1
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Masiero C, Aresi C, Forlino A, Tonelli F. Zebrafish Models for Skeletal and Extraskeletal Osteogenesis Imperfecta Features: Unveiling Pathophysiology and Paving the Way for Drug Discovery. Calcif Tissue Int 2024:10.1007/s00223-024-01282-5. [PMID: 39320469 DOI: 10.1007/s00223-024-01282-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 08/27/2024] [Indexed: 09/26/2024]
Abstract
In the last decades, the easy genetic manipulation, the external fertilization, the high percentage of homology with human genes and the reduced husbandry costs compared to rodents, made zebrafish a valid model for studying human diseases and for developing new therapeutical strategies. Since zebrafish shares with mammals the same bone cells and ossification types, it became widely used to dissect mechanisms and possible new therapeutic approaches in the field of common and rare bone diseases, such as osteoporosis and osteogenesis imperfecta (OI), respectively. OI is a heritable skeletal disorder caused by defects in gene encoding collagen I or proteins/enzymes necessary for collagen I synthesis and secretion. Nevertheless, OI patients can be also characterized by extraskeletal manifestations such as dentinogenesis imperfecta, muscle weakness, cardiac valve and pulmonary abnormalities and skin laxity. In this review, we provide an overview of the available zebrafish models for both dominant and recessive forms of OI. An updated description of all the main similarities and differences between zebrafish and mammal skeleton, muscle, heart and skin, will be also discussed. Finally, a list of high- and low-throughput techniques available to exploit both larvae and adult OI zebrafish models as unique tools for the discovery of new therapeutic approaches will be presented.
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Affiliation(s)
- Cecilia Masiero
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3B, 27100, Pavia, Italy
| | - Carla Aresi
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3B, 27100, Pavia, Italy
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3B, 27100, Pavia, Italy.
| | - Francesca Tonelli
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3B, 27100, Pavia, Italy
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2
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Belleville AE, Thomas JD, Tonnies J, Gabel AM, Borrero Rossi A, Singh P, Queitsch C, Bradley RK. An autoregulatory poison exon in Smndc1 is conserved across kingdoms and influences organism growth. PLoS Genet 2024; 20:e1011363. [PMID: 39150991 PMCID: PMC11357089 DOI: 10.1371/journal.pgen.1011363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 08/28/2024] [Accepted: 07/08/2024] [Indexed: 08/18/2024] Open
Abstract
Many of the most highly conserved elements in the human genome are "poison exons," alternatively spliced exons that contain premature termination codons and permit post-transcriptional regulation of mRNA abundance through induction of nonsense-mediated mRNA decay (NMD). Poison exons are widely assumed to be highly conserved due to their presumed importance for organismal fitness, but this functional importance has never been tested in the context of a whole organism. Here, we report that a poison exon in Smndc1 is conserved across mammals and plants and plays a molecular autoregulatory function in both kingdoms. We generated mouse and A. thaliana models lacking this poison exon to find its loss leads to deregulation of SMNDC1 protein levels, pervasive alterations in mRNA processing, and organismal size restriction. Together, these models demonstrate the importance of poison exons for both molecular and organismal phenotypes that likely explain their extraordinary conservation.
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Affiliation(s)
- Andrea E. Belleville
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - James D. Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Graduate Program in Biology, University of Washington, Seattle, Washington, United States of America
| | - Austin M. Gabel
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Andrea Borrero Rossi
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Priti Singh
- Preclinical Modeling Core, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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3
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Khan AEMA, Arutla V, Srivenugopal KS. Human NQO1 as a Selective Target for Anticancer Therapeutics and Tumor Imaging. Cells 2024; 13:1272. [PMID: 39120303 PMCID: PMC11311714 DOI: 10.3390/cells13151272] [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: 06/22/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
Human NAD(P)H-quinone oxidoreductase1 (HNQO1) is a two-electron reductase antioxidant enzyme whose expression is driven by the NRF2 transcription factor highly active in the prooxidant milieu found in human malignancies. The resulting abundance of NQO1 expression (up to 200-fold) in cancers and a barely detectable expression in body tissues makes it a selective marker of neoplasms. NQO1 can catalyze the repeated futile redox cycling of certain natural and synthetic quinones to their hydroxyquinones, consuming NADPH and generating rapid bursts of cytotoxic reactive oxygen species (ROS) and H2O2. A greater level of this quinone bioactivation due to elevated NQO1 content has been recognized as a tumor-specific therapeutic strategy, which, however, has not been clinically exploited. We review here the natural and new quinones activated by NQO1, the catalytic inhibitors, and the ensuing cell death mechanisms. Further, the cancer-selective expression of NQO1 has opened excellent opportunities for distinguishing cancer cells/tissues from their normal counterparts. Given this diagnostic, prognostic, and therapeutic importance, we and others have engineered a large number of specific NQO1 turn-on small molecule probes that remain latent but release intense fluorescence groups at near-infrared and other wavelengths, following enzymatic cleavage in cancer cells and tumor masses. This sensitive visualization/quantitation and powerful imaging technology based on NQO1 expression offers promise for guided cancer surgery, and the reagents suggest a theranostic potential for NQO1-targeted chemotherapy.
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Affiliation(s)
| | | | - Kalkunte S. Srivenugopal
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, 1406 Amarillo Research Bldg., Rm. 1102, Amarillo, TX 79106, USA; (A.E.M.A.K.); (V.A.)
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4
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Cai Z, Iso-Touru T, Sanchez MP, Kadri N, Bouwman AC, Chitneedi PK, MacLeod IM, Vander Jagt CJ, Chamberlain AJ, Gredler-Grandl B, Spengeler M, Lund MS, Boichard D, Kühn C, Pausch H, Vilkki J, Sahana G. Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance. Genet Sel Evol 2024; 56:54. [PMID: 39009986 PMCID: PMC11247842 DOI: 10.1186/s12711-024-00920-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 06/26/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Mastitis is a disease that incurs significant costs in the dairy industry. A promising approach to mitigate its negative effects is to genetically improve the resistance of dairy cattle to mastitis. A meta-analysis of genome-wide association studies (GWAS) across multiple breeds for clinical mastitis (CM) and its indicator trait, somatic cell score (SCS), is a powerful method to identify functional genetic variants that impact mastitis resistance. RESULTS We conducted meta-analyses of eight and fourteen GWAS on CM and SCS, respectively, using 30,689 and 119,438 animals from six dairy cattle breeds. Methods for the meta-analyses were selected to properly account for the multi-breed structure of the GWAS data. Our study revealed 58 lead markers that were associated with mastitis incidence, including 16 loci that did not overlap with previously identified quantitative trait loci (QTL), as curated at the Animal QTLdb. Post-GWAS analysis techniques such as gene-based analysis and genomic feature enrichment analysis enabled prioritization of 31 candidate genes and 14 credible candidate causal variants that affect mastitis. CONCLUSIONS Our list of candidate genes can help to elucidate the genetic architecture underlying mastitis resistance and provide better tools for the prevention or treatment of mastitis, ultimately contributing to more sustainable animal production.
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Affiliation(s)
- Zexi Cai
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Terhi Iso-Touru
- Natural Resources Institute Finland (Luke), 31600, Jokioinen, Finland
| | - Marie-Pierre Sanchez
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Naveen Kadri
- Animal Genomics, ETH Zurich, 8092, Zurich, Switzerland
| | - Aniek C Bouwman
- Wageningen University and Research, Animal Breeding and Genomics, P.O. Box 338, 6700, AH, Wageningen, The Netherlands
| | - Praveen Krishna Chitneedi
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | | | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
| | - Birgit Gredler-Grandl
- Wageningen University and Research, Animal Breeding and Genomics, P.O. Box 338, 6700, AH, Wageningen, The Netherlands
| | | | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark
| | - Didier Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Christa Kühn
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
- Agricultural and Environmental Faculty, University Rostock, 18059, Rostock, Germany
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, 8092, Zurich, Switzerland
| | - Johanna Vilkki
- Natural Resources Institute Finland (Luke), 31600, Jokioinen, Finland
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark
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5
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Krishnamoorthy GP, Glover AR, Untch BR, Sigcha-Coello N, Xu B, Vukel D, Liu Y, Tiedje V, Berman K, Tamarapu PP, Acuña-Ruiz A, Saqcena M, de Stanchina E, Boucai L, Ghossein RA, Knauf JA, Abdel-Wahab O, Bradley RK, Fagin JA. RBM10 loss induces aberrant splicing of cytoskeletal and extracellular matrix mRNAs and promotes metastatic fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602730. [PMID: 39026820 PMCID: PMC11257529 DOI: 10.1101/2024.07.09.602730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
RBM10 modulates transcriptome-wide cassette exon splicing. Loss-of-function RBM10 mutations are enriched in thyroid cancers with distant metastases. Analysis of transcriptomes and genes mis-spliced by RBM10 loss showed pro-migratory and RHO/RAC signaling signatures. RBM10 loss increases cell velocity. Cytoskeletal and ECM transcripts subject to exon-inclusion events included vinculin (VCL), tenascin C (TNC) and CD44. Knockdown of the VCL exon inclusion transcript in RBM10-null cells reduced cell velocity, whereas knockdown of TNC and CD44 exon-inclusion isoforms reduced invasiveness. RAC1-GTP levels were increased in RBM10-null cells. Mouse Hras G12V /Rbm1O KO thyrocytes develop metastases that are reversed by RBM10 or by combined knockdown of VCL, CD44 and TNC inclusion isoforms. Thus, RBM10 loss generates exon inclusions in transcripts regulating ECM-cytoskeletal interactions, leading to RAC1 activation and metastatic competency. Moreover, a CRISPR-Cas9 screen for synthetic lethality with RBM10 loss identified NFkB effectors as central to viability, providing a therapeutic target for these lethal thyroid cancers.
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Affiliation(s)
- Gnana P. Krishnamoorthy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthony R. Glover
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian R. Untch
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nickole Sigcha-Coello
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dina Vukel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yi Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vera Tiedje
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katherine Berman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Prasanna P. Tamarapu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adrian Acuña-Ruiz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mahesh Saqcena
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura Boucai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronald A. Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James A. Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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6
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Kim SR, Kim YJ, Kim JH, Kim SN, Park WS, Kim SH, Chung J, Choi MS, Kim M, Park BC. Comprehensive transcriptome profiling between balding and non-balding scalp of female pattern hair loss in Asian. Arch Dermatol Res 2024; 316:360. [PMID: 38850442 DOI: 10.1007/s00403-024-03114-w] [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: 02/13/2024] [Revised: 02/13/2024] [Accepted: 04/26/2024] [Indexed: 06/10/2024]
Abstract
While many gene expression studies have focused on male pattern baldness (MPB), few studies have investigated the genetic differences between bald and non-bald hair follicles in female pattern hair loss (FPHL). This study aimed to identify molecular biomarkers associated with FPHL through genetic analysis of paired bald and non-bald hair follicles from 18 FPHL patients, using next-generation sequencing (NGS) techniques. RNA transcriptome analysis was performed to identify differentially expressed genes (DEGs) between bald and non-bald hair follicles in FPHL. The DEGs were validated using real-time PCR, and protein expression was confirmed through immunohistochemistry and western blot analysis. Our findings suggest that HOXB13, SFRP2, PTGDS, CXCR3, SFRP4, SOD3, and DCN are significantly upregulated in bald hair follicles compared to non-bald hair follicles in FPHL. SFRP2 and PTGDS were found to be consistently highly expressed in bald hair follicles in all 18 samples. Additionally, elevated protein levels of SFRP2 and PTGDS were confirmed through western blot and immunohistochemical analysis. Our study identified SFRP2 and PTGDS as potential biomarkers for FPHL and suggests that they may play a role in inducing hair loss in this condition. These findings provide a foundation for further research on the pathogenesis of FPHL and potential therapeutic targets.
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Affiliation(s)
- Soon Re Kim
- Basic and Clinical Hair institute, Dankook University, Cheonan, Republic of Korea
- Beckman Laser Institute Korea, DanKook University, Cheonan, Republic of Korea
| | - Yun Ji Kim
- Theragen Bio Institute, Seongnam, Republic of Korea
| | - Ju-Hee Kim
- Basic and Clinical Hair institute, Dankook University, Cheonan, Republic of Korea
| | - Su Na Kim
- AmorePacific R&D Center, Yongin, Republic of Korea
| | | | - Se Hwan Kim
- Beckman Laser Institute Korea, DanKook University, Cheonan, Republic of Korea
- Department of Biomedical Engineering, School of Medicine, Dankook University, Cheonan, Republic of Korea
| | - Juhyun Chung
- Department of Dermatology, Dankook University Hospital, Cheonan, Republic of Korea
| | - Mi Soo Choi
- Department of Dermatology, Dankook University Hospital, Cheonan, Republic of Korea
| | - MyungHwa Kim
- Department of Dermatology, Dankook University Hospital, Cheonan, Republic of Korea
| | - Byung Cheol Park
- Basic and Clinical Hair institute, Dankook University, Cheonan, Republic of Korea.
- Department of Dermatology, Dankook University Hospital, Cheonan, Republic of Korea.
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7
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Pineda JMB, Bradley RK. DUX4 is a common driver of immune evasion and immunotherapy failure in metastatic cancers. eLife 2024; 12:RP89017. [PMID: 38829686 PMCID: PMC11147511 DOI: 10.7554/elife.89017] [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] [Indexed: 06/05/2024] Open
Abstract
Cancer immune evasion contributes to checkpoint immunotherapy failure in many patients with metastatic cancers. The embryonic transcription factor DUX4 was recently characterized as a suppressor of interferon-γ signaling and antigen presentation that is aberrantly expressed in a small subset of primary tumors. Here, we report that DUX4 expression is a common feature of metastatic tumors, with ~10-50% of advanced bladder, breast, kidney, prostate, and skin cancers expressing DUX4. DUX4 expression is significantly associated with immune cell exclusion and decreased objective response to PD-L1 blockade in a large cohort of urothelial carcinoma patients. DUX4 expression is a significant predictor of survival even after accounting for tumor mutational burden and other molecular and clinical features in this cohort, with DUX4 expression associated with a median reduction in survival of over 1 year. Our data motivate future attempts to develop DUX4 as a biomarker and therapeutic target for checkpoint immunotherapy resistance.
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Affiliation(s)
- Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Medical Scientist Training Program, University of WashingtonSeattleUnited States
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
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8
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Deyell RJ, Shen Y, Titmuss E, Dixon K, Williamson LM, Pleasance E, Nelson JMT, Abbasi S, Krzywinski M, Armstrong L, Bonakdar M, Ch'ng C, Chuah E, Dunham C, Fok A, Jones M, Lee AF, Ma Y, Moore RA, Mungall AJ, Mungall KL, Rogers PC, Schrader KA, Virani A, Wee K, Young SS, Zhao Y, Jones SJM, Laskin J, Marra MA, Rassekh SR. Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers. Nat Commun 2024; 15:4165. [PMID: 38755180 PMCID: PMC11099106 DOI: 10.1038/s41467-024-48363-5] [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: 05/08/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
The role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in children and adolescents with relapsed, refractory or poor prognosis malignancies who underwent somatic WGTA and matched germline sequencing. Seventy-nine participants with a median age at enrollment of 8.8 y (range 6 months to 21.2 y) are included. Germline pathogenic/likely pathogenic variants are identified in 12% of participants, of which 60% were not known prior. Therapeutically actionable variants are identified by targeted gene report and whole genome in 32% and 62% of participants, respectively, and increase to 96% after integrating transcriptome analyses. Thirty-two molecularly informed therapies are pursued in 28 participants with 54% achieving a clinical benefit rate; objective response or stable disease ≥6 months. Integrated WGTA identifies therapeutically actionable variants in almost all tumors and are directly translatable to clinical care of children with poor prognosis cancers.
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Affiliation(s)
- Rebecca J Deyell
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada.
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Katherine Dixon
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Jessica M T Nelson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Sanna Abbasi
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Martin Krzywinski
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Chris Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alexandra Fok
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Martin Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Paul C Rogers
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada
| | - Kasmintan A Schrader
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Alice Virani
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Kathleen Wee
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Sean S Young
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Cancer Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Shahrad R Rassekh
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada.
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9
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Benbarche S, Pineda JMB, Galvis LB, Biswas J, Liu B, Wang E, Zhang Q, Hogg SJ, Lyttle K, Dahi A, Lewis AM, Sarchi M, Rahman J, Fox N, Ai Y, Mehta S, Garippa R, Ortiz-Pacheco J, Li Z, Monetti M, Stanley RF, Doulatov S, Bradley RK, Abdel-Wahab O. GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies. Mol Cell 2024; 84:1886-1903.e10. [PMID: 38688280 PMCID: PMC11102302 DOI: 10.1016/j.molcel.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/04/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
Mutations in the RNA splicing factor gene SF3B1 are common across hematologic and solid cancers and result in widespread alterations in splicing, yet there is currently no therapeutic means to correct this mis-splicing. Here, we utilize synthetic introns uniquely responsive to mutant SF3B1 to identify trans factors required for aberrant mutant SF3B1 splicing activity. This revealed the G-patch domain-containing protein GPATCH8 as required for mutant SF3B1-induced splicing alterations and impaired hematopoiesis. GPATCH8 is involved in quality control of branchpoint selection, interacts with the RNA helicase DHX15, and functionally opposes SURP and G-patch domain containing 1 (SUGP1), a G-patch protein recently implicated in SF3B1-mutant diseases. Silencing of GPATCH8 corrected one-third of mutant SF3B1-dependent splicing defects and was sufficient to improve dysfunctional hematopoiesis in SF3B1-mutant mice and primary human progenitors. These data identify GPATCH8 as a novel splicing factor required for mis-splicing by mutant SF3B1 and highlight the therapeutic impact of correcting aberrant splicing in SF3B1-mutant cancers.
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Affiliation(s)
- Salima Benbarche
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jose Mario Bello Pineda
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Laura Baquero Galvis
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jeetayu Biswas
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bo Liu
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qian Zhang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon J Hogg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kadeen Lyttle
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ariana Dahi
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander M Lewis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martina Sarchi
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jahan Rahman
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nina Fox
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuxi Ai
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sanjoy Mehta
- Gene Editing and Screening Core Facility, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Ralph Garippa
- Gene Editing and Screening Core Facility, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Juliana Ortiz-Pacheco
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Mara Monetti
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Robert F Stanley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergei Doulatov
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Robert K Bradley
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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10
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Deng B, Kong W, Shen X, Han C, Zhao Z, Chen S, Zhou C, Bae-Jump V. The role of DGAT1 and DGAT2 in regulating tumor cell growth and their potential clinical implications. J Transl Med 2024; 22:290. [PMID: 38500157 PMCID: PMC10946154 DOI: 10.1186/s12967-024-05084-z] [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: 12/20/2023] [Accepted: 03/10/2024] [Indexed: 03/20/2024] Open
Abstract
Lipid metabolism is widely reprogrammed in tumor cells. Lipid droplet is a common organelle existing in most mammal cells, and its complex and dynamic functions in maintaining redox and metabolic balance, regulating endoplasmic reticulum stress, modulating chemoresistance, and providing essential biomolecules and ATP have been well established in tumor cells. The balance between lipid droplet formation and catabolism is critical to maintaining energy metabolism in tumor cells, while the process of energy metabolism affects various functions essential for tumor growth. The imbalance of synthesis and catabolism of fatty acids in tumor cells leads to the alteration of lipid droplet content in tumor cells. Diacylglycerol acyltransferase 1 and diacylglycerol acyltransferase 2, the enzymes that catalyze the final step of triglyceride synthesis, participate in the formation of lipid droplets in tumor cells and in the regulation of cell proliferation, migration and invasion, chemoresistance, and prognosis in tumor. Several diacylglycerol acyltransferase 1 and diacylglycerol acyltransferase 2 inhibitors have been developed over the past decade and have shown anti-tumor effects in preclinical tumor models and improvement of metabolism in clinical trials. In this review, we highlight key features of fatty acid metabolism and different paradigms of diacylglycerol acyltransferase 1 and diacylglycerol acyltransferase 2 activities on cell proliferation, migration, chemoresistance, and prognosis in tumor, with the hope that these scientific findings will have potential clinical implications.
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Affiliation(s)
- Boer Deng
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, People's Republic of China
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Weimin Kong
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, People's Republic of China
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Xiaochang Shen
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, People's Republic of China
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chao Han
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, People's Republic of China
| | - Ziyi Zhao
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, People's Republic of China
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Shuning Chen
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, People's Republic of China
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chunxiao Zhou
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Victoria Bae-Jump
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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11
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Gabel AM, Belleville AE, Thomas JD, McKellar SA, Nicholas TR, Banjo T, Crosse EI, Bradley RK. Multiplexed screening reveals how cancer-specific alternative polyadenylation shapes tumor growth in vivo. Nat Commun 2024; 15:959. [PMID: 38302465 PMCID: PMC10834521 DOI: 10.1038/s41467-024-44931-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
Alternative polyadenylation (APA) is strikingly dysregulated in many cancers. Although global APA dysregulation is frequently associated with poor prognosis, the importance of most individual APA events is controversial simply because few have been functionally studied. Here, we address this gap by developing a CRISPR-Cas9-based screen to manipulate endogenous polyadenylation and systematically quantify how APA events contribute to tumor growth in vivo. Our screen reveals individual APA events that control mouse melanoma growth in an immunocompetent host, with concordant associations in clinical human cancer. For example, forced Atg7 3' UTR lengthening in mouse melanoma suppresses ATG7 protein levels, slows tumor growth, and improves host survival; similarly, in clinical human melanoma, a long ATG7 3' UTR is associated with significantly prolonged patient survival. Overall, our study provides an easily adaptable means to functionally dissect APA in physiological systems and directly quantifies the contributions of recurrent APA events to tumorigenic phenotypes.
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Affiliation(s)
- Austin M Gabel
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Andrea E Belleville
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - James D Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Siegen A McKellar
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Taylor R Nicholas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Toshihiro Banjo
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Edie I Crosse
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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12
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Liu C, Bian C, Gao Q, Gao Z, Huang Y, Wang L, Shi Q, Song L. Whole genome sequencing of a novel sea anemone (Actinostola sp.) from a deep-sea hydrothermal vent. Sci Data 2024; 11:102. [PMID: 38253640 PMCID: PMC10803348 DOI: 10.1038/s41597-024-02944-7] [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: 09/11/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Deep-sea hydrothermal vents are usually considered as extreme environments with high pressure, high temperature, scarce food, and chemical toxicity, while many local inhabitants have evolved special adaptive mechanisms for residence in this representative ecosystem. In this study, we constructed a high-quality genome assembly for a novel deep-sea anemone species (Actinostola sp.) that was resident at a depth of 2,971 m in an Edmond vent along the central Indian Ocean ridge, with a total size of 424.3 Mb and a scaffold N50 of 383 kb. The assembled genome contained 265 Mb of repetitive sequences and 20,812 protein-coding genes. Taken together, our reference genome provides a valuable genetic resource for exploring the evolution and adaptive clues of this deep-sea anemone.
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Affiliation(s)
- Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
| | - Chao Bian
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China
| | - Qiang Gao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, China
| | - Zijian Gao
- Shenzhen Key Lab of Marine Genomics, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, China.
| | - Qiong Shi
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China.
- Shenzhen Key Lab of Marine Genomics, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, China.
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13
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Benjelloun B, Leempoel K, Boyer F, Stucki S, Streeter I, Orozco-terWengel P, Alberto FJ, Servin B, Biscarini F, Alberti A, Engelen S, Stella A, Colli L, Coissac E, Bruford MW, Ajmone-Marsan P, Negrini R, Clarke L, Flicek P, Chikhi A, Joost S, Taberlet P, Pompanon F. Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints. Mol Ecol 2023:e17257. [PMID: 38149334 DOI: 10.1111/mec.17257] [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: 09/15/2022] [Revised: 08/18/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.
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Affiliation(s)
- Badr Benjelloun
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Florian J Alberto
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Castanet-Tolosan, France
| | - Filippo Biscarini
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stefan Engelen
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- AIA Associazione Italiana Allevatori, Roma, Italy
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Abdelkader Chikhi
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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14
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Cai Z, Wu X, Thomsen B, Lund MS, Sahana G. Genome-wide association study identifies functional genomic variants associated with young stock survival in Nordic Red Dairy Cattle. J Dairy Sci 2023; 106:7832-7845. [PMID: 37641238 DOI: 10.3168/jds.2023-23252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/01/2023] [Indexed: 08/31/2023]
Abstract
Identifying quantitative trait loci (QTL) associated with calf survival is essential for both reducing economic loss in cattle industry and understanding the genetic basis of the trait. To identify mutations and genes underlying young stock survival (YSS), we performed GWAS using de-regressed estimated breeding values of a YSS index and its component traits defined by sex and age in 3,077 Nordic Red Dairy Cattle (RDC) bulls and 2 stillbirth traits (first lactation and later lactations) in 5,141 RDC bulls. Two associated QTL regions on Bos taurus autosome (BTA) 4 and 6 were identified for the YSS index. The results of 4 YSS component traits indicate that same QTL regions were associated with bull and heifer calf mortality, but the effects were different over the growing period and suggested an additional QTL on BTA23. The GWAS on stillbirth identified 3 additional QTL regions on BTA5, 14, and 24 compared with YSS and its component traits. The conditional test of BTA6 showed at least 2 closely located QTL segregating for YSS component traits and stillbirth. We found 2 independent QTL for stillbirth on BTA23. The post-GWAS revealed LCORL, PPM1K, SSP1, MED28, and LAP3 are putative causal genes on BTA6, and a frame shift variant within LCORL, BTA6:37401770 (rs384548488) could be the putative causal variant. On BTA4, the GRB10 gene is the putative causal gene and BTA4:5296018 is the putative causal variant. In addition, NDUFA9 and FGF23 on BTA5, LYN on BTA14, and KCNK5 on BTA23 are putative causal genes for QTL for stillbirth. The gene analysis also proposed several candidate genes. Our findings shed new light on the candidate genes affecting calf survival, and the knowledge could be utilized to reduce calf mortality and thereby enhance welfare of dairy cattle.
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Affiliation(s)
- Zexi Cai
- Center for Quantitative Genetics and Genomics, Aarhus University, DK-8000 Aarhus C, Denmark.
| | - Xiaoping Wu
- Center for Quantitative Genetics and Genomics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Bo Thomsen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, DK-8000 Aarhus C, Denmark
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15
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Cameron DP, Grosser J, Ladigan S, Kuzin V, Iliopoulou E, Wiegard A, Benredjem H, Jackson K, Liffers ST, Lueong S, Cheung PF, Vangala D, Pohl M, Viebahn R, Teschendorf C, Wolters H, Usta S, Geng K, Kutter C, Arsenian-Henriksson M, Siveke JT, Tannapfel A, Schmiegel W, Hahn SA, Baranello L. Coinhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcription. SCIENCE ADVANCES 2023; 9:eadg5109. [PMID: 37831776 PMCID: PMC10575591 DOI: 10.1126/sciadv.adg5109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Pancreatic carcinoma lacks effective therapeutic strategies resulting in poor prognosis. Transcriptional dysregulation due to alterations in KRAS and MYC affects initiation, development, and survival of this tumor type. Using patient-derived xenografts of KRAS- and MYC-driven pancreatic carcinoma, we show that coinhibition of topoisomerase 1 (TOP1) and bromodomain-containing protein 4 (BRD4) synergistically induces tumor regression by targeting promoter pause release. Comparing the nascent transcriptome with the recruitment of elongation and termination factors, we found that coinhibition of TOP1 and BRD4 disrupts recruitment of transcription termination factors. Thus, RNA polymerases transcribe downstream of genes for hundreds of kilobases leading to readthrough transcription. This occurs during replication, perturbing replisome progression and inducing DNA damage. The synergistic effect of TOP1 + BRD4 inhibition is specific to cancer cells leaving normal cells unaffected, highlighting the tumor's vulnerability to transcriptional defects. This preclinical study provides a mechanistic understanding of the benefit of combining TOP1 and BRD4 inhibitors to treat pancreatic carcinomas addicted to oncogenic drivers of transcription and replication.
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Affiliation(s)
- Donald P. Cameron
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Grosser
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Swetlana Ladigan
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Vladislav Kuzin
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Evanthia Iliopoulou
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anika Wiegard
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hajar Benredjem
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kathryn Jackson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sven T. Liffers
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Smiths Lueong
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Phyllis F. Cheung
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Deepak Vangala
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Michael Pohl
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Richard Viebahn
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Surgery, Bochum, Germany
| | | | - Heiner Wolters
- Department of Visceral and General Surgery, St. Josef-Hospital, Dortmund, Germany
| | - Selami Usta
- Department of Visceral and General Surgery, St. Josef-Hospital, Dortmund, Germany
| | - Keyi Geng
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Jens T. Siveke
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, Essen, Germany
| | | | - Wolff Schmiegel
- Ruhr University Bochum, Knappschaftskrankenhaus, Department of Internal Medicine, Bochum, Germany
| | - Stephan A. Hahn
- Ruhr University Bochum, Faculty of Medicine, Department of Molecular GI Oncology, Bochum, Germany
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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16
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Jain A, Begum T, Ahmad S. Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates. J Mol Biol 2023; 435:168208. [PMID: 37479078 DOI: 10.1016/j.jmb.2023.168208] [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: 02/27/2023] [Revised: 06/20/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Identification of key sequence, expression and function related features of nucleic acid-sensing host proteins is of fundamental importance to understand the dynamics of pathogen-specific host responses. To meet this objective, we considered toll-like receptors (TLRs), a representative class of membrane-bound sensor proteins, from 17 vertebrate species covering mammals, birds, reptiles, amphibians, and fishes in this comparative study. We identified the molecular signatures of host TLRs that are responsible for sensing pathogen nucleic acids or other pathogen-associated molecular patterns (PAMPs), and potentially play important roles in host defence mechanism. Interestingly, our findings reveal that such host-specific features are directly related to the strand (single or double) specificity of nucleic acid from pathogens. However, during host-pathogen interactions, such features were unable to explain the pathogenic PAMP (i.e., DNA, RNA or other) selectivity, suggesting a more complex mechanism. Using these features, we developed a number of machine learning models, of which Random Forest achieved a high performance (94.57% accuracy) to predict strand specificity of TLRs from protein-derived features. We applied the trained model to propose strand specificity of some previously uncharacterized distinct fish-specific novel TLRs (TLR18, TLR23, TLR24, TLR25, TLR27).
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Affiliation(s)
- Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India. https://twitter.com/@Anuja334
| | - Tina Begum
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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17
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Kashyap Y, He Y, Sadhu N, Yao Y, Wilkie DJ, Molokie RE, Wang ZJ. An alcohol dehydrogenase 7 gene polymorphism associates with both acute and chronic pain in sickle cell disease. Pharmacogenomics 2023; 24:641-649. [PMID: 37712142 PMCID: PMC10621759 DOI: 10.2217/pgs-2023-0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/04/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction: As the most distressing complication of sickle cell disease (SCD), pain is marked by considerable heterogenicity. In this study we explored the potential association of alcohol dehydrogenase 7 gene (ADH7) polymorphism rs971074 with sickle cell pain. Methods: We analyzed clinical phenotypes and the rs971074 single-nucleotide polymorphism in ADH7 by MassARRAY-iPlex analysis in a cohort of SCD patients. Results: The synonymous rs971074 was significantly associated with both acute and chronic pain in SCD. Patients with the minor T allele(s) recorded significantly more crisis episodes and severe chronic pain symptoms. Conclusion: Our study has identified the rs971074 minor T allele as a genetic biomarker potentially influencing acute and chronic pain. These findings may ultimately help inform strategies to develop precision pain therapies in SCD.
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Affiliation(s)
- Yavnika Kashyap
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, Chicago, IL 60612, USA
| | - Ying He
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, Chicago, IL 60612, USA
- Comprehensive Sickle Cell Center, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Nilanjana Sadhu
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, Chicago, IL 60612, USA
| | - Yingwei Yao
- Department of Biobehavioral Nursing Science, University of Florida College of Nursing, Gainesville, FL 32610, USA
| | - Diana J Wilkie
- Department of Biobehavioral Nursing Science, University of Florida College of Nursing, Gainesville, FL 32610, USA
| | - Robert E Molokie
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, Chicago, IL 60612, USA
- Comprehensive Sickle Cell Center, University of Illinois Chicago, Chicago, IL 60612, USA
- Jesse Brown Veteran's Administration Medical Center, Chicago, IL 60612, USA
- Division of Hematology/Oncology, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Zaijie Jim Wang
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, Chicago, IL 60612, USA
- Comprehensive Sickle Cell Center, University of Illinois Chicago, Chicago, IL 60612, USA
- Department of Neurology & Rehabilitation, University of Illinois College of Medicine, Chicago, IL 60612, USA
- Department of Biomedical Engineering, University of Illinois Chicago College of Engineering, Chicago, IL 60607, USA
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18
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Hoppe ER, Udy DB, Bradley RK. Recursive splicing discovery using lariats in total RNA sequencing. Life Sci Alliance 2023; 6:e202201889. [PMID: 37137707 PMCID: PMC10156609 DOI: 10.26508/lsa.202201889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
Recursive splicing is a non-canonical splicing mechanism in which an intron is removed in segments via multiple splicing reactions. Relatively few recursive splice sites have been identified with high confidence in human introns, and more comprehensive analyses are needed to better characterize where recursive splicing happens and whether or not it has a regulatory function. In this study, we use an unbiased approach using intron lariats to search for recursive splice sites in constitutive introns and alternative exons in the human transcriptome. We find evidence for recursive splicing in a broader range of intron sizes than previously reported and detail a new location for recursive splicing at the distal ends of cassette exons. In addition, we identify evidence for the conservation of these recursive splice sites among higher vertebrates and the use of these sites to influence alternative exon exclusion. Together, our data demonstrate the prevalence of recursive splicing and its potential influence on gene expression through alternatively spliced isoforms.
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Affiliation(s)
- Emma R Hoppe
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Dylan B Udy
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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19
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Dunker W, Zaver SA, Pineda JMB, Howard CJ, Bradley RK, Woodward JJ. The proto-oncogene SRC phosphorylates cGAS to inhibit an antitumor immune response. JCI Insight 2023; 8:e167270. [PMID: 37166992 PMCID: PMC10371251 DOI: 10.1172/jci.insight.167270] [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: 11/16/2022] [Accepted: 05/09/2023] [Indexed: 05/12/2023] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) is a DNA sensor and responsible for inducing an antitumor immune response. Recent studies reveal that cGAS is frequently inhibited in cancer, and therapeutic targets to promote antitumor cGAS function remain elusive. SRC is a proto-oncogene tyrosine kinase and is expressed at elevated levels in numerous cancers. Here, we demonstrate that SRC expression in primary and metastatic bladder cancer negatively correlates with innate immune gene expression and immune cell infiltration. We determine that SRC restricts cGAS signaling in human cell lines through SRC small molecule inhibitors, depletion, and overexpression. cGAS and SRC interact in cells and in vitro, while SRC directly inhibits cGAS enzymatic activity and DNA binding in a kinase-dependent manner. SRC phosphorylates cGAS, and inhibition of cGAS Y248 phosphorylation partially reduces SRC inhibition. Collectively, our study demonstrates that cGAS antitumor signaling is hindered by the proto-oncogene SRC and describes how cancer-associated proteins can regulate the innate immune system.
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Affiliation(s)
| | - Shivam A. Zaver
- Department of Microbiology and
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
| | - Jose Mario Bello Pineda
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Robert K. Bradley
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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20
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Xu X, Ma J, Li W, You Y, Jiang Q, Long P, Liu K, Mo T, Jiang J, Wang W, Lei Y, Diao T, Ruan S, Wang X, Guo H, Chen W, Wu T. Polycyclic aromatic hydrocarbons exposure and plasma lncRNA signature: A profile and functional analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162932. [PMID: 36934921 DOI: 10.1016/j.scitotenv.2023.162932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants that pose detrimental effects on human health, and the exploration of the associations of PAHs exposure with long non-coding RNA (lncRNA) may provide novel clues to the underlying mechanisms. In the present study, we detected 10 urinary PAHs metabolites by GC-MS and plasma lncRNAs levels by Human LncRNA Array v4 among 230 participants from two panels (160 in the Shiyan panel and 70 in the Wuhan-Zhuhai panel). We applied linear regression models to assess the associations between PAHs metabolites and lncRNAs separately in each panel and combined the results using fixed-effect meta-analysis. To explore the potential origin of PAHs-related lncRNAs in plasma, we estimated their tissue-specificity and associations between lncRNAs levels in plasma and leukocytes. Leukocytes mRNA sequencing data and RNA binding proteins were utilized to explore implicated pathways of identified lncRNAs. We found that urinary 1-hydroxyphenanthrene (1-OH-Phe) was inversely associated with 8 lncRNAs and positively associated with 1 lncRNA, as well as 9-hydroxyphenanthrene (9-OH-Phe) was inversely associated with 11 lncRNAs (FDR < 0.1). Tissue specificity analysis using Genome Tissue Expression database suggested that several identified lncRNAs might specifically express in organs targeted by PAHs exposure (lung, liver, heart, kidney, and brain). Besides, plasma levels of 1-OH-Phe related ENSG00000260616 and 9-OH-Phe related STARD4-AS1 were inversely associated with their intra-leukocytes levels (P value < 0.05). Notably, STARD4-AS1 was positively associated with the expression levels of its neighboring protein-coding gene (CAMK4 and STARD4) in leukocytes and were involved in pathways related to cellular response to DNA damage, which we further confirmed using DNA damage biomarker, 8-hydroxydeoxyguanosine. Functional analysis also revealed vital pathways related to cytokine-mediated signaling and glucose homeostasis. Our findings provided novel insights into plausible biological mechanisms underlying the adverse effects of PAHs exposure.
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Affiliation(s)
- Xuedan Xu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jixuan Ma
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wending Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yutong You
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qin Jiang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Pinpin Long
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kang Liu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; School of Public Health, Guangzhou Medical University, Guangzhou 511436, China
| | - Tingting Mo
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jing Jiang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Wang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yanshou Lei
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tingyue Diao
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuping Ruan
- Health Management Center, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan 442008, China
| | - Xiaozheng Wang
- Health Management Center, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan 442008, China
| | - Huan Guo
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weihong Chen
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tangchun Wu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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21
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Wei C, Zeng H, Zhong Z, Cai X, Teng J, Liu Y, Zhao Y, Wu X, Li J, Zhang Z. Integration of non-additive genome-wide association study with a multi-tissue transcriptome analysis of growth and carcass traits in Duroc pigs. Animal 2023; 17:100817. [PMID: 37196577 DOI: 10.1016/j.animal.2023.100817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 05/19/2023] Open
Abstract
Growth and carcass traits are of economic importance in the pig production, which affect pork quality and profitability of finishing pig production. This study used whole-genome and transcriptome sequencing technologies to identify potential candidate genes affecting growth and carcass traits in Duroc pigs. The medium (50-60 k) single nucleotide polymorphism (SNP) arrays of 4 154 Duroc pigs from three populations were imputed to whole-genome sequence data, yielding 10 463 227 markers on 18 autosomes. The dominance heritabilities estimated for growth and carcass traits ranged from 0.000 ± 0.041 to 0.161 ± 0.054. Using non-additive genome-wide association study (GWAS), we identified 80 dominance quantitative trait loci for growth and carcass traits at genome-wide significance (false discovery rate < 5%), 15 of which were also detected in our additive GWAS. After fine mapping, 31 candidate genes for dominance GWAS were annotated, and 8 of them were highlighted that have been previously reported to be associated with growth and development (e.g. SNX14, RELN and ENPP2), autosomal recessive diseases (e.g. AMPH, SNX14, RELN and CACNB4) and immune response (e.g. UNC93B1 and PPM1D). By integrating the lead SNPs with RNA-seq data of 34 pig tissues from the Pig Genotype-Tissue Expression project (https://piggtex.farmgtex.org/), we found that the rs691128548, rs333063869, and rs1110730611 have significantly dominant effects for the expression of SNX14, AMPH and UNC93B1 genes in tissues related to growth and development for pig, respectively. Finally, the identified candidate genes were significantly enriched for biological processes involved in the cell and organ development, lipids catabolic process and phosphatidylinositol 3-kinase signalling (P < 0.05). These results provide new molecular markers for meat production and quality selection of pig as well as basis for deciphering the genetic mechanisms of growth and carcass traits.
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Affiliation(s)
- Chen Wei
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Haonan Zeng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Zhanming Zhong
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Xiaodian Cai
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Jingyan Teng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Yuqiang Liu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Yunxiang Zhao
- School of Life Science and Engineering, Foshan University, Foshan 528225, PR China
| | - Xibo Wu
- Guangxi Guiken Yongxin Animal Husbandry Group Co. Ltd, Nanning 530000, PR China
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China.
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22
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Wang E, Pineda JMB, Kim WJ, Chen S, Bourcier J, Stahl M, Hogg SJ, Bewersdorf JP, Han C, Singer ME, Cui D, Erickson CE, Tittley SM, Penson AV, Knorr K, Stanley RF, Rahman J, Krishnamoorthy G, Fagin JA, Creger E, McMillan E, Mak CC, Jarvis M, Bossard C, Beaupre DM, Bradley RK, Abdel-Wahab O. Modulation of RNA splicing enhances response to BCL2 inhibition in leukemia. Cancer Cell 2023; 41:164-180.e8. [PMID: 36563682 PMCID: PMC9839614 DOI: 10.1016/j.ccell.2022.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
Therapy resistance is a major challenge in the treatment of cancer. Here, we performed CRISPR-Cas9 screens across a broad range of therapies used in acute myeloid leukemia to identify genomic determinants of drug response. Our screens uncover a selective dependency on RNA splicing factors whose loss preferentially enhances response to the BCL2 inhibitor venetoclax. Loss of the splicing factor RBM10 augments response to venetoclax in leukemia yet is completely dispensable for normal hematopoiesis. Combined RBM10 and BCL2 inhibition leads to mis-splicing and inactivation of the inhibitor of apoptosis XIAP and downregulation of BCL2A1, an anti-apoptotic protein implicated in venetoclax resistance. Inhibition of splicing kinase families CLKs (CDC-like kinases) and DYRKs (dual-specificity tyrosine-regulated kinases) leads to aberrant splicing of key splicing and apoptotic factors that synergize with venetoclax, and overcomes resistance to BCL2 inhibition. Our findings underscore the importance of splicing in modulating response to therapies and provide a strategy to improve venetoclax-based treatments.
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Affiliation(s)
- Eric Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Jose Mario Bello Pineda
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Won Jun Kim
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sisi Chen
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessie Bourcier
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Simon J Hogg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jan Phillipp Bewersdorf
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cuijuan Han
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael E Singer
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Cui
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caroline E Erickson
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven M Tittley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katherine Knorr
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert F Stanley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jahan Rahman
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gnana Krishnamoorthy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Division of Endocrinology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Division of Endocrinology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | | | | | - Robert K Bradley
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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23
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Morales-Sanchez A, Shissler SC, Cowan JE, Bhandoola A. Revelations in Thymic Epithelial Cell Biology and Heterogeneity from Single-Cell RNA Sequencing and Lineage Tracing Methodologies. Methods Mol Biol 2023; 2580:25-49. [PMID: 36374449 PMCID: PMC10802793 DOI: 10.1007/978-1-0716-2740-2_2] [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] [Indexed: 06/16/2023]
Abstract
Thymic epithelial cells (TECs) make up the thymic microenvironments that support the generation of a functionally competent and self-tolerant T-cell repertoire. Cortical (c)TECs, present in the cortex, are essential for early thymocyte development including selection of thymocytes expressing functional TCRs (positive selection). Medullary (m)TECs, located in the medulla, play a key role in late thymocyte development, including depletion of self-reactive T cells (negative selection) and selection of regulatory T cells. In recent years, transcriptomic analysis by single-cell (sc)RNA sequencing (Seq) has revealed TEC heterogeneity previously masked by population-level RNA-Seq or phenotypic studies. We summarize the discoveries made possible by scRNA-Seq, including the identification of novel mTEC subsets, advances in understanding mTEC promiscuous gene expression, and TEC alterations from embryonic to adult stages. Whereas pseudotime analyses of scRNA-Seq data can suggest relationships between TEC subsets, experimental methods such as lineage tracing and reaggregate thymic organ culture (RTOC) are required to test these hypotheses. Lineage tracing - namely, of β5t or Aire expressing cells - has exposed progenitor and parent-daughter cellular relationships within TEC.
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Affiliation(s)
- Abigail Morales-Sanchez
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
- Children's Hospital of Mexico Federico Gomez, Mexico City, Mexico.
| | - Susannah C Shissler
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer E Cowan
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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24
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Lagman D, Haines HJ, Abalo XM, Larhammar D. Ancient multiplicity in cyclic nucleotide-gated (CNG) cation channel repertoire was reduced in the ancestor of Olfactores before re-expansion by whole genome duplications in vertebrates. PLoS One 2022; 17:e0279548. [PMID: 36584110 PMCID: PMC9803222 DOI: 10.1371/journal.pone.0279548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
Cyclic nucleotide-gated (CNG) cation channels are important heterotetrameric proteins in the retina, with different subunit composition in cone and rod photoreceptor cells: three CNGA3 and one CNGB3 in cones and three CNGA1 and one CNGB1 in rods. CNGA and CNGB subunits form separate subfamilies. We have analyzed the evolution of the CNG gene family in metazoans, with special focus on vertebrates by using sequence-based phylogeny and conservation of chromosomal synteny to deduce paralogons resulting from the early vertebrate whole genome duplications (WGDs). Our analyses show, unexpectedly, that the CNGA subfamily had four sister subfamilies in the ancestor of bilaterians and cnidarians that we named CNGC, CNGD, CNGE and CNGF. Of these, CNGC, CNGE and CNGF were lost in the ancestor of Olfactores while CNGD was lost in the vertebrate ancestor. The remaining CNGA and CNGB genes were expanded by a local duplication of CNGA and the subsequent chromosome duplications in the basal vertebrate WGD events. Upon some losses, this resulted in the gnathostome ancestor having three members in the visual CNGA subfamily (CNGA1-3), a single CNGA4 gene, and two members in the CNGB subfamily (CNGB1 and CNGB3). The nature of chromosomal rearrangements in the vertebrate CNGA paralogon was resolved by including the genomes of a non-teleost actinopterygian and an elasmobranch. After the teleost-specific WGD, additional duplicates were generated and retained for CNGA1, CNGA2, CNGA3 and CNGB1. Furthermore, teleosts retain a local duplicate of CNGB3. The retention of duplicated CNG genes is explained by their subfunctionalisation and photoreceptor-specific expression. In conclusion, this study provides evidence for four previously unknown CNG subfamilies in metazoans and further evidence that the early vertebrate WGD events were instrumental in the evolution of the vertebrate visual and central nervous systems.
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Affiliation(s)
- David Lagman
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Helen J. Haines
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Xesús M. Abalo
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Dan Larhammar
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
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25
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Kim SJ, Park SJ, Park J, Cho HJ, Shim JK, Seon J, Choi RJ, Yoon SJ, Moon JH, Kim EH, Seo EK, Kim SH, Kim HS, Teo WY, Chang JH, Yook JI, Kang SG. Dual inhibition of CPT1A and G6PD suppresses glioblastoma tumorspheres. J Neurooncol 2022; 160:677-689. [PMID: 36396930 DOI: 10.1007/s11060-022-04189-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/01/2022] [Indexed: 11/18/2022]
Abstract
PURPOSE Limited treatment options are currently available for glioblastoma (GBM), an extremely lethal type of brain cancer. For a variety of tumor types, bioenergetic deprivation through inhibition of cancer-specific metabolic pathways has proven to be an effective therapeutic strategy. Here, we evaluated the therapeutic effects and underlying mechanisms of dual inhibition of carnitine palmitoyltransferase 1A (CPT1A) and glucose-6-phosphate dehydrogenase (G6PD) critical for fatty acid oxidation (FAO) and the pentose phosphate pathway (PPP), respectively, against GBM tumorspheres (TSs). METHODS Therapeutic efficacy against GBM TSs was determined by assessing cell viability, neurosphere formation, and 3D invasion. Liquid chromatography-mass spectrometry (LC-MS) and RNA sequencing were employed for metabolite and gene expression profiling, respectively. Anticancer efficacy in vivo was examined using an orthotopic xenograft model. RESULTS CPT1A and G6PD were highly expressed in GBM tumor tissues. Notably, siRNA-mediated knockdown of both genes led to reduced viability, ATP levels, and expression of genes associated with stemness and invasiveness. Similar results were obtained upon combined treatment with etomoxir and dehydroepiandrosterone (DHEA). Transcriptome analyses further confirmed these results. Data from LC-MS analysis showed that this treatment regimen induced a considerable reduction in the levels of metabolites associated with the TCA cycle and PPP. Additionally, the combination of etomoxir and DHEA inhibited tumor growth and extended survival in orthotopic xenograft model mice. CONCLUSION Our collective findings support the utility of dual suppression of CPT1A and G6PD with selective inhibitors, etomoxir and DHEA, as an efficacious therapeutic approach for GBM.
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Affiliation(s)
- Seo Jin Kim
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Soo Jeong Park
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Department of Neurosurgery, Ewha Womans University Seoul Hospital, Ewha Womans University College of Medicine, Seoul, Republic of Korea
| | - Junseong Park
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hye Joung Cho
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jin-Kyoung Shim
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jieun Seon
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Ran Joo Choi
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Seon-Jin Yoon
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Ju Hyung Moon
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Eui Hyun Kim
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Eui Kyo Seo
- Department of Neurosurgery, Ewha Womans University Seoul Hospital, Ewha Womans University College of Medicine, Seoul, Republic of Korea
| | - Sun Ho Kim
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Department of Neurosurgery, Ewha Womans University Seoul Hospital, Ewha Womans University College of Medicine, Seoul, Republic of Korea
| | - Hyun Sil Kim
- Department of Oral Pathology, Oral Cancer Research Institute, Yonsei University College of Dentistry, Seoul, Republic of Korea
| | - Wan-Yee Teo
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Jong Hee Chang
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jong In Yook
- Department of Oral Pathology, Oral Cancer Research Institute, Yonsei University College of Dentistry, Seoul, Republic of Korea
| | - Seok-Gu Kang
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- Department of Medical Science, Yonsei University Graduate School, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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Varghese DM, Nussinov R, Ahmad S. Predictive modeling of moonlighting DNA-binding proteins. NAR Genom Bioinform 2022; 4:lqac091. [PMID: 36474806 PMCID: PMC9716651 DOI: 10.1093/nargab/lqac091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 09/10/2024] Open
Abstract
Moonlighting proteins are multifunctional, single-polypeptide chains capable of performing multiple autonomous functions. Most moonlighting proteins have been discovered through work unrelated to their multifunctionality. We believe that prediction of moonlighting proteins from first principles, that is, using sequence, predicted structure, evolutionary profiles, and global gene expression profiles, for only one functional class of proteins in a single organism at a time will significantly advance our understanding of multifunctional proteins. In this work, we investigated human moonlighting DNA-binding proteins (mDBPs) in terms of properties that distinguish them from other (non-moonlighting) proteins with the same DNA-binding protein (DBP) function. Following a careful and comprehensive analysis of discriminatory features, a machine learning model was developed to assess the predictability of mDBPs from other DBPs (oDBPs). We observed that mDBPs can be discriminated from oDBPs with high accuracy of 74% AUC of ROC using these first principles features. A number of novel predicted mDBPs were found to have literature support for their being moonlighting and others are proposed as candidates, for which the moonlighting function is currently unknown. We believe that this work will help in deciphering and annotating novel moonlighting DBPs and scale up other functions. The source codes and data sets used for this work are freely available at https://zenodo.org/record/7299265#.Y2pO3ctBxPY.
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Affiliation(s)
- Dana Mary Varghese
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Ruth Nussinov
- Computational Structural Biology Section, Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
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27
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Ahi EP, Richter F, Sefc KM. Gene expression patterns associated with caudal fin shape in the cichlid Lamprologus tigripictilis. HYDROBIOLOGIA 2022; 850:2257-2273. [PMID: 37325486 PMCID: PMC10261199 DOI: 10.1007/s10750-022-05068-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 06/17/2023]
Abstract
Variation in fin shape is one of the most prominent features of morphological diversity among fish. Regulation of fin growth has mainly been studied in zebrafish, and it is not clear whether the molecular mechanisms underlying shape variation are equally diverse or rather conserved across species. In the present study, expression levels of 37 candidate genes were tested for association with fin shape in the cichlid fish Lamprologus tigripictilis. The tested genes included members of a fin shape-associated gene regulatory network identified in a previous study and novel candidates selected within this study. Using both intact and regenerating fin tissue, we tested for expression differences between the elongated and the short regions of the spade-shaped caudal fin and identified 20 genes and transcription factors (including angptl5, cd63, csrp1a, cx43, esco2, gbf1, and rbpj), whose expression patterns were consistent with a role in fin growth. Collated with available gene expression data of two other cichlid species, our study not only highlights several genes that were correlated with fin growth in all three species (e.g., angptl5, cd63, cx43, and mmp9), but also reveals species-specific gene expression and correlation patterns, which indicate considerable divergence in the regulatory mechanisms of fin growth across cichlids. Supplementary Information The online version contains supplementary material available at 10.1007/s10750-022-05068-4.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Florian Richter
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Kristina M. Sefc
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
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Prostaglandin E2 receptor Ptger4b regulates female-specific peptidergic neurons and female sexual receptivity in medaka. Commun Biol 2022; 5:1215. [PMID: 36357668 PMCID: PMC9649691 DOI: 10.1038/s42003-022-04195-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
In vertebrates, female receptivity to male courtship is highly dependent on ovarian secretion of estrogens and prostaglandins. We recently identified female-specific neurons in the medaka (Oryzias latipes) preoptic area that express Npba, a neuropeptide mediating female sexual receptivity, in response to ovarian estrogens. Here we show by transcriptomic analysis that these neurons express a multitude of neuropeptides, in addition to Npba, in an ovarian-dependent manner, and we thus termed them female-specific, sex steroid-responsive peptidergic (FeSP) neurons. Our results further revealed that FeSP neurons express a prostaglandin E2 receptor gene, ptger4b, in an ovarian estrogen-dependent manner. Behavioral and physiological examination of ptger4b-deficient female medaka found that they exhibit increased sexual receptivity while retaining normal ovarian function and that their FeSP neurons have reduced firing activity and impaired neuropeptide release. Collectively, this work provides evidence that prostaglandin E2/Ptger4b signaling mediates the estrogenic regulation of FeSP neuron activity and female sexual receptivity. Prostaglandin E2 signaling mediates the estrogenic regulation of peptidergic neuronal activity and female receptivity via the ptger4b gene pathway in Japanese rice fish.
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29
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Zhang X, Smith DR. An overview of online resources for intra-species detection of gene duplications. Front Genet 2022; 13:1012788. [PMID: 36313461 PMCID: PMC9606816 DOI: 10.3389/fgene.2022.1012788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Gene duplication plays an important role in evolutionary mechanism, which can act as a new source of genetic material in genome evolution. However, detecting duplicate genes from genomic data can be challenging. Various bioinformatics resources have been developed to identify duplicate genes from single and/or multiple species. Here, we summarize the metrics used to measure sequence identity among gene duplicates within species, compare several computational approaches that have been used to predict gene duplicates, and review recent advancements of a Basic Local Alignment Search Tool (BLAST)-based web tool and database, allowing future researchers to easily identify intra-species gene duplications. This article is a quick reference guide for research tools used for detecting gene duplicates.
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
| | - David Roy Smith
- Department of Biology, Western University, London, ON, Canada
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30
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Shim JK, Choi S, Yoon SJ, Choi RJ, Park J, Lee EH, Cho HJ, Lee S, Teo WY, Moon JH, Kim HS, Kim EH, Cheong JH, Chang JH, Yook JI, Kang SG. Etomoxir, a carnitine palmitoyltransferase 1 inhibitor, combined with temozolomide reduces stemness and invasiveness in patient-derived glioblastoma tumorspheres. Cancer Cell Int 2022; 22:309. [PMID: 36221088 PMCID: PMC9552483 DOI: 10.1186/s12935-022-02731-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/22/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction The importance of fatty acid oxidation (FAO) in the bioenergetics of glioblastoma (GBM) is being realized. Etomoxir (ETO), a carnitine palmitoyltransferase 1 (CPT1) inhibitor exerts cytotoxic effects in GBM, which involve interrupting the FAO pathway. We hypothesized that FAO inhibition could affect the outcomes of current standard temozolomide (TMZ) chemotherapy against GBM. Methods The FAO-related gene expression was compared between GBM and the tumor-free cortex. Using four different GBM tumorspheres (TSs), the effects of ETO and/or TMZ was analyzed on cell viability, tricarboxylate (TCA) cycle intermediates and adenosine triphosphate (ATP) production to assess metabolic changes. Alterations in tumor stemness, invasiveness, and associated transcriptional changes were also measured. Mouse orthotopic xenograft model was used to elucidate the combinatory effect of TMZ and ETO. Results GBM tissues exhibited overexpression of FAO-related genes, especially CPT1A, compared to the tumor-free cortex. The combined use of ETO and TMZ further inhibited TCA cycle and ATP production than single uses. This combination treatment showed superior suppression effects compared to treatment with individual agents on the viability, stemness, and invasiveness of GBM TSs, as well as better downregulation of FAO-related gene expression. The results of in vivo study showed prolonged survival outcomes in the combination treatment group. Conclusion ETO, an FAO inhibitor, causes a lethal energy reduction in the GBM TSs. When used in combination with TMZ, ETO effectively reduces GBM cell stemness and invasiveness and further improves survival. These results suggest a potential novel treatment option for GBM. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02731-7.
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Affiliation(s)
- Jin-Kyoung Shim
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Seonah Choi
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Seon-Jin Yoon
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Ran Joo Choi
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Junseong Park
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, 03722, Republic of Korea
| | - Eun Hee Lee
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hye Joung Cho
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Suji Lee
- Department of Medical Science, BK21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Wan-Yee Teo
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore.,Institute of Molecular and Cell Biology, A*STAR, Singapore, 169857, Singapore
| | - Ju Hyung Moon
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hyun Sil Kim
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Eui Hyun Kim
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jae-Ho Cheong
- Department of Surgery, BK21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jong Hee Chang
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jong In Yook
- Department of Oral Pathology, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Seok-Gu Kang
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea. .,Brain Tumor Translational Research Laboratory, Severance Biomedical Research Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea. .,Departments of Medical Science, Yonsei University Graduate School, Seoul, 03722, Republic of Korea.
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A lignan from Alnus japonica inhibits glioblastoma tumorspheres by suppression of FOXM1. Sci Rep 2022; 12:13990. [PMID: 35978012 PMCID: PMC9385634 DOI: 10.1038/s41598-022-18185-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
Forkhead Box M1 (FOXM1) is known to regulate cell proliferation, apoptosis and tumorigenesis. The lignan, (-)-(2R,3R)-1,4-O-diferuloylsecoisolariciresinol (DFS), from Alnus japonica has shown anti-cancer effects against colon cancer cells by suppressing FOXM1. The present study hypothesized that DFS can have anti-cancer effects against glioblastoma (GBM) tumorspheres (TSs). Immunoprecipitation and luciferase reporter assays were performed to evaluate the ability of DFS to suppress nuclear translocation of β-catenin through β-catenin/FOXM1 binding. DFS-pretreated GBM TSs were evaluated to assess the ability of DFS to inhibit GBM TSs and their transcriptional profiles. The in vivo efficacy was examined in orthotopic xenograft models of GBM. Expression of FOXM1 was higher in GBM than in normal tissues. DFS-induced FOXM1 protein degradation blocked β-catenin translocation into the nucleus and consequently suppressed downstream target genes of FOXM1 pathways. DFS inhibited cell viability and ATP levels, while increasing apoptosis, and it reduced tumorsphere formation and the invasiveness of GBM TSs. And DFS reduced the activities of transcription factors related to tumorigenesis, stemness, and invasiveness. DFS significantly inhibited tumor growth and prolonged the survival rate of mice in orthotopic xenograft models of GBM. It suggests that DFS inhibits the proliferation of GBM TSs by suppressing FOXM1. DFS may be a potential therapeutic agent to treat GBM.
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32
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Astudillo-Clavijo V, Stiassny MLJ, Ilves KL, Musilova Z, Salzburger W, López-Fernández H. Exon-based phylogenomics and the relationships of African cichlid fishes: tackling the challenges of reconstructing phylogenies with repeated rapid radiations. Syst Biol 2022; 72:134-149. [PMID: 35880863 DOI: 10.1093/sysbio/syac051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system.
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Affiliation(s)
- Viviana Astudillo-Clavijo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, 10024-5102, USA
| | - Katriina L Ilves
- Research & Collections, Zoology, Canadian Museum of Nature, Ottawa, K1P 6P4, Canada
| | - Zuzana Musilova
- Department of Zoology, Charles University in Prague, Vinicna 7, Prague, CZ-128 44, Czech Republic
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
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North K, Benbarche S, Liu B, Pangallo J, Chen S, Stahl M, Bewersdorf JP, Stanley RF, Erickson C, Cho H, Pineda JMB, Thomas JD, Polaski JT, Belleville AE, Gabel AM, Udy DB, Humbert O, Kiem HP, Abdel-Wahab O, Bradley RK. Synthetic introns enable splicing factor mutation-dependent targeting of cancer cells. Nat Biotechnol 2022; 40:1103-1113. [PMID: 35241838 PMCID: PMC9288984 DOI: 10.1038/s41587-022-01224-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/17/2022] [Indexed: 11/16/2022]
Abstract
Many cancers carry recurrent, change-of-function mutations affecting RNA splicing factors. Here, we describe a method to harness this abnormal splicing activity to drive splicing factor mutation-dependent gene expression to selectively eliminate tumor cells. We engineered synthetic introns that were efficiently spliced in cancer cells bearing SF3B1 mutations, but unspliced in otherwise isogenic wild-type cells, to yield mutation-dependent protein production. A massively parallel screen of 8,878 introns delineated ideal intronic size and mapped elements underlying mutation-dependent splicing. Synthetic introns enabled mutation-dependent expression of herpes simplex virus-thymidine kinase (HSV-TK) and subsequent ganciclovir (GCV)-mediated killing of SF3B1-mutant leukemia, breast cancer, uveal melanoma and pancreatic cancer cells in vitro, while leaving wild-type cells unaffected. Delivery of synthetic intron-containing HSV-TK constructs to leukemia, breast cancer and uveal melanoma cells and GCV treatment in vivo significantly suppressed the growth of these otherwise lethal xenografts and improved mouse host survival. Synthetic introns provide a means to exploit tumor-specific changes in RNA splicing for cancer gene therapy.
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Affiliation(s)
- Khrystyna North
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Salima Benbarche
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bo Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph Pangallo
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Sisi Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maximilian Stahl
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jan Philipp Bewersdorf
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert F Stanley
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caroline Erickson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hana Cho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - James D Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jacob T Polaski
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrea E Belleville
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Austin M Gabel
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Dylan B Udy
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Olivier Humbert
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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Starskaia I, Laajala E, Grönroos T, Härkönen T, Junttila S, Kattelus R, Kallionpää H, Laiho A, Suni V, Tillmann V, Lund R, Elo LL, Lähdesmäki H, Knip M, Kalim UU, Lahesmaa R. Early DNA methylation changes in children developing beta cell autoimmunity at a young age. Diabetologia 2022; 65:844-860. [PMID: 35142878 PMCID: PMC8960578 DOI: 10.1007/s00125-022-05657-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022]
Abstract
AIMS/HYPOTHESIS Type 1 diabetes is a chronic autoimmune disease of complex aetiology, including a potential role for epigenetic regulation. Previous epigenomic studies focused mainly on clinically diagnosed individuals. The aim of the study was to assess early DNA methylation changes associated with type 1 diabetes already before the diagnosis or even before the appearance of autoantibodies. METHODS Reduced representation bisulphite sequencing (RRBS) was applied to study DNA methylation in purified CD4+ T cell, CD8+ T cell and CD4-CD8- cell fractions of 226 peripheral blood mononuclear cell samples longitudinally collected from seven type 1 diabetes-specific autoantibody-positive individuals and control individuals matched for age, sex, HLA risk and place of birth. We also explored correlations between DNA methylation and gene expression using RNA sequencing data from the same samples. Technical validation of RRBS results was performed using pyrosequencing. RESULTS We identified 79, 56 and 45 differentially methylated regions in CD4+ T cells, CD8+ T cells and CD4-CD8- cell fractions, respectively, between type 1 diabetes-specific autoantibody-positive individuals and control participants. The analysis of pre-seroconversion samples identified DNA methylation signatures at the very early stage of disease, including differential methylation at the promoter of IRF5 in CD4+ T cells. Further, we validated RRBS results using pyrosequencing at the following CpG sites: chr19:18118304 in the promoter of ARRDC2; chr21:47307815 in the intron of PCBP3; and chr14:81128398 in the intergenic region near TRAF3 in CD4+ T cells. CONCLUSIONS/INTERPRETATION These preliminary results provide novel insights into cell type-specific differential epigenetic regulation of genes, which may contribute to type 1 diabetes pathogenesis at the very early stage of disease development. Should these findings be validated, they may serve as a potential signature useful for disease prediction and management.
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Affiliation(s)
- Inna Starskaia
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Essi Laajala
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Toni Grönroos
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Taina Härkönen
- Pediatric Research Center, Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Roosa Kattelus
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Henna Kallionpää
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Veronika Suni
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Vallo Tillmann
- Children's Clinic of Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Riikka Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Mikael Knip
- Pediatric Research Center, Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
- Institute of Biomedicine, University of Turku, Turku, Finland.
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35
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Grissa D, Junge A, Oprea TI, Jensen LJ. Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration. Database (Oxford) 2022; 2022:6554833. [PMID: 35348648 PMCID: PMC9216524 DOI: 10.1093/database/baac019] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/14/2022] [Accepted: 03/11/2022] [Indexed: 12/04/2022]
Abstract
The scientific knowledge about which genes are involved in which diseases grows rapidly, which makes it difficult to keep up with new publications and genetics datasets. The DISEASES database aims to provide a comprehensive overview by systematically integrating and assigning confidence scores to evidence for disease–gene associations from curated databases, genome-wide association studies (GWAS) and automatic text mining of the biomedical literature. Here, we present a major update to this resource, which greatly increases the number of associations from all these sources. This is especially true for the text-mined associations, which have increased by at least 9-fold at all confidence cutoffs. We show that this dramatic increase is primarily due to adding full-text articles to the text corpus, secondarily due to improvements to both the disease and gene dictionaries used for named entity recognition, and only to a very small extent due to the growth in number of PubMed abstracts. DISEASES now also makes use of a new GWAS database, Target Illumination by GWAS Analytics, which considerably increased the number of GWAS-derived disease–gene associations. DISEASES itself is also integrated into several other databases and resources, including GeneCards/MalaCards, Pharos/Target Central Resource Database and the Cytoscape stringApp. All data in DISEASES are updated on a weekly basis and is available via a web interface at https://diseases.jensenlab.org, from where it can also be downloaded under open licenses. Database URL: https://diseases.jensenlab.org
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Affiliation(s)
- Dhouha Grissa
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Alexander Junge
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Tudor I Oprea
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Internal Medicine, Division of Translational Informatics, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
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Siqueira E, Obiols-Guardia A, Jorge-Torres OC, Oliveira-Mateos C, Soler M, Ramesh-Kumar D, Setién F, van Rossum D, Pascual-Alonso A, Xiol C, Ivan C, Shimizu M, Armstrong J, Calin GA, Pasterkamp RJ, Esteller M, Guil S. Analysis of the circRNA and T-UCR populations identifies convergent pathways in mouse and human models of Rett syndrome. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:621-644. [PMID: 35036070 PMCID: PMC8749388 DOI: 10.1016/j.omtn.2021.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/17/2021] [Indexed: 01/07/2023]
Abstract
Noncoding RNAs play regulatory roles in physiopathology, but their involvement in neurodevelopmental diseases is poorly understood. Rett syndrome is a severe, progressive neurodevelopmental disorder linked to loss-of-function mutations of the MeCP2 gene for which no cure is yet available. Analysis of the noncoding RNA profile corresponding to the brain-abundant circular RNA (circRNA) and transcribed-ultraconserved region (T-UCR) populations in a mouse model of the disease reveals widespread dysregulation and enrichment in glutamatergic excitatory signaling and microtubule cytoskeleton pathways of the corresponding host genes. Proteomic analysis of hippocampal samples from affected individuals confirms abnormal levels of several cytoskeleton-related proteins together with key alterations in neurotransmission. Importantly, the glutamate receptor GRIA3 gene displays altered biogenesis in affected individuals and in vitro human cells and is influenced by expression of two ultraconserved RNAs. We also describe post-transcriptional regulation of SIRT2 by circRNAs, which modulates acetylation and total protein levels of GluR-1. As a consequence, both regulatory mechanisms converge on the biogenesis of AMPA receptors, with an effect on neuronal differentiation. In both cases, the noncoding RNAs antagonize MeCP2-directed regulation. Our findings indicate that noncoding transcripts may contribute to key alterations in Rett syndrome and are not only useful tools for revealing dysregulated processes but also molecules of biomarker value.
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Affiliation(s)
- Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, 08916 Catalonia, Spain
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908 Catalonia, Spain
- National Council for Scientific and Technological Development (CNPq), Brasilia, 71605-001 Federal District, Brazil
| | - Aida Obiols-Guardia
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, 08916 Catalonia, Spain
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908 Catalonia, Spain
| | - Olga C. Jorge-Torres
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, 08916 Catalonia, Spain
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908 Catalonia, Spain
| | | | - Marta Soler
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, 08916 Catalonia, Spain
| | - Deepthi Ramesh-Kumar
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, 08916 Catalonia, Spain
| | - Fernando Setién
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, 08916 Catalonia, Spain
| | - Daniëlle van Rossum
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Ainhoa Pascual-Alonso
- Fundación San Juan de Dios, Barcelona, 08950 Catalonia, Spain
- Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu, Barcelona, 08950 Catalonia, Spain
| | - Clara Xiol
- Fundación San Juan de Dios, Barcelona, 08950 Catalonia, Spain
- Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu, Barcelona, 08950 Catalonia, Spain
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Masayoshi Shimizu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Judith Armstrong
- Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu, Barcelona, 08950 Catalonia, Spain
- Servei de Medicina Genètica i Molecular, Hospital Sant Joan de Déu, Barcelona, 08950 Catalonia, Spain
- CIBER-ER (Biomedical Network Research Center for Rare Diseases), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - R. Jeroen Pasterkamp
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, 08916 Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010 Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, 08907 Catalonia, Spain
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, 08916 Catalonia, Spain
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908 Catalonia, Spain
- Germans Trias i Pujol Health Science Research Institute, Badalona, Barcelona, 08916 Catalonia, Spain
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Cai Z, Christensen OF, Lund MS, Ostersen T, Sahana G. Large-scale association study on daily weight gain in pigs reveals overlap of genetic factors for growth in humans. BMC Genomics 2022; 23:133. [PMID: 35168569 PMCID: PMC8845347 DOI: 10.1186/s12864-022-08373-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/08/2022] [Indexed: 01/10/2023] Open
Abstract
Background Imputation from genotyping array to whole-genome sequence variants using resequencing of representative reference populations enhances our ability to map genetic factors affecting complex phenotypes in livestock species. The accumulation of knowledge about gene function in human and laboratory animals can provide substantial advantage for genomic research in livestock species. Results In this study, 201,388 pigs from three commercial Danish breeds genotyped with low to medium (8.5k to 70k) SNP arrays were imputed to whole genome sequence variants using a two-step approach. Both imputation steps achieved high accuracies, and in total this yielded 26,447,434 markers on 18 autosomes. The average estimated imputation accuracy of markers with minor allele frequency ≥ 0.05 was 0.94. To overcome the memory consumption of running genome-wide association study (GWAS) for each breed, we performed within-breed subpopulation GWAS then within-breed meta-analysis for average daily weight gain (ADG), followed by a multi-breed meta-analysis of GWAS summary statistics. We identified 15 quantitative trait loci (QTL). Our post-GWAS analysis strategy to prioritize of candidate genes including information like gene ontology, mammalian phenotype database, differential expression gene analysis of high and low feed efficiency pig and human GWAS catalog for height, obesity, and body mass index, we proposed MRAP2, LEPROT, PMAIP1, ENSSSCG00000036234, BMP2, ELFN1, LIG4 and FAM155A as the candidate genes with biological support for ADG in pigs. Conclusion Our post-GWAS analysis strategy helped to identify candidate genes not just by distance to the lead SNP but also by multiple sources of biological evidence. Besides, the identified QTL overlap with genes which are known for their association with human growth-related traits. The GWAS with this large data set showed the power to map the genetic factors associated with ADG in pigs and have added to our understanding of the genetics of growth across mammalian species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08373-3.
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Affiliation(s)
- Zexi Cai
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.
| | | | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
| | - Tage Ostersen
- SEGES Danish Pig Research Centre, Agro Food Park 15, 8200, Aarhus N, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
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38
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Rubio-Alarcón M, Cámara-Checa A, Dago M, Crespo-García T, Nieto-Marín P, Marín M, Merino JL, Toquero J, Salguero-Bodes R, Tamargo J, Cebrián J, Delpón E, Caballero R. Zfhx3 Transcription Factor Represses the Expression of SCN5A Gene and Decreases Sodium Current Density (I Na). Int J Mol Sci 2021; 22:13031. [PMID: 34884836 PMCID: PMC8657907 DOI: 10.3390/ijms222313031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 02/02/2023] Open
Abstract
The ZFHX3 and SCN5A genes encode the zinc finger homeobox 3 (Zfhx3) transcription factor (TF) and the human cardiac Na+ channel (Nav1.5), respectively. The effects of Zfhx3 on the expression of the Nav1.5 channel, and in cardiac excitability, are currently unknown. Additionally, we identified three Zfhx3 variants in probands diagnosed with familial atrial fibrillation (p.M1260T) and Brugada Syndrome (p.V949I and p.Q2564R). Here, we analyzed the effects of native (WT) and mutated Zfhx3 on Na+ current (INa) recorded in HL-1 cardiomyocytes. ZFHX3 mRNA can be detected in human atrial and ventricular samples. In HL-1 cardiomyocytes, transfection of Zfhx3 strongly reduced peak INa density, while the silencing of endogenous expression augmented it (from -65.9 ± 8.9 to -104.6 ± 10.8 pA/pF; n ≥ 8, p < 0.05). Zfhx3 significantly reduced the transcriptional activity of human SCN5A, PITX2, TBX5, and NKX25 minimal promoters. Consequently, the mRNA and/or protein expression levels of Nav1.5 and Tbx5 were diminished (n ≥ 6, p < 0.05). Zfhx3 also increased the expression of Nedd4-2 ubiquitin-protein ligase, enhancing Nav1.5 proteasomal degradation. p.V949I, p.M1260T, and p.Q2564R Zfhx3 produced similar effects on INa density and time- and voltage-dependent properties in WT. WT Zfhx3 inhibits INa as a result of a direct repressor effect on the SCN5A promoter, the modulation of Tbx5 increasing on the INa, and the increased expression of Nedd4-2. We propose that this TF participates in the control of cardiac excitability in human adult cardiac tissue.
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Affiliation(s)
- Marcos Rubio-Alarcón
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Gregorio Marañón, CIBERCV, 28040 Madrid, Spain; (M.R.-A.); (A.C.-C.);; (T.C.-G.); (P.N.-M.); (M.M.); (J.T.); (E.D.); (R.C.)
| | - Anabel Cámara-Checa
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Gregorio Marañón, CIBERCV, 28040 Madrid, Spain; (M.R.-A.); (A.C.-C.);; (T.C.-G.); (P.N.-M.); (M.M.); (J.T.); (E.D.); (R.C.)
| | - María Dago
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Gregorio Marañón, CIBERCV, 28040 Madrid, Spain; (M.R.-A.); (A.C.-C.);; (T.C.-G.); (P.N.-M.); (M.M.); (J.T.); (E.D.); (R.C.)
| | - Teresa Crespo-García
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Gregorio Marañón, CIBERCV, 28040 Madrid, Spain; (M.R.-A.); (A.C.-C.);; (T.C.-G.); (P.N.-M.); (M.M.); (J.T.); (E.D.); (R.C.)
| | - Paloma Nieto-Marín
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Gregorio Marañón, CIBERCV, 28040 Madrid, Spain; (M.R.-A.); (A.C.-C.);; (T.C.-G.); (P.N.-M.); (M.M.); (J.T.); (E.D.); (R.C.)
| | - María Marín
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Gregorio Marañón, CIBERCV, 28040 Madrid, Spain; (M.R.-A.); (A.C.-C.);; (T.C.-G.); (P.N.-M.); (M.M.); (J.T.); (E.D.); (R.C.)
| | - José Luis Merino
- Department of Cardiology, Hospital Universitario La Paz, Instituto de Investigación Sanitaria la Paz, CIBERCV, 28046 Madrid, Spain;
| | - Jorge Toquero
- Department of Cardiology, Hospital Universitario Puerta de Hierro, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, CIBERCV, Majadahonda, 28222 Madrid, Spain;
| | - Rafael Salguero-Bodes
- Department of Cardiology, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre, CIBERCV, 28041 Madrid, Spain;
| | - Juan Tamargo
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Gregorio Marañón, CIBERCV, 28040 Madrid, Spain; (M.R.-A.); (A.C.-C.);; (T.C.-G.); (P.N.-M.); (M.M.); (J.T.); (E.D.); (R.C.)
| | - Jorge Cebrián
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Gregorio Marañón, CIBERCV, 28040 Madrid, Spain; (M.R.-A.); (A.C.-C.);; (T.C.-G.); (P.N.-M.); (M.M.); (J.T.); (E.D.); (R.C.)
| | - Eva Delpón
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Gregorio Marañón, CIBERCV, 28040 Madrid, Spain; (M.R.-A.); (A.C.-C.);; (T.C.-G.); (P.N.-M.); (M.M.); (J.T.); (E.D.); (R.C.)
| | - Ricardo Caballero
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Gregorio Marañón, CIBERCV, 28040 Madrid, Spain; (M.R.-A.); (A.C.-C.);; (T.C.-G.); (P.N.-M.); (M.M.); (J.T.); (E.D.); (R.C.)
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Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants. Am J Hum Genet 2021; 108:2301-2318. [PMID: 34762822 DOI: 10.1016/j.ajhg.2021.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying whether a given genetic mutation results in a gene product with increased (gain-of-function; GOF) or diminished (loss-of-function; LOF) activity is an important step toward understanding disease mechanisms because they may result in markedly different clinical phenotypes. Here, we generated an extensive database of documented germline GOF and LOF pathogenic variants by employing natural language processing (NLP) on the available abstracts in the Human Gene Mutation Database. We then investigated various gene- and protein-level features of GOF and LOF variants and applied machine learning and statistical analyses to identify discriminative features. We found that GOF variants were enriched in essential genes, for autosomal-dominant inheritance, and in protein binding and interaction domains, whereas LOF variants were enriched in singleton genes, for protein-truncating variants, and in protein core regions. We developed a user-friendly web-based interface that enables the extraction of selected subsets from the GOF/LOF database by a broad set of annotated features and downloading of up-to-date versions. These results improve our understanding of how variants affect gene/protein function and may ultimately guide future treatment options.
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The Levels of Circulating MicroRNAs at 6-Hour Cardiac Arrest Can Predict 6-Month Poor Neurological Outcome. Diagnostics (Basel) 2021; 11:diagnostics11101905. [PMID: 34679603 PMCID: PMC8534364 DOI: 10.3390/diagnostics11101905] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Early prognostication in cardiac arrest survivors is challenging for physicians. Unlike other prognostic modalities, biomarkers are easily accessible and provide an objective assessment method. We hypothesized that in cardiac arrest patients with targeted temperature management (TTM), early circulating microRNA (miRNA) levels are associated with the 6-month neurological outcome. In the discovery phase, we identified candidate miRNAs associated with cardiac arrest patients who underwent TTM by comparing circulating expression levels in patients and healthy controls. Next, using a larger cohort, we validated the prognostic values of the identified early miRNAs by measuring the serum levels of miRNAs, neuron-specific enolase (NSE), and S100 calcium-binding protein B (S100B) 6 h after cardiac arrest. The validation cohort consisted of 54 patients with TTM. The areas under the curve (AUCs) for poor outcome were 0.85 (95% CI (confidence interval), 0.72–0.93), 0.82 (95% CI, 0.70–0.91), 0.78 (95% CI, 0.64–0.88), and 0.77 (95% CI, 0.63–0.87) for miR-6511b-5p, -125b-1-3p, -122-5p, and -124-3p, respectively. When the cut-off was based on miRNA levels predicting poor outcome with 100% specificity, sensitivities were 67.7% (95% CI, 49.5–82.6), 50.0% (95% CI, 32.4–67.7), 35.3% (95% CI, 19.7–53.5), and 26.5% (95% CI, 12.9–44.4) for the above miRNAs, respectively. The models combining early miRNAs with protein biomarkers demonstrated superior prognostic performance to those of protein biomarkers.
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Lee J, Cho S, Hong SE, Kang D, Choi H, Lee JM, Yoon JH, Cho BS, Lee S, Kim HJ, Kim M, Kim Y. Integrative Analysis of Gene Expression Data by RNA Sequencing for Differential Diagnosis of Acute Leukemia: Potential Application of Machine Learning. Front Oncol 2021; 11:717616. [PMID: 34497767 PMCID: PMC8419339 DOI: 10.3389/fonc.2021.717616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/21/2021] [Indexed: 11/24/2022] Open
Abstract
BCR-ABL1–positive acute leukemia can be classified into three disease categories: B-lymphoblastic leukemia (B-ALL), acute myeloid leukemia (AML), and mixed-phenotype acute leukemia (MPAL). We conducted an integrative analysis of RNA sequencing (RNA-seq) data obtained from 12 BCR-ABL1–positive B-ALL, AML, and MPAL samples to evaluate its diagnostic utility. RNA-seq facilitated the identification of all p190 BCR-ABL1 with accurate splicing sites and a new gene fusion involving MAP2K2. Most of the clinically significant mutations were also identified including single-nucleotide variations, insertions, and deletions. In addition, RNA-seq yielded differential gene expression profile according to the disease category. Therefore, we selected 368 genes differentially expressed between AML and B-ALL and developed two differential diagnosis models based on the gene expression data using 1) scoring algorithm and 2) machine learning. Both models showed an excellent diagnostic accuracy not only for our 12 BCR-ABL1–positive cases but also for 427 public gene expression datasets from acute leukemias regardless of specific genetic aberration. This is the first trial to develop models of differential diagnosis using RNA-seq, especially to evaluate the potential role of machine learning in identifying the disease category of acute leukemia. The integrative analysis of gene expression data by RNA-seq facilitates the accurate differential diagnosis of acute leukemia with successful detection of significant gene fusion and/or mutations, which warrants further investigation.
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Affiliation(s)
- Jaewoong Lee
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | | | - Seong-Eui Hong
- Next Generation Sequencing (NGS) Division, Theragen Bio Co. Ltd., Seongnam-si, South Korea
| | - Dain Kang
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jong-Mi Lee
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jae-Ho Yoon
- Department of Hematology, Catholic Hematology Hospital and Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Byung-Sik Cho
- Department of Hematology, Catholic Hematology Hospital and Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Seok Lee
- Department of Hematology, Catholic Hematology Hospital and Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hee-Je Kim
- Department of Hematology, Catholic Hematology Hospital and Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
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Wen H, Luo H, Yang M, Augustino SMA, Wang D, Mi S, Guo Y, Zhang Y, Xiao W, Wang Y, Yu Y. Genetic parameters and weighted single-step genome-wide association study for supernumerary teats in Holstein cattle. J Dairy Sci 2021; 104:11867-11877. [PMID: 34482976 DOI: 10.3168/jds.2020-19943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/29/2021] [Indexed: 01/22/2023]
Abstract
Supernumerary teats (SNT) are a common epidermal abnormality of udders in mammals. The SNT negatively affect machine milking ability, udder health, and animal welfare and sometimes act as reservoirs for undesirable bacteria, resulting in economic losses on calves and lactating cows due to the cost of SNT removal surgery, early culling, and low milk yield. This study aimed to analyze the incidence and genetic parameter of SNT and detect SNT-related genes in Chinese Holstein cattle. In this study, the incidence of SNT was recorded in 4,670 Chinese Holstein cattle (born between 2008 and 2017) from 2 farms, including 734 genotyped cows with 114,485 SNPs. The SNT had a total frequency of 9.8% and estimated heritability of 0.22 (SE = 0.07), which were obtained using a threshold model in the studied Chinese Holstein population. Furthermore, we calculated approximate genetic correlations between SNT and the following indicator traits: 12 milk production, 28 body conformation, 5 fertility and reproduction, 5 health, and 9 longevity. Generally, the estimated correlations, such as 305-d milk yield for third parity (-0.55; SE = 0.02) and age at first calving in heifer (0.19; SE = 0.03), were low to moderate. A single-step GWAS was implemented, and 10 genes associated with SNT located in BTA4 were identified. The region (112.70-112.90 Mb) on BTA4 showed the highest genetic variance for SNT. The quantitative trait loci on BTA4 was mapped into the RARRES2 gene, which was previously shown to affect adipogenesis and hormone secretion. The WIF1 gene, which was located in BTA5, was also considered as a candidate gene for SNT. Overall, these findings provide useful information for breeders who are interested in reducing SNT.
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Affiliation(s)
- H Wen
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - H Luo
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - M Yang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - S M A Augustino
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - D Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - S Mi
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Y Guo
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU 75007, Uppsala, Sweden
| | - Y Zhang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - W Xiao
- Beijing Animal Husbandry Station, No. 15A Anwaibeiyuan Road, 100029, Beijing, China
| | - Y Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
| | - Y Yu
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
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Beauchamp EM, Leventhal M, Bernard E, Hoppe ER, Todisco G, Creignou M, Gallì A, Castellano CA, McConkey M, Tarun A, Wong W, Schenone M, Stanclift C, Tanenbaum B, Malolepsza E, Nilsson B, Bick AG, Weinstock JS, Miller M, Niroula A, Dunford A, Taylor-Weiner A, Wood T, Barbera A, Anand S, Psaty BM, Desai P, Cho MH, Johnson AD, Loos R, MacArthur DG, Lek M, Neuberg DS, Lage K, Carr SA, Hellstrom-Lindberg E, Malcovati L, Papaemmanuil E, Stewart C, Getz G, Bradley RK, Jaiswal S, Ebert BL. ZBTB33 is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing. Blood Cancer Discov 2021; 2:500-517. [PMID: 34568833 PMCID: PMC8462124 DOI: 10.1158/2643-3230.bcd-20-0224] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/14/2021] [Accepted: 07/07/2021] [Indexed: 12/17/2022] Open
Abstract
Clonal hematopoiesis results from somatic mutations in cancer driver genes in hematopoietic stem cells. We sought to identify novel drivers of clonal expansion using an unbiased analysis of sequencing data from 84,683 persons and identified common mutations in the 5-methylcytosine reader, ZBTB33, as well as in YLPM1, SRCAP, and ZNF318. We also identified these mutations at low frequency in myelodysplastic syndrome patients. Zbtb33 edited mouse hematopoietic stem and progenitor cells exhibited a competitive advantage in vivo and increased genome-wide intron retention. ZBTB33 mutations potentially link DNA methylation and RNA splicing, the two most commonly mutated pathways in clonal hematopoiesis and MDS.
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Affiliation(s)
- Ellen M Beauchamp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Matthew Leventhal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Elsa Bernard
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emma R Hoppe
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Gabriele Todisco
- Department of Molecular Medicine, University of Pavia, and Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Creignou
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Gallì
- Department of Molecular Medicine, University of Pavia, and Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Cecilia A Castellano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Marie McConkey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Akansha Tarun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Waihay Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Monica Schenone
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Caroline Stanclift
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Benjamin Tanenbaum
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Edyta Malolepsza
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Björn Nilsson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Alexander G Bick
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Mendy Miller
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Abhishek Niroula
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Andrew Dunford
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Amaro Taylor-Weiner
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Timothy Wood
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Alex Barbera
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, Washington
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medical College, New York, New York
| | - Michael H Cho
- Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Andrew D Johnson
- National Heart, Lung, and Blood Institute Center for Population Studies, the Framingham Heart Study, Framingham, Massachusetts
| | - Ruth Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Daniel G MacArthur
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Monkol Lek
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kasper Lage
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Eva Hellstrom-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, and Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elli Papaemmanuil
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chip Stewart
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, Massachusetts
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Fan HP, Zhu ZX, Xu JJ, Li YT, Guo CW, Yan H. The lncRNA CASC9 alleviates lipopolysaccharide-induced acute kidney injury by regulating the miR-424-5p/TXNIP pathway. J Int Med Res 2021; 49:3000605211037495. [PMID: 34407684 PMCID: PMC8381429 DOI: 10.1177/03000605211037495] [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] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE This study aimed to clarify the mechanism by which the long non-coding RNA cancer susceptibility candidate 9 (CASC9) alleviates sepsis-related acute kidney injury (S-AKI). METHODS A lipopolysaccharide (LPS)-induced AKI model was established to simulate S-AKI. HK-2 human renal tubular epithelial cells were treated with LPS to establish an in vitro model, and mice were intraperitoneally injected with LPS to generate an in vivo model. Subsequently, the mRNA expression of inflammatory and antioxidant factors was validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Reactive oxygen species (ROS) production was assessed using an assay kit. Apoptosis was detected by western blotting and fluorescence-activated cell sorting. RESULTS CASC9 was significantly downregulated in the LPS-induced AKI model. CASC9 attenuated cell inflammation and apoptosis and enhanced the antioxidant capacity of cells. Regarding the mechanism, miR-424-5p was identified as the downstream target of CASC9, and the interaction between CASC9 and miR-424-5p promoted thioredoxin-interacting protein (TXNIP) expression. CONCLUSIONS CASC9 alleviates LPS-induced AKI in vivo and in vitro, and CASC9 directly targets miR-424-5p and further promotes the expression of TXNIP. We have provided a possible reference strategy for the treatment of S-AKI.
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Affiliation(s)
- Hai-Peng Fan
- Department of Emergency, First Hospital of Quanzhou affiliated to Fujian Medical University, Fujian, Quanzhou, China
| | - Zhi-Xia Zhu
- Department of Emergency, First Hospital of Quanzhou affiliated to Fujian Medical University, Fujian, Quanzhou, China
| | - Jia-Jun Xu
- Department of Emergency, First Hospital of Quanzhou affiliated to Fujian Medical University, Fujian, Quanzhou, China
| | - Yu-Tang Li
- Department of Emergency, First Hospital of Quanzhou affiliated to Fujian Medical University, Fujian, Quanzhou, China
| | - Chun-Wen Guo
- Department of Emergency, First Hospital of Quanzhou affiliated to Fujian Medical University, Fujian, Quanzhou, China
| | - Hong Yan
- Department of Emergency, First Hospital of Quanzhou affiliated to Fujian Medical University, Fujian, Quanzhou, China
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Gao Z, You X, Zhang X, Chen J, Xu T, Huang Y, Lin X, Xu J, Bian C, Shi Q. A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus). Genomics 2021; 113:3349-3356. [PMID: 34343676 DOI: 10.1016/j.ygeno.2021.07.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 07/13/2021] [Accepted: 07/28/2021] [Indexed: 12/15/2022]
Abstract
Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of Illumina short reads, Nanopore long reads and Hi-C data. A 731.7-Mb genome assembly was finally obtained, with a contig N50 of 3.5 Mb, a scaffold N50 of 29.5 Mb, and anchoring of 98.46% of the assembly onto 30 pseudochromosomes. The genome contained 36.9% repeat sequences, and a total 18,895 protein-coding genes were predicted. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be related to the high fat content in striped catfish. Meanwhile, the FABP1-2 and -3 isoforms differed from FABP1-1 by several missense mutations including R126T, which may affect the fatty acid binding properties. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and lays a solid foundation for practical aquaculture and molecular breeding of this international teleost species.
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Affiliation(s)
- Zijian Gao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Jieming Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Tengfei Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xueqiang Lin
- BGI Marine-Hainan, BGI Marine, BGI, Wenchang 571327, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Chao Bian
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
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Lu SX, De Neef E, Thomas JD, Sabio E, Rousseau B, Gigoux M, Knorr DA, Greenbaum B, Elhanati Y, Hogg SJ, Chow A, Ghosh A, Xie A, Zamarin D, Cui D, Erickson C, Singer M, Cho H, Wang E, Lu B, Durham BH, Shah H, Chowell D, Gabel AM, Shen Y, Liu J, Jin J, Rhodes MC, Taylor RE, Molina H, Wolchok JD, Merghoub T, Diaz LA, Abdel-Wahab O, Bradley RK. Pharmacologic modulation of RNA splicing enhances anti-tumor immunity. Cell 2021; 184:4032-4047.e31. [PMID: 34171309 PMCID: PMC8684350 DOI: 10.1016/j.cell.2021.05.038] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/26/2021] [Accepted: 05/24/2021] [Indexed: 01/26/2023]
Abstract
Although mutations in DNA are the best-studied source of neoantigens that determine response to immune checkpoint blockade, alterations in RNA splicing within cancer cells could similarly result in neoepitope production. However, the endogenous antigenicity and clinical potential of such splicing-derived epitopes have not been tested. Here, we demonstrate that pharmacologic modulation of splicing via specific drug classes generates bona fide neoantigens and elicits anti-tumor immunity, augmenting checkpoint immunotherapy. Splicing modulation inhibited tumor growth and enhanced checkpoint blockade in a manner dependent on host T cells and peptides presented on tumor MHC class I. Splicing modulation induced stereotyped splicing changes across tumor types, altering the MHC I-bound immunopeptidome to yield splicing-derived neoepitopes that trigger an anti-tumor T cell response in vivo. These data definitively identify splicing modulation as an untapped source of immunogenic peptides and provide a means to enhance response to checkpoint blockade that is readily translatable to the clinic.
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Affiliation(s)
- Sydney X Lu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Emma De Neef
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - James D Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Erich Sabio
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Center for Immunotherapy and Precision-Oncology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Benoit Rousseau
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Mathieu Gigoux
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - David A Knorr
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Benjamin Greenbaum
- Department of Epidemiology and Biostatistics, Computational Oncology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Yuval Elhanati
- Department of Epidemiology and Biostatistics, Computational Oncology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Simon J Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Andrew Chow
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Arnab Ghosh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Abigail Xie
- Medical Scientist Training Program, Weill Cornell Medical School, New York, NY 10065, USA
| | - Dmitriy Zamarin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Daniel Cui
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Caroline Erickson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Michael Singer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Hana Cho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Eric Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Bin Lu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Benjamin H Durham
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Harshal Shah
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Diego Chowell
- Center for Immunotherapy and Precision-Oncology, Cleveland Clinic, Cleveland, OH 44195, USA; The Precision Immunology Institute, The Tisch Cancer Institute, Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Austin M Gabel
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Yudao Shen
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jing Liu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew C Rhodes
- The Warren Family Research Center for Drug Discovery and Development and the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Richard E Taylor
- The Warren Family Research Center for Drug Discovery and Development and the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Jedd D Wolchok
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Taha Merghoub
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA.
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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Armaos A, Colantoni A, Proietti G, Rupert J, Tartaglia G. catRAPID omics v2.0: going deeper and wider in the prediction of protein-RNA interactions. Nucleic Acids Res 2021; 49:W72-W79. [PMID: 34086933 PMCID: PMC8262727 DOI: 10.1093/nar/gkab393] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Prediction of protein-RNA interactions is important to understand post-transcriptional events taking place in the cell. Here we introduce catRAPID omics v2.0, an update of our web server dedicated to the computation of protein-RNA interaction propensities at the transcriptome- and RNA-binding proteome-level in 8 model organisms. The server accepts multiple input protein or RNA sequences and computes their catRAPID interaction scores on updated precompiled libraries. Additionally, it is now possible to predict the interactions between a custom protein set and a custom RNA set. Considerable effort has been put into the generation of a new database of RNA-binding motifs that are searched within the predicted RNA targets of proteins. In this update, the sequence fragmentation scheme of the catRAPID fragment module has been included, which allows the server to handle long linear RNAs and to analyse circular RNAs. For the top-scoring protein-RNA pairs, the web server shows the predicted binding sites in both protein and RNA sequences and reports whether the predicted interactions are conserved in orthologous protein-RNA pairs. The catRAPID omics v2.0 web server is a powerful tool for the characterization and classification of RNA-protein interactions and is freely available at http://service.tartaglialab.com/page/catrapid_omics2_group along with documentation and tutorial.
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Affiliation(s)
- Alexandros Armaos
- Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Gabriele Proietti
- Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
- Dipartimento di Neuroscienze, University of Genova, Genoa 16126, Italy
| | - Jakob Rupert
- Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Gian Gaetano Tartaglia
- Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy
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Zhao B, Luo H, Huang X, Wei C, Di J, Tian Y, Fu X, Li B, Liu GE, Fang L, Zhang S, Tian K. Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep. Genet Sel Evol 2021; 53:56. [PMID: 34193030 PMCID: PMC8247193 DOI: 10.1186/s12711-021-00649-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). RESULTS Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from - 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. CONCLUSIONS Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.
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Affiliation(s)
- Bingru Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hanpeng Luo
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Chen Wei
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jiang Di
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Yuezhen Tian
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Bingjie Li
- Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, EH25 9RG, UK
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
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49
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Investigation of monogenic causes of familial breast cancer: data from the BEACCON case-control study. NPJ Breast Cancer 2021; 7:76. [PMID: 34117267 PMCID: PMC8196173 DOI: 10.1038/s41523-021-00279-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 05/03/2021] [Indexed: 01/19/2023] Open
Abstract
Breast cancer (BC) has a significant heritable component but the genetic contribution remains unresolved in the majority of high-risk BC families. This study aims to investigate the monogenic causes underlying the familial aggregation of BC beyond BRCA1 and BRCA2, including the identification of new predisposing genes. A total of 11,511 non-BRCA familial BC cases and population-matched cancer-free female controls in the BEACCON study were investigated in two sequencing phases: 1303 candidate genes in up to 3892 cases and controls, followed by validation of 145 shortlisted genes in an additional 7619 subjects. The coding regions and exon–intron boundaries of all candidate genes and 14 previously proposed BC genes were sequenced using custom designed sequencing panels. Pedigree and pathology data were analysed to identify genotype-specific associations. The contribution of ATM, PALB2 and CHEK2 to BC predisposition was confirmed, but not RAD50 and NBN. An overall excess of loss-of-function (LoF) (OR 1.27, p = 9.05 × 10−9) and missense (OR 1.27, p = 3.96 × 10−73) variants was observed in the cases for the 145 candidate genes. Leading candidates harbored LoF variants with observed ORs of 2–4 and individually accounted for no more than 0.79% of the cases. New genes proposed by this study include NTHL1, WRN, PARP2, CTH and CDK9. The new candidate BC predisposition genes identified in BEACCON indicate that much of the remaining genetic causes of high-risk BC families are due to genes in which pathogenic variants are both very rare and convey only low to moderate risk.
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Seong RK, Lee JK, Cho GJ, Kumar M, Shin OS. mRNA and miRNA profiling of Zika virus-infected human umbilical cord mesenchymal stem cells identifies miR-142-5p as an antiviral factor. Emerg Microbes Infect 2021; 9:2061-2075. [PMID: 32902370 PMCID: PMC7534337 DOI: 10.1080/22221751.2020.1821581] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Zika virus (ZIKV) infection during pregnancy is associated with congenital brain abnormalities, a finding that highlights the urgent need to understand mother-to-fetus transmission mechanisms. Human umbilical cord mesenchymal stem cells (hUCMSCs) are susceptible to ZIKV infection but the underlying mechanisms of viral susceptibility remain largely unexplored. In this study, we have characterized and compared host mRNA and miRNA expression profiles in hUCMSCs after infection with two lineages of ZIKV, African (MR766) and Asian (PRVABC59). RNA sequencing analysis identified differentially expressed genes involved in anti-viral immunity and mitochondrial dynamics following ZIKV infection. In particular, ZIKV-infected hUCMSCs displayed mitochondrial elongation and the treatment of hUCMSCs with mitochondrial fission inhibitor led to a dose-dependent increase in ZIKV gene expression and decrease in anti-viral signalling pathways. Moreover, small RNA sequencing analysis identified several significantly up- or down-regulated microRNAs. Interestingly, miR-142-5p was significantly downregulated upon ZIKV infection, whereas cellular targets of miR-142-5p, IL6ST and ITGAV, were upregulated. Overexpression of miR-142-5p resulted in the suppression of ZIKV replication. Furthermore, blocking ITGAV expression resulted in a significant suppression of ZIKV binding to cells, suggesting a potential role of ITGAV in ZIKV entry. In conclusion, these results demonstrate both common and specific host responses to African and Asian ZIKV lineages and indicate miR-142-5p as a key regulator of ZIKV replication in the umbilical cords.
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Affiliation(s)
- Rak-Kyun Seong
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jae Kyung Lee
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Geum Joon Cho
- Department of Obstetrics and Gynaecology, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Mukesh Kumar
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Ok Sarah Shin
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
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