealed that a closely related homolog, Zrsr1, expressed in the murine hematopoietic cells, but not in human cells contributes to splicing of U12-type introns. Depletion of Zrsr1 in Zrsr2 KO myeloid cells exacerbated retention of the U12-type introns, thus highlighting a collective role of ZRSR1 and ZRSR2 in murine U12-spliceosome. We also demonstrate that aberrant retention of U12-type introns of MAPK9 and MAPK14 leads to their reduced protein expression. Overall, our findings highlight that both ZRSR1 and ZRSR2 are functional components of the murine U12-spliceosome, and depletion of both proteins is required to accurately model ZRSR2-mutant MDS in mice.
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Affiliation(s)
- Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
| | - Zeya Cao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Weoi Woon Teoh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lin Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Maya Jeitany
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore
| | - Siqin Zhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jia Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - JiZhong Shi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Shuizhou Yu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Md Zakir Hossain
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Hematology-Oncology, National University Cancer Institute, NUHS, Singapore
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, USA; National University Cancer Institute, National University Hospital Singapore, Singapore
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10
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Jeitany M, Prabhu A, Dakle P, Pathak E, Madan V, Kanojia D, Mukundan V, Jiang YY, Landesman Y, Tam WL, Kappei D, Koeffler HP. Novel carfilzomib-based combinations as potential therapeutic strategies for liposarcomas. Cell Mol Life Sci 2021; 78:1837-1851. [PMID: 32851475 PMCID: PMC7904719 DOI: 10.1007/s00018-020-03620-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/19/2020] [Accepted: 08/07/2020] [Indexed: 01/09/2023]
Abstract
Proteasome inhibitors, such as bortezomib and carfilzomib, have shown efficacy in anti-cancer therapy in hematological diseases but not in solid cancers. Here, we found that liposarcomas (LPS) are susceptible to proteasome inhibition, and identified drugs that synergize with carfilzomib, such as selinexor, an inhibitor of XPO1-mediated nuclear export. Through quantitative nuclear protein profiling and phospho-kinase arrays, we identified potential mode of actions of this combination, including interference with ribosome biogenesis and inhibition of pro-survival kinase PRAS40. Furthermore, by assessing global protein levels changes, FADS2, a key enzyme regulating fatty acids synthesis, was found down-regulated after proteasome inhibition. Interestingly, SC26196, an inhibitor of FADS2, synergized with carfilzomib. Finally, to identify further combinational options, we performed high-throughput drug screening and uncovered novel drug interactions with carfilzomib. For instance, cyclosporin A, a known immunosuppressive agent, enhanced carfilzomib's efficacy in vitro and in vivo. Altogether, these results demonstrate that carfilzomib and its combinations could be repurposed for LPS clinical management.
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Affiliation(s)
- Maya Jeitany
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Aishvaryaa Prabhu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Elina Pathak
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Deepika Kanojia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vineeth Mukundan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yan Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Wai Leong Tam
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, CA, USA
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Hospital, Singapore, Singapore
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11
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Jiang YY, Jiang Y, Li CQ, Zhang Y, Dakle P, Kaur H, Deng JW, Lin RYT, Han L, Xie JJ, Yan Y, Doan N, Zheng Y, Mayakonda A, Hazawa M, Xu L, Li Y, Aswad L, Jeitany M, Kanojia D, Guan XY, Said JW, Yang W, Fullwood MJ, Lin DC, Koeffler HP. TP63, SOX2, and KLF5 Establish a Core Regulatory Circuitry That Controls Epigenetic and Transcription Patterns in Esophageal Squamous Cell Carcinoma Cell Lines. Gastroenterology 2020; 159:1311-1327.e19. [PMID: 32619460 DOI: 10.1053/j.gastro.2020.06.050] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 06/12/2020] [Accepted: 06/21/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS We investigated the transcriptome of esophageal squamous cell carcinoma (ESCC) cells, activity of gene regulatory (enhancer and promoter regions), and the effects of blocking epigenetic regulatory proteins. METHODS We performed chromatin immunoprecipitation sequencing with antibodies against H3K4me1, H3K4me3, and H3K27ac and an assay for transposase-accessible chromatin to map the enhancer regions and accessible chromatin in 8 ESCC cell lines. We used the CRC_Mapper algorithm to identify core regulatory circuitry transcription factors in ESCC cell lines, and determined genome occupancy profiles for 3 of these factors. In ESCC cell lines, expression of transcription factors was knocked down with small hairpin RNAs, promoter and enhancer regions were disrupted by CRISPR/Cas9 genome editing, or bromodomains and extraterminal (BET) family proteins and histone deacetylases (HDACs) were inhibited with ARV-771 and romidepsin, respectively. ESCC cell lines were then analyzed by whole-transcriptome sequencing, immunoprecipitation, immunoblots, immunohistochemistry, and viability assays. Interactions between distal enhancers and promoters were identified and verified with circular chromosome conformation capture sequencing. NOD-SCID mice were given injections of modified ESCC cells, some mice where given injections of HDAC or BET inhibitors, and growth of xenograft tumors was measured. RESULTS We identified super-enhancer-regulated circuits and transcription factors TP63, SOX2, and KLF5 as core regulatory factors in ESCC cells. Super-enhancer regulation of ALDH3A1 mediated by core regulatory factors was required for ESCC viability. We observed direct interactions between the promoter region of TP63 and functional enhancers, mediated by the core regulatory circuitry transcription factors. Deletion of enhancer regions from ESCC cells decreased expression of the core regulatory circuitry transcription factors and reduced cell viability; these same results were observed with knockdown of each core regulatory circuitry transcription factor. Incubation of ESCC cells with BET and HDAC disrupted the core regulatory circuitry program and the epigenetic modifications observed in these cells; mice given injections of HDAC or BET inhibitors developed smaller xenograft tumors from the ESCC cell lines. Xenograft tumors grew more slowly in mice given the combination of ARV-771 and romidepsin than mice given either agent alone. CONCLUSIONS In epigenetic and transcriptional analyses of ESCC cell lines, we found the transcription factors TP63, SOX2, and KLF5 to be part of a core regulatory network that determines chromatin accessibility, epigenetic modifications, and gene expression patterns in these cells. A combination of epigenetic inhibitors slowed growth of xenograft tumors derived from ESCC cells in mice.
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Affiliation(s)
- Yan-Yi Jiang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yuan Jiang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California; Cancer Science Institute of Singapore, National University of Singapore, Singapore.
| | - Chun-Quan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Ying Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Harvinder Kaur
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jian-Wen Deng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ruby Yu-Tong Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lin Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jian-Jun Xie
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Yiwu Yan
- Cedars-Sinai Medical Center, Departments of Surgery and Biomedical Sciences, Los Angeles, California
| | - Ngan Doan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Yueyuan Zheng
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Masaharu Hazawa
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - YanYu Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Luay Aswad
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore
| | - Maya Jeitany
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Deepika Kanojia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xin-Yuan Guan
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jonathan W Said
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Wei Yang
- Cedars-Sinai Medical Center, Departments of Surgery and Biomedical Sciences, Los Angeles, California
| | - Melissa J Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore.
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California.
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California; Cancer Science Institute of Singapore, National University of Singapore, Singapore; National University Cancer Institute, National University Hospital Singapore, Singapore
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12
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Kanojia D, Dakle P, Mayakonda A, Parameswaran R, Puhaindran ME, Min VLK, Madan V, Koeffler P. Identification of somatic alterations in lipoma using whole exome sequencing. Sci Rep 2019; 9:14370. [PMID: 31591430 PMCID: PMC6779901 DOI: 10.1038/s41598-019-50805-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/19/2019] [Indexed: 01/09/2023] Open
Abstract
Lipomas are benign fatty tumors with a high prevalence rate, mostly found in adults but have a good prognosis. Until now, reason for lipoma occurrence not been identified. We performed whole exome sequencing to define the mutational spectrum in ten lipoma patients along with their matching control samples. We presented genomic insight into the development of lipomas, the most common benign tumor of soft tissue. Our analysis identified 412 somatic variants including missense mutations, splice site variants, frameshift indels, and stop gain/lost. Copy number variation analysis highlighted minor aberrations in patients. Kinase genes and transcriptions factors were among the validated mutated genes critical for cell proliferation and survival. Pathway analysis revealed enrichment of calcium, Wnt and phospholipase D signaling in patients. In conclusion, whole exome sequencing in lipomas identified mutations in genes with a possible role in development and progression of lipomas.
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Affiliation(s)
- Deepika Kanojia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rajeev Parameswaran
- Division of Surgical Oncology, National University Cancer Institute, Singapore, Singapore
| | - Mark E Puhaindran
- Department of Hand and Reconstructive Microsurgery, National University Hospital, Singapore, Singapore
| | | | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, School of Medicine, Los Angeles, California, USA
- National University Cancer Institute, National University Hospital, Singapore, Singapore
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13
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Loh XY, Sun QY, Ding LW, Mayakonda A, Venkatachalam N, Yeo MS, Silva TC, Xiao JF, Doan NB, Said JW, Ran XB, Zhou SQ, Dakle P, Shyamsunder P, Koh APF, Huang RYJ, Berman BP, Tan SY, Yang H, Lin DC, Koeffler HP. RNA-Binding Protein ZFP36L1 Suppresses Hypoxia and Cell-Cycle Signaling. Cancer Res 2019; 80:219-233. [PMID: 31551365 DOI: 10.1158/0008-5472.can-18-2796] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 06/28/2019] [Accepted: 09/16/2019] [Indexed: 11/16/2022]
Abstract
ZFP36L1 is a tandem zinc-finger RNA-binding protein that recognizes conserved adenylate-uridylate-rich elements (ARE) located in 3'untranslated regions (UTR) to mediate mRNA decay. We hypothesized that ZFP36L1 is a negative regulator of a posttranscriptional hub involved in mRNA half-life regulation of cancer-related transcripts. Analysis of in silico data revealed that ZFP36L1 was significantly mutated, epigenetically silenced, and downregulated in a variety of cancers. Forced expression of ZFP36L1 in cancer cells markedly reduced cell proliferation in vitro and in vivo, whereas silencing of ZFP36L1 enhanced tumor cell growth. To identify direct downstream targets of ZFP36L1, systematic screening using RNA pull-down of wild-type and mutant ZFP36L1 as well as whole transcriptome sequencing of bladder cancer cells {plus minus} tet-on ZFP36L1 was performed. A network of 1,410 genes was identified as potential direct targets of ZFP36L1. These targets included a number of key oncogenic transcripts such as HIF1A, CCND1, and E2F1. ZFP36L1 specifically bound to the 3'UTRs of these targets for mRNA degradation, thus suppressing their expression. Dual luciferase reporter assays and RNA electrophoretic mobility shift assays showed that wild-type, but not zinc-finger mutant ZFP36L1, bound to HIF1A 3'UTR and mediated HIF1A mRNA degradation, leading to reduced expression of HIF1A and its downstream targets. Collectively, our findings reveal an indispensable role of ZFP36L1 as a posttranscriptional safeguard against aberrant hypoxic signaling and abnormal cell-cycle progression. SIGNIFICANCE: RNA-binding protein ZFP36L1 functions as a tumor suppressor by regulating the mRNA stability of a number of mRNAs involved in hypoxia and cell-cycle signaling.
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Affiliation(s)
- Xin-Yi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Qiao-Yang Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Mei-Shi Yeo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tiago C Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ngan B Doan
- Pathology and Laboratory Medicine, Ronald Reagan UCLA Medical Center, Los Angeles, California
| | - Jonathan W Said
- Pathology and Laboratory Medicine, Ronald Reagan UCLA Medical Center, Los Angeles, California
| | - Xue-Bin Ran
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Si-Qin Zhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Angele Pei-Fern Koh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ruby Yun-Ju Huang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California.,Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Soo-Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California.,National University Cancer Institute of Singapore, National University Hospital, Singapore
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14
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Han L, Madan V, Mayakonda A, Dakle P, Woon TW, Shyamsunder P, Nordin HBM, Cao Z, Sundaresan J, Lei I, Wang Z, Koeffler HP. Chromatin remodeling mediated by ARID1A is indispensable for normal hematopoiesis in mice. Leukemia 2019; 33:2291-2305. [PMID: 30858552 PMCID: PMC6756219 DOI: 10.1038/s41375-019-0438-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/30/2019] [Accepted: 02/21/2019] [Indexed: 11/17/2022]
Abstract
Precise regulation of chromatin architecture is vital to physiological processes including hematopoiesis. ARID1A is a core component of the mammalian SWI/SNF complex, which is one of the ATP-dependent chromatin remodeling complexes. To uncover the role of ARID1A in hematopoietic development, we utilized hematopoietic cell-specific deletion of Arid1a in mice. We demonstrate that ARID1A is essential for maintaining the frequency and function of hematopoietic stem cells and its loss impairs the differentiation of both myeloid and lymphoid lineages. ARID1A deficiency led to a global reduction in open chromatin and ensuing transcriptional changes affected key genes involved in hematopoietic development. We also observed that silencing of ARID1A affected ATRA-induced differentiation of NB4 cells, suggesting its role in granulocytic differentiation of human leukemic cells. Overall, our study provides a comprehensive elucidation of the function of ARID1A in hematopoiesis and highlights the central role of ARID1A-containing SWI/SNF complex in maintaining chromatin dynamics in hematopoietic cells.
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Affiliation(s)
- Lin Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Teoh Weoi Woon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Zeya Cao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Janani Sundaresan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ienglam Lei
- Department of Cardiac Surgery, Cardiovascular Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Zhong Wang
- Department of Cardiac Surgery, Cardiovascular Research Center, University of Michigan, Ann Arbor, MI, USA
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, CA, USA.,Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Hospital, Singapore, Singapore
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15
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Madan V, Han L, Hattori N, Teoh WW, Mayakonda A, Sun QY, Ding LW, Nordin HBM, Lim SL, Shyamsunder P, Dakle P, Sundaresan J, Doan NB, Sanada M, Sato-Otsubo A, Meggendorfer M, Yang H, Said JW, Ogawa S, Haferlach T, Liang DC, Shih LY, Nakamaki T, Wang QT, Koeffler HP. ASXL2 regulates hematopoiesis in mice and its deficiency promotes myeloid expansion. Haematologica 2018; 103:1980-1990. [PMID: 30093396 PMCID: PMC6269306 DOI: 10.3324/haematol.2018.189928] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
Chromosomal translocation t(8;21)(q22;q22) which leads to the generation of oncogenic RUNX1-RUNX1T1 (AML1-ETO) fusion is observed in approximately 10% of acute myelogenous leukemia (AML). To identify somatic mutations that co-operate with t(8;21)-driven leukemia, we performed whole and targeted exome sequencing of an Asian cohort at diagnosis and relapse. We identified high frequency of truncating alterations in ASXL2 along with recurrent mutations of KIT, TET2, MGA, FLT3, and DHX15 in this subtype of AML. To investigate in depth the role of ASXL2 in normal hematopoiesis, we utilized a mouse model of ASXL2 deficiency. Loss of ASXL2 caused progressive hematopoietic defects characterized by myeloid hyperplasia, splenomegaly, extramedullary hematopoiesis, and poor reconstitution ability in transplantation models. Parallel analyses of young and >1-year old Asxl2-deficient mice revealed age-dependent perturbations affecting, not only myeloid and erythroid differentiation, but also maturation of lymphoid cells. Overall, these findings establish a critical role for ASXL2 in maintaining steady state hematopoiesis, and provide insights into how its loss primes the expansion of myeloid cells.
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Affiliation(s)
- Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore
| | - Lin Han
- Cancer Science Institute of Singapore, National University of Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
| | - Norimichi Hattori
- Cancer Science Institute of Singapore, National University of Singapore .,Division of Hematology, Department of Medicine, School of Medicine, Showa University, Shinagawa-Ku, Tokyo, Japan
| | - Weoi Woon Teoh
- Cancer Science Institute of Singapore, National University of Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore
| | - Qiao-Yang Sun
- Cancer Science Institute of Singapore, National University of Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore
| | | | - Su Lin Lim
- Cancer Science Institute of Singapore, National University of Singapore
| | | | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore
| | - Janani Sundaresan
- Cancer Science Institute of Singapore, National University of Singapore
| | - Ngan B Doan
- Department of Pathology and Laboratory Medicine, Santa Monica-University of California-Los Angeles Medical Center, Los Angeles, CA, USA
| | - Masashi Sanada
- Department of Advanced Diagnosis, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Japan.,Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Japan
| | - Aiko Sato-Otsubo
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Japan
| | | | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore
| | - Jonathan W Said
- Department of Pathology and Laboratory Medicine, Santa Monica-University of California-Los Angeles Medical Center, Los Angeles, CA, USA
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Japan
| | | | - Der-Cherng Liang
- Division of Pediatric Hematology-Oncology, Mackay Memorial Hospital and Mackay Medical College, Taipei, Taiwan
| | - Lee-Yung Shih
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan
| | - Tsuyoshi Nakamaki
- Division of Hematology, Department of Medicine, School of Medicine, Showa University, Shinagawa-Ku, Tokyo, Japan
| | - Q Tian Wang
- Department of Biological Sciences, University of Illinois at Chicago, IL, USA
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore.,Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, CA, USA.,Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Hospital, Singapore
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16
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Shyamsunder P, Sankar H, Mayakonda A, Han L, Nordin HBM, Woon TW, Shanmugasundaram M, Dakle P, Madan V, Koeffler HP. CARD10, a CEBPE target involved in granulocytic differentiation. Haematologica 2018; 103:1269-1277. [PMID: 29773596 PMCID: PMC6068032 DOI: 10.3324/haematol.2018.190280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 05/14/2018] [Indexed: 12/29/2022] Open
Abstract
Maturation of granulocytes is dependent on controlled gene expression by myeloid lineage restricted transcription factors. CEBPE is one of the essential transcription factors required for granulocytic differentiation. Identification of downstream targets of CEBPE is vital to understand better its role in terminal granulopoiesis. In this study, we have identified Card10 as a novel target of CEBPE. We show that CEBPE binds to regulatory elements upstream of the murine Card10 locus, and expression of CARD10 is significantly reduced in Cebpe knock-out mice. Silencing Card10 in a human cell line and in murine primary cells impaired granulopoiesis, affecting expression of genes involved in myeloid cell development and function. Taken together, our data demonstrate for the first time that Card10 is expressed in granulocytes and is a direct target of CEBPE with functions extending to myeloid differentiation.
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Affiliation(s)
- Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Haresh Sankar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lin Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
| | | | - Teoh Weoi Woon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, CA, USA.,Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Hospital, Singapore
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17
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Netravathi M, Kumari R, Kapoor S, Dakle P, Dwivedi MK, Roy SD, Pandey P, Saini J, Ramakrishna A, Navalli D, Satishchandra P, Pal PK, Kumar A, Faruq M. Whole exome sequencing in an Indian family links Coats plus syndrome and dextrocardia with a homozygous novel CTC1 and a rare HES7 variation. BMC Med Genet 2015; 16:5. [PMID: 25928698 PMCID: PMC4422476 DOI: 10.1186/s12881-015-0151-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 01/30/2015] [Indexed: 01/10/2023]
Abstract
Background Coats plus syndrome is an autosomal recessive, pleiotropic, multisystem disorder characterized by retinal telangiectasia and exudates, intracranial calcification with leukoencephalopathy and brain cysts, osteopenia with predisposition to fractures, bone marrow suppression, gastrointestinal bleeding and portal hypertension. It is caused by compound heterozygous mutations in the CTC1 gene. Case presentation We encountered a case of an eight-year old boy from an Indian family with manifestations of Coats plus syndrome along with an unusual occurrence of dextrocardia and situs inversus. Targeted resequencing of the CTC1 gene as well as whole exome sequencing (WES) were conducted in this family to identify the causal variations. The identified candidate variations were screened in ethnicity matched healthy controls. The effect of CTC1 variation on telomere length was assessed using Southern blot. A novel homozygous missense mutation c.1451A > C (p.H484P) in exon 9 of the CTC1 gene and a rare 3′UTR known dbSNP variation (c.*556 T > C) in HES7 were identified as the plausible candidates associated with this complex phenotype of Coats plus and dextrocardia. This CTC1 variation was absent in the controls and we also observed a reduced telomere length in the affected individual’s DNA, suggesting its likely pathogenic nature. The reported p.H484P mutation is located in the N-terminal 700 amino acid regionthat is important for the binding of CTC1 to ssDNA through its two OB domains. WES data also showed a rare homozygous missense variation in the TEK gene in the affected individual. Both HES7 and TEK are targets of the Notch signaling pathway. Conclusions This is the first report of a genetically confirmed case of Coats plus syndrome from India. By means of WES, the genetic variations in this family with unique and rare complex phenotype could be traced effectively. We speculate the important role of Notch signaling in this complex phenotypic presentation of Coats plus syndrome and dextrocardia. The present finding will be useful for genetic diagnosis and carrier detection in the family and for other patients with similar disease manifestations. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0151-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manjunath Netravathi
- Department of Neurology, National Institute of mental health & Neurosciences (NIMHANS), Bangalore, 560029, India.
| | - Renu Kumari
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, New Delhi, India.
| | - Saketh Kapoor
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India.
| | - Pushkar Dakle
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, New Delhi, India.
| | - Manish Kumar Dwivedi
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, New Delhi, India.
| | - Sumitabho Deb Roy
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, New Delhi, India.
| | - Paritosh Pandey
- Department of Neurosurgery, National Institute of mental health & Neurosciences (NIMHANS), Bangalore, 560029, India.
| | - Jitender Saini
- Department of Neuroimaging & Interventional Neuroradiology, National Institute of mental health & Neurosciences (NIMHANS), Bangalore, 560034, India.
| | - Anil Ramakrishna
- Department of Neurology, National Institute of mental health & Neurosciences (NIMHANS), Bangalore, 560029, India.
| | - Devaraddi Navalli
- Department of Neurology, National Institute of mental health & Neurosciences (NIMHANS), Bangalore, 560029, India.
| | - Parthasarathy Satishchandra
- Department of Neurology, National Institute of mental health & Neurosciences (NIMHANS), Bangalore, 560029, India.
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of mental health & Neurosciences (NIMHANS), Bangalore, 560029, India.
| | - Arun Kumar
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India.
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, New Delhi, India.
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