1
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Ibrahim H, Balboa D, Saarimäki-Vire J, Montaser H, Dyachok O, Lund PE, Omar-Hmeadi M, Kvist J, Dwivedi OP, Lithovius V, Barsby T, Chandra V, Eurola S, Ustinov J, Tuomi T, Miettinen PJ, Barg S, Tengholm A, Otonkoski T. RFX6 haploinsufficiency predisposes to diabetes through impaired beta cell function. Diabetologia 2024:10.1007/s00125-024-06163-y. [PMID: 38743124 DOI: 10.1007/s00125-024-06163-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/21/2024] [Indexed: 05/16/2024]
Abstract
AIMS/HYPOTHESIS Regulatory factor X 6 (RFX6) is crucial for pancreatic endocrine development and differentiation. The RFX6 variant p.His293LeufsTer7 is significantly enriched in the Finnish population, with almost 1:250 individuals as a carrier. Importantly, the FinnGen study indicates a high predisposition for heterozygous carriers to develop type 2 and gestational diabetes. However, the precise mechanism of this predisposition remains unknown. METHODS To understand the role of this variant in beta cell development and function, we used CRISPR technology to generate allelic series of pluripotent stem cells. We created two isogenic stem cell models: a human embryonic stem cell model; and a patient-derived stem cell model. Both were differentiated into pancreatic islet lineages (stem-cell-derived islets, SC-islets), followed by implantation in immunocompromised NOD-SCID-Gamma mice. RESULTS Stem cell models of the homozygous variant RFX6-/- predictably failed to generate insulin-secreting pancreatic beta cells, mirroring the phenotype observed in Mitchell-Riley syndrome. Notably, at the pancreatic endocrine stage, there was an upregulation of precursor markers NEUROG3 and SOX9, accompanied by increased apoptosis. Intriguingly, heterozygous RFX6+/- SC-islets exhibited RFX6 haploinsufficiency (54.2% reduction in protein expression), associated with reduced beta cell maturation markers, altered calcium signalling and impaired insulin secretion (62% and 54% reduction in basal and high glucose conditions, respectively). However, RFX6 haploinsufficiency did not have an impact on beta cell number or insulin content. The reduced insulin secretion persisted after in vivo implantation in mice, aligning with the increased risk of variant carriers to develop diabetes. CONCLUSIONS/INTERPRETATION Our allelic series isogenic SC-islet models represent a powerful tool to elucidate specific aetiologies of diabetes in humans, enabling the sensitive detection of aberrations in both beta cell development and function. We highlight the critical role of RFX6 in augmenting and maintaining the pancreatic progenitor pool, with an endocrine roadblock and increased cell death upon its loss. We demonstrate that RFX6 haploinsufficiency does not affect beta cell number or insulin content but does impair function, predisposing heterozygous carriers of loss-of-function variants to diabetes. DATA AVAILABILITY Ultra-deep bulk RNA-seq data for pancreatic differentiation stages 3, 5 and 7 of H1 RFX6 genotypes are deposited in the Gene Expression Omnibus database with accession code GSE234289. Original western blot images are deposited at Mendeley ( https://data.mendeley.com/datasets/g75drr3mgw/2 ).
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Affiliation(s)
- Hazem Ibrahim
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Diego Balboa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jonna Saarimäki-Vire
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hossam Montaser
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Oleg Dyachok
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Per-Eric Lund
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | | | - Jouni Kvist
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Om P Dwivedi
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, Helsinki, Finland
- Research Program of Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Väinö Lithovius
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tom Barsby
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vikash Chandra
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Solja Eurola
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jarkko Ustinov
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, Helsinki, Finland
- Research Program of Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Finland
- Abdominal Center, Endocrinology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Päivi J Miettinen
- Department of Pediatrics, Helsinki University Hospital, Helsinki, Finland
| | - Sebastian Barg
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Anders Tengholm
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Pediatrics, Helsinki University Hospital, Helsinki, Finland.
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2
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Coykendall VM, Qian MF, Tellez K, Bautista A, Bevacqua RJ, Gu X, Hang Y, Neukam M, Zhao W, Chang C, MacDonald PE, Kim SK. RFX6 Maintains Gene Expression and Function of Adult Human Islet α-Cells. Diabetes 2024; 73:448-460. [PMID: 38064570 PMCID: PMC10882151 DOI: 10.2337/db23-0483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/21/2023] [Indexed: 02/22/2024]
Abstract
Mutations in the gene encoding the transcription factor regulatory factor X-box binding 6 (RFX6) are associated with human diabetes. Within pancreatic islets, RFX6 expression is most abundant in islet α-cells, and α-cell RFX6 expression is altered in diabetes. However, the roles of RFX6 in regulating gene expression, glucagon output, and other crucial human adult α-cell functions are not yet understood. We developed a method for selective genetic targeting of human α-cells and assessed RFX6-dependent α-cell function. RFX6 suppression with RNA interference led to impaired α-cell exocytosis and dysregulated glucagon secretion in vitro and in vivo. By contrast, these phenotypes were not observed with RFX6 suppression across all islet cells. Transcriptomics in α-cells revealed RFX6-dependent expression of genes governing nutrient sensing, hormone processing, and secretion, with some of these exclusively expressed in human α-cells. Mapping of RFX6 DNA-binding sites in primary human islet cells identified a subset of direct RFX6 target genes. Together, these data unveil RFX6-dependent genetic targets and mechanisms crucial for regulating adult human α-cell function. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Vy M.N. Coykendall
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Mollie F. Qian
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Krissie Tellez
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Austin Bautista
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Romina J. Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Xueying Gu
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA
| | - Martin Neukam
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Weichen Zhao
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Charles Chang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Patrick E. MacDonald
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Seung K. Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
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3
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Litif CG, Flom LT, Sandum KL, Hodgins SL, Vaccaro L, Stitzel JA, Blouin NA, Mannino MC, Gigley JP, Schoborg TA, Bobadilla AC. Differential genetic expression within reward-specific ensembles in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.02.565378. [PMID: 37961222 PMCID: PMC10635086 DOI: 10.1101/2023.11.02.565378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Maladaptive reward seeking is a hallmark of cocaine use disorder. To develop therapeutic targets, it is critical to understand the neurobiological changes specific to cocaine-seeking without altering the seeking of natural rewards, e.g., sucrose. The prefrontal cortex (PFC) and the nucleus accumbens core (NAcore) are known regions associated with cocaine- and sucrose-seeking ensembles, i.e., a sparse population of co-activated neurons. Within ensembles, transcriptomic alterations in the PFC and NAcore underlie the learning and persistence of cocaine- and sucrose-seeking behavior. However, transcriptomes exclusively driving cocaine seeking independent from sucrose seeking have not yet been defined using a within-subject approach. Using Ai14:cFos-TRAP2 transgenic mice in a dual cocaine and sucrose self-administration model, we fluorescently sorted (FACS) and characterized (RNAseq) the transcriptomes defining cocaine- and sucrose-seeking ensembles. We found reward- and region-specific transcriptomic changes that will help develop clinically relevant genetic approaches to decrease cocaine-seeking behavior without altering non-drug reward-based positive reinforcement.
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Affiliation(s)
- Carl G. Litif
- School of Pharmacy, University of Wyoming, Laramie, Wyoming, USA
| | - Levi T. Flom
- School of Pharmacy, University of Wyoming, Laramie, Wyoming, USA
| | | | | | - Lucio Vaccaro
- School of Pharmacy, University of Wyoming, Laramie, Wyoming, USA
| | - Jerry A. Stitzel
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, USA
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Nicolas A. Blouin
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
| | | | - Jason P. Gigley
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
| | - Todd A. Schoborg
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
| | - Ana-Clara Bobadilla
- School of Pharmacy, University of Wyoming, Laramie, Wyoming, USA
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
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4
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Nakamura T, Fujikura J, Ito R, Keidai Y, Inagaki N. Human RFX6 regulates endoderm patterning at the primitive gut tube stage. PNAS NEXUS 2024; 3:pgae001. [PMID: 38239755 PMCID: PMC10794167 DOI: 10.1093/pnasnexus/pgae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/26/2023] [Indexed: 01/22/2024]
Abstract
Transcriptional factor RFX6 is known to be a causal gene of Mitchell-Riley syndrome (MRS), an autosomal recessive neonatal diabetes associated with pancreatic hypoplasia and intestinal atresia/malformation. The morphological defects are limited to posterior foregut and mid-hindgut endodermal lineages and do not occur in the anterior foregut lineage; the mechanism remains to be fully elucidated. In this study, we generated RFX6+/eGFP heterozygous knockin and RFX6eGFP/eGFP homozygous knockin/knockout human-induced pluripotent stem cell (hiPSC) lines and performed in vitro endoderm differentiation to clarify the role of RFX6 in early endoderm development. RFX6 expression was found to surge at the primitive gut tube (PGT) stage in comparison with that in the undifferentiated or definitive endoderm stage. At the PGT stage, the expression of PDX1 and CDX2, posterior foregut and mid-hindgut master regulators, respectively, was decreased by the RFX6 deficit. PDX1+ and CDX2+ cells were mostly green fluorescent protein (GFP)+ in RFX6+/eGFP hiPSCs, but their cell number was markedly decreased in RFX6eGFP/eGFP hiPSCs. The expression of SOX2, an anterior foregut marker, was not affected by the RFX6 deficit. In addition, we found a putative RFX6-binding X-box motif using cap analysis of gene expression-seq and the motif-containing sequences in the enhancer regions of PDX1 and CDX2 bound to RFX6 in vitro. Thus, RFX6 regulates the ParaHox genes PDX1 and CDX2 but does not affect SOX2 in early endodermal differentiation, suggesting that defects in early stage endoderm patterning account for the morphological pathology of MRS.
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Affiliation(s)
- Toshihiro Nakamura
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Junji Fujikura
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Ryo Ito
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Yamato Keidai
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Nobuya Inagaki
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Medical Research Institute, Kitano Hospital, PIIF Tazuke-kofukai, Osaka 530-8480, Japan
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5
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Qiu Z, Wang C, Huang P, Yuan Y, Shi Y, Lin Z, Huang Z, Zuo D, Qiu J, He W, Shen J, Niu Y, Yuan Y, Li B. RFX6 facilitates aerobic glycolysis-mediated growth and metastasis of hepatocellular carcinoma through targeting PGAM1. Clin Transl Med 2023; 13:e1511. [PMID: 38093528 PMCID: PMC10719540 DOI: 10.1002/ctm2.1511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) cells undergo reprogramming of glucose metabolism to support uncontrolled proliferation, of which the intrinsic mechanism still merits further investigation. Although regulatory factor X6 (RFX6) is aberrantly expressed in different cancers, its precise role in cancer development remains ambiguous. METHODS Microarrays of HCC tissues were employed to investigate the expression of RFX6 in tumour and adjacent non-neoplastic tissues. Functional assays were employed to explore the role of RFX6 in HCC development. Chromatin immunoprecipitation, untargeted metabolome profiling and sequencing were performed to identify potential downstream genes and pathways regulated by RFX6. Metabolic assays were employed to investigate the effect of RFX6 on glycolysis in HCC cells. Bioinformatics databases were used to validate the above findings. RESULTS HCC tissues exhibited elevated expression of RFX6. High RFX6 expression represented as an independent hazard factor correlated to poor prognosis in patients with HCC. RFX6 deficiency inhibited HCC development in vitro and in vivo, while its overexpression exerted opposite functions. Mechanistically, RFX6 bound to the promoter area of phosphoglycerate mutase 1 (PGAM1) and upregulated its expression. The increased PGAM1 protein levels enhanced glycolysis and further promoted the development of HCC. CONCLUSIONS RFX6 acted as a novel driver for HCC development by promoting aerobic glycolysis, disclosing the potential of the RFX6-PGAM1 axis for therapeutic targeting.
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Affiliation(s)
- Zhiyu Qiu
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
- Department of Liver SurgerySun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Chenwei Wang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
- Department of Liver SurgerySun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Pinzhu Huang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease and Department of Colon and Rectum SurgeryThe Sixth Affiliated Hospital of Sun Yat‐Sen UniversityGuangzhouP. R. China
| | - Yichuan Yuan
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
- Department of Liver SurgerySun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Yunxing Shi
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
- Department of Liver SurgerySun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Zhu Lin
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
- Department of Liver SurgerySun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Zhenkun Huang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
- Department of Liver SurgerySun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Dinglan Zuo
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Jiliang Qiu
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
- Department of Liver SurgerySun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Wei He
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
- Department of Liver SurgerySun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Jingxian Shen
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
- Department of RadiologySun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Yi Niu
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Yunfei Yuan
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
- Department of Liver SurgerySun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
| | - Binkui Li
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer MedicineSun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
- Department of Liver SurgerySun Yat‐Sen University Cancer CenterSun Yat‐Sen UniversityGuangzhouP. R. China
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6
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Hirasawa I, Odagiri H, Park G, Sanghavi R, Oshita T, Togi A, Yoshikawa K, Mizutani K, Takeuchi Y, Kobayashi H, Katagiri S, Iwata T, Aoki A. Anti-inflammatory effects of cold atmospheric plasma irradiation on the THP-1 human acute monocytic leukemia cell line. PLoS One 2023; 18:e0292267. [PMID: 37851686 PMCID: PMC10584116 DOI: 10.1371/journal.pone.0292267] [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: 06/21/2023] [Accepted: 09/15/2023] [Indexed: 10/20/2023] Open
Abstract
Cold atmospheric plasma (CAP) has been studied and clinically applied to treat chronic wounds, cancer, periodontitis, and other diseases. CAP exerts cytotoxic, bactericidal, cell-proliferative, and anti-inflammatory effects on living tissues by generating reactive species. Therefore, CAP holds promise as a treatment for diseases involving chronic inflammation and bacterial infections. However, the cellular mechanisms underlying these anti-inflammatory effects of CAP are still unclear. Thus, this study aimed to elucidate the anti-inflammatory mechanisms of CAP in vitro. The human acute monocytic leukemia cell line, THP-1, was stimulated with lipopolysaccharide and irradiated with CAP, and the cytotoxic effects of CAP were evaluated. Time-course differentiation of gene expression was analyzed, and key transcription factors were identified via transcriptome analysis. Additionally, the nuclear localization of the CAP-induced transcription factor was examined using western blotting. The results indicated that CAP showed no cytotoxic effects after less than 70 s of irradiation and significantly inhibited interleukin 6 (IL6) expression after more than 40 s of irradiation. Transcriptome analysis revealed many differentially expressed genes (DEGs) following CAP irradiation at all time points. Cluster analysis classified the DEGs into four distinct groups, each with time-dependent characteristics. Gene ontology and gene set enrichment analyses revealed CAP-induced suppression of IL6 production, other inflammatory responses, and the expression of genes related to major histocompatibility complex (MHC) class II. Transcription factor analysis suggested that nuclear factor erythroid 2-related factor 2 (NRF2), which suppresses intracellular oxidative stress, is the most activated transcription factor. Contrarily, regulatory factor X5, which regulates MHC class II expression, is the most suppressed transcription factor. Western blotting revealed the nuclear localization of NRF2 following CAP irradiation. These data suggest that CAP suppresses the inflammatory response, possibly by promoting NRF2 nuclear translocation.
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Affiliation(s)
- Ito Hirasawa
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Sekisui Chemical Co., Ltd., Ibaraki, Japan
| | | | - Giri Park
- Sekisui Chemical Co., Ltd., Ibaraki, Japan
| | | | | | - Akiko Togi
- Sekisui Chemical Co., Ltd., Ibaraki, Japan
| | | | - Koji Mizutani
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuo Takeuchi
- Department of Lifetime Oral Health Care Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Kobayashi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akira Aoki
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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7
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Moyers BA, Partridge EC, Mackiewicz M, Betti MJ, Darji R, Meadows SK, Newberry KM, Brandsmeier LA, Wold BJ, Mendenhall EM, Myers RM. Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells. Genome Res 2023; 33:gr.278205.123. [PMID: 37852782 PMCID: PMC10760452 DOI: 10.1101/gr.278205.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
Abstract
Transcription factors (TFs) are trans-acting proteins that bind cis-regulatory elements (CREs) in DNA to control gene expression. Here, we analyzed the genomic localization profiles of 529 sequence-specific TFs and 151 cofactors and chromatin regulators in the human cancer cell line HepG2, for a total of 680 broadly termed DNA-associated proteins (DAPs). We used this deep collection to model each TF's impact on gene expression, and identified a cohort of 26 candidate transcriptional repressors. We examine high occupancy target (HOT) sites in the context of three-dimensional genome organization and show biased motif placement in distal-promoter connections involving HOT sites. We also found a substantial number of closed chromatin regions with multiple DAPs bound, and explored their properties, finding that a MAFF/MAFK TF pair correlates with transcriptional repression. Altogether, these analyses provide novel insights into the regulatory logic of the human cell line HepG2 genome and show the usefulness of large genomic analyses for elucidation of individual TF functions.
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Affiliation(s)
- Belle A Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Michael J Betti
- Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Roshan Darji
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sarah K Meadows
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | | | - Barbara J Wold
- Merkin Institute for Translational Research, California Institute of Technology, Pasadena, California 91125, USA
| | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
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8
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Samadli S, Zhou Q, Zheng B, Gu W, Zhang A. From glucose sensing to exocytosis: takes from maturity onset diabetes of the young. Front Endocrinol (Lausanne) 2023; 14:1188301. [PMID: 37255971 PMCID: PMC10226665 DOI: 10.3389/fendo.2023.1188301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
Monogenic diabetes gave us simplified models of complex molecular processes occurring within β-cells, which allowed to explore the roles of numerous proteins from single protein perspective. Constellation of characteristic phenotypic features and wide application of genetic sequencing techniques to clinical practice, made the major form of monogenic diabetes - the Maturity Onset Diabetes of the Young to be distinguishable from type 1, type 2 as well as neonatal diabetes mellitus and understanding underlying molecular events for each type of MODY contributed to the advancements of antidiabetic therapy and stem cell research tremendously. The functional analysis of MODY-causing proteins in diabetes development, not only provided better care for patients suffering from diabetes, but also enriched our comprehension regarding the universal cellular processes including transcriptional and translational regulation, behavior of ion channels and transporters, cargo trafficking, exocytosis. In this review, we will overview structure and function of MODY-causing proteins, alterations in a particular protein arising from the deleterious mutations to the corresponding gene and their consequences, and translation of this knowledge into new treatment strategies.
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Affiliation(s)
- Sama Samadli
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Department of Pediatric Diseases II, Azerbaijan Medical University, Baku, Azerbaijan
| | - Qiaoli Zhou
- Department of Endocrinology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Bixia Zheng
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Gu
- Department of Endocrinology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Aihua Zhang
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
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9
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Mattis KK, Krentz NAJ, Metzendorf C, Abaitua F, Spigelman AF, Sun H, Ikle JM, Thaman S, Rottner AK, Bautista A, Mazzaferro E, Perez-Alcantara M, Manning Fox JE, Torres JM, Wesolowska-Andersen A, Yu GZ, Mahajan A, Larsson A, MacDonald PE, Davies B, den Hoed M, Gloyn AL. Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression. Diabetologia 2023; 66:674-694. [PMID: 36633628 PMCID: PMC9947029 DOI: 10.1007/s00125-022-05856-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/17/2022] [Indexed: 01/13/2023]
Abstract
AIMS/HYPOTHESIS Genome-wide studies have uncovered multiple independent signals at the RREB1 locus associated with altered type 2 diabetes risk and related glycaemic traits. However, little is known about the function of the zinc finger transcription factor Ras-responsive element binding protein 1 (RREB1) in glucose homeostasis or how changes in its expression and/or function influence diabetes risk. METHODS A zebrafish model lacking rreb1a and rreb1b was used to study the effect of RREB1 loss in vivo. Using transcriptomic and cellular phenotyping of a human beta cell model (EndoC-βH1) and human induced pluripotent stem cell (hiPSC)-derived beta-like cells, we investigated how loss of RREB1 expression and activity affects pancreatic endocrine cell development and function. Ex vivo measurements of human islet function were performed in donor islets from carriers of RREB1 type 2 diabetes risk alleles. RESULTS CRISPR/Cas9-mediated loss of rreb1a and rreb1b function in zebrafish supports an in vivo role for the transcription factor in beta cell mass, beta cell insulin expression and glucose levels. Loss of RREB1 also reduced insulin gene expression and cellular insulin content in EndoC-βH1 cells and impaired insulin secretion under prolonged stimulation. Transcriptomic analysis of RREB1 knockdown and knockout EndoC-βH1 cells supports RREB1 as a novel regulator of genes involved in insulin secretion. In vitro differentiation of RREB1KO/KO hiPSCs revealed dysregulation of pro-endocrine cell genes, including RFX family members, suggesting that RREB1 also regulates genes involved in endocrine cell development. Human donor islets from carriers of type 2 diabetes risk alleles in RREB1 have altered glucose-stimulated insulin secretion ex vivo, consistent with a role for RREB1 in regulating islet cell function. CONCLUSIONS/INTERPRETATION Together, our results indicate that RREB1 regulates beta cell function by transcriptionally regulating the expression of genes involved in beta cell development and function.
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Affiliation(s)
- Katia K Mattis
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nicole A J Krentz
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Endocrinology, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Christoph Metzendorf
- Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | - Fernando Abaitua
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Aliya F Spigelman
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Han Sun
- Division of Endocrinology, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Jennifer M Ikle
- Division of Endocrinology, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Swaraj Thaman
- Division of Endocrinology, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Antje K Rottner
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Austin Bautista
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Eugenia Mazzaferro
- Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | | | - Jocelyn E Manning Fox
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Jason M Torres
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Grace Z Yu
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Anders Larsson
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Patrick E MacDonald
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Marcel den Hoed
- Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Division of Endocrinology, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK.
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10
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Schwab K, Coronel L, Riege K, Sacramento EK, Rahnis N, Häckes D, Cirri E, Groth M, Hoffmann S, Fischer M. Multi-omics analysis identifies RFX7 targets involved in tumor suppression and neuronal processes. Cell Death Discov 2023; 9:80. [PMID: 36864036 PMCID: PMC9981735 DOI: 10.1038/s41420-023-01378-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 03/04/2023] Open
Abstract
Recurrently mutated in lymphoid neoplasms, the transcription factor RFX7 is emerging as a tumor suppressor. Previous reports suggested that RFX7 may also have a role in neurological and metabolic disorders. We recently reported that RFX7 responds to p53 signaling and cellular stress. Furthermore, we found RFX7 target genes to be dysregulated in numerous cancer types also beyond the hematological system. However, our understanding of RFX7's target gene network and its role in health and disease remains limited. Here, we generated RFX7 knock-out cells and employed a multi-omics approach integrating transcriptome, cistrome, and proteome data to obtain a more comprehensive picture of RFX7 targets. We identify novel target genes linked to RFX7's tumor suppressor function and underscoring its potential role in neurological disorders. Importantly, our data reveal RFX7 as a mechanistic link that enables the activation of these genes in response to p53 signaling.
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Affiliation(s)
- Katjana Schwab
- grid.418245.e0000 0000 9999 5706Computational Biology Group, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Luis Coronel
- grid.418245.e0000 0000 9999 5706Computational Biology Group, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Konstantin Riege
- grid.418245.e0000 0000 9999 5706Computational Biology Group, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Erika K. Sacramento
- grid.418245.e0000 0000 9999 5706Core Facility for Proteomics, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Norman Rahnis
- grid.418245.e0000 0000 9999 5706Core Facility for Proteomics, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - David Häckes
- grid.418245.e0000 0000 9999 5706Computational Biology Group, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Emilio Cirri
- grid.418245.e0000 0000 9999 5706Core Facility for Proteomics, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Marco Groth
- grid.418245.e0000 0000 9999 5706Core Facility for Next-Generation Sequencing, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Steve Hoffmann
- grid.418245.e0000 0000 9999 5706Computational Biology Group, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany.
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11
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Ledger ML, Kaare M, Mailo JA, Jain-Ghai S. Phenotype expansion and neurological manifestations of neurobehavioural disease caused by a variant in RFX7. Eur J Med Genet 2023; 66:104657. [PMID: 36334883 DOI: 10.1016/j.ejmg.2022.104657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/20/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022]
Abstract
The RFX7 gene is one of eight genes within the regulatory factor X family. RFX7 is highly expressed in the brain and plays an important role in cell maturation and differentiation. It has only recently been implicated in disease in humans. Reports from 15 individuals have described RFX-associated phenotype as a neurobehavioural disease, manifesting primarily with global developmental delay and intellectual disability. Autism spectrum disorder and attention deficit hyperactivity disorder have also been described in some children. Here we report a case of a 19-month-old with a de novo missense variant in RFX7 resulting in severe global developmental delay including significant speech delay, microcephaly, dyskinetic movements, and failure to thrive. This is the first association between variants in RFX7 and failure to thrive, expanding the phenotype of this newly described gene. In this report we will also show RFX7 associated progressive central nervous system involvement through serial brain imaging.
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Affiliation(s)
- Marissa L Ledger
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
| | - Milja Kaare
- Blueprint Genetics, A Quest Diagnostics Company, Espoo, Finland
| | - Janette A Mailo
- Department of Pediatrics, Division of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Shailly Jain-Ghai
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
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12
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The genetics of monogenic intestinal epithelial disorders. Hum Genet 2022; 142:613-654. [PMID: 36422736 PMCID: PMC10182130 DOI: 10.1007/s00439-022-02501-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/23/2022] [Indexed: 11/27/2022]
Abstract
Monogenic intestinal epithelial disorders, also known as congenital diarrheas and enteropathies (CoDEs), are a group of rare diseases that result from mutations in genes that primarily affect intestinal epithelial cell function. Patients with CoDE disorders generally present with infantile-onset diarrhea and poor growth, and often require intensive fluid and nutritional management. CoDE disorders can be classified into several categories that relate to broad areas of epithelial function, structure, and development. The advent of accessible and low-cost genetic sequencing has accelerated discovery in the field with over 45 different genes now associated with CoDE disorders. Despite this increasing knowledge in the causal genetics of disease, the underlying cellular pathophysiology remains incompletely understood for many disorders. Consequently, clinical management options for CoDE disorders are currently limited and there is an urgent need for new and disorder-specific therapies. In this review, we provide a general overview of CoDE disorders, including a historical perspective of the field and relationship to other monogenic disorders of the intestine. We describe the genetics, clinical presentation, and known pathophysiology for specific disorders. Lastly, we describe the major challenges relating to CoDE disorders, briefly outline key areas that need further study, and provide a perspective on the future genetic and therapeutic landscape.
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13
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Chen J, Li X, Huang J, Wang Q, Wang S, Wei S, Qin Q, Yang M. The transcription factor RFX5 positively regulates expression of MHCIa in the red-spotted grouper (Epinephelus akaara). FISH & SHELLFISH IMMUNOLOGY 2022; 121:370-379. [PMID: 35051562 DOI: 10.1016/j.fsi.2022.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Regulatory factor X 5 (RFX 5) is a member of the RFX family, and it forms the transcription factor complex RFX with RFXANK/B and RFXAP. The RFX complex can activate MHC expression by binding to the MHC promoter. However, the regulate mechanism of RFX in fish species is not been fully elucidated. In this study, we investigated the transcriptional regulation of Epinephelus akaara RFX5 (EaRFX5) on EaMHCI, and its effect on immune pathways. The genomic sequence of EaRFX5 was 35,774 bp and consisted of ten exons and nine introns. The length of EaRFX5 ORF sequence is 2,160 bp, encoding 719 amino acids. By qRT-PCR, EaRFX5 was detected constitutively expressed in twelve selected tissues, showing a wide range of expression. EaRFX5 expression parttern in response to poly (I:C), LPS, Zymosan A, SGIV, and NNV challenges showed that EaRFX5 plays a differentiated immunomodulatory role in response to various stimuli in different tissues, and EaRFX5 was most significantly upregulated in the kidney after challenge with SGIV. Subcellular localization assays showed that EaRFX5 is a typical nuclear protein. Based on the in vitro overexpression experiments, EaRFX5 appeared to promote the expression of EaMHCIa gene, interferon signalling pathway and inflammatory cytokine. Luciferase reporter assay showed that the -267 bp to +82 bp region of EaMHCIa promoter was the core region where EaRFX5 modulated. Additionally, point mutations and electrophoretic mobility shift assays indicating M3 is the EaRFX5 binding sites in the EaMHCIa promoter. These results contribute to elucidating the function of EaRFX5 in fish immune response, and provide the first evidence of positive regulation of MHCIa expression by RFX5 in fish.
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Affiliation(s)
- Jinpeng Chen
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xinshuai Li
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jianling Huang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qing Wang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shaowen Wang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shina Wei
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qiwei Qin
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, 519000, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
| | - Min Yang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
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14
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Khan SA, Khan S, Muhammad N, Rehman ZU, Khan MA, Nasir A, Kalsoom UE, Khan AK, Khan H, Wasif N. The First Report of a Missense Variant in RFX2 Causing Non-Syndromic Tooth Agenesis in a Consanguineous Pakistani Family. Front Genet 2022; 12:782653. [PMID: 35145545 PMCID: PMC8822170 DOI: 10.3389/fgene.2021.782653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background: The syndromic and non-syndromic congenital missing teeth phenotype is termed tooth agenesis. Since tooth agenesis is a heterogeneous disorder hence, the patients show diverse absent teeth phenotypes. Thus identifying novel genes involved in the morphogenesis of ectodermal appendages, including teeth, paves the way for establishing signaling pathways.Methods and Results: We have recruited an autosomal recessive non-syndromic tooth agenesis family with two affected members. The exome sequencing technology identified a novel missense sequence variant c.1421T > C; p.(Ile474Thr) in a regulatory factor X (RFX) family member (RFX2, OMIM: 142,765). During the data analysis eight rare variants on various chromosomal locations were identified, but the co-segregation analysis using Sanger sequencing confirmed the segregation of only two variants RFX2: c.1421T > C; p.(Ile474Thr), DOHH: c.109C > G; p.(Pro37Ala) lying in a common 7.1 MB region of homozygosity on chromosome 19p13.3. Furthermore, the online protein prediction algorithms and protein modeling analysis verified the RFX2 variant as a damaging genetic alteration and ACMG pathogenicity criteria classified it as likely pathogenic. On the other hand, the DOHH variant showed benign outcomes.Conclusion:RFX2 regulates the Hedgehog and fibroblast growth factor signaling pathways, which are involved in the epithelial and mesenchymal interactions during tooth development. Prior animal model studies have confirmed the expression of rfx2 at a developmental stage governing mouth formation. Moreover, its regulatory role and close association with ciliary and non-ciliary genes causing various dental malformations makes it a potential candidate gene for tooth agenesis phenotype. Further studies will contribute to exploring the direct role of RFX2 in human tooth development.
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Affiliation(s)
- Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
- *Correspondence: Saadullah Khan, ; Naveed Wasif,
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Zia Ur Rehman
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Muhammad Adnan Khan
- Dental Material, Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Peshawar, Pakistan
| | - Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Umm-e- Kalsoom
- Department of Biochemistry, Hazara University, Mansehra, Pakistan
| | - Anwar Kamal Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Hassan Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Naveed Wasif
- Institute of Human Genetics, University of Ulm, Ulm, Germany
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
- *Correspondence: Saadullah Khan, ; Naveed Wasif,
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Sun Y, Yu Z, Zhang Y, Wang H, Chi Z, Chen X, Xu D. Downregulation of microRNA?342-3p eases insulin resistance and liver gluconeogenesis via regulating Rfx3 in gestational diabetes mellitus. Crit Rev Eukaryot Gene Expr 2022; 32:83-95. [DOI: 10.1615/critreveukaryotgeneexpr.2022043275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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16
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Construction of miRNA-mRNA-TF Regulatory Network for Diagnosis of Gastric Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9121478. [PMID: 34840985 PMCID: PMC8616677 DOI: 10.1155/2021/9121478] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/27/2021] [Indexed: 12/30/2022]
Abstract
Gastric cancer (GC), as an epidemic cancer worldwide, has more than 1 million new cases and an estimated 769,000 deaths worldwide in 2020, ranking fifth and fourth in global morbidity and mortality. In mammals, both miRNAs and transcription factors (TFs) play a partial role in gene expression regulation. The mRNA expression profile and miRNA expression profile of GEO database were screened by GEO2R for differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs). Then, DAVID annotated the functions of DEGs to understand the functions played in biological processes. The prediction of potential target genes of miRNA and key TFs of mRNA was performed by mipathDB V2.0 and CHEA3, respectively, and the gene list comparison was performed to look for overlapping genes coregulated by key TFs and DEMs. Finally, the obtained miRNAs, TF, and overlapping genes were used to construct the miRNA-mRNA-TF regulatory network, which was verified by RT-qPCR. 76 upregulated DEGs, 199 downregulated DEGs, and 3 upregulated miRNAs (miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p) were identified from the expression profiles of mRNA (GSE26899, GSE29998, GSE51575, and GSE13911) and miRNA (GSE93415), respectively. Through database prediction and gene list comparison, it was found that among the 199 downregulated DEGs, 61, 71, and 69 genes were the potential targets of miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p, respectively. 199 downregulated DEGs were used as the gene list for the prediction of key TFs, and the results showed that RFX6 ranked the highest. The potential target overlap genes of miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p were 4 genes (SH3GL2, ATP4B, CTSE, and SORBS2), 7 genes (SLC7A8, RNASE4, ESRRG, PGC, MUC6, Fam3B, and FMO5), and 6 genes (CHGA, PDK4, TMPRSS2, CLIC6, GPX3, and PSCA), respectively. Finally, we constructed a miRNA-mRNA-TF regulatory network based on the above 17 mRNAs, 3 miRNAs, and 1 TF and verified by RT-qPCR and western blot results that the expression of RFX6 was downregulated in GC tissues. These identified miRNAs, mRNAs, and TF have a certain reference value for further exploration of the regulatory mechanism of GC.
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Jung S, Ye BD, Lee HS, Baek J, Kim G, Park D, Park SH, Yang SK, Han B, Liu J, Song K. Identification of Three Novel Susceptibility Loci for Inflammatory Bowel Disease in Koreans in an Extended Genome-Wide Association Study. J Crohns Colitis 2021; 15:1898-1907. [PMID: 33853113 DOI: 10.1093/ecco-jcc/jjab060] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Genome-wide association studies [GWAS] of inflammatory bowel disease [IBD] in multiple populations have identified over 240 susceptibility loci. We previously performed a largest-to-date Asian-specific IBD GWAS to identify two new IBD risk loci and confirm associations with 28 established loci. To identify additional susceptibility loci in Asians, we expanded our previous study design by doubling the case size with an additional dataset of 1726 cases and 378 controls. METHODS An inverse-variance fixed-effects meta-analysis was performed between the previous and the new GWAS dataset, comprising a total of 3195 cases and 4419 controls, followed by replication in an additional 1088 cases and 845 controls. RESULTS The meta-analysis of Korean GWAS identified one novel locus for ulcerative colitis at rs76227733 on 10q24 [pcombined = 6.56 × 10-9] and two novel loci for Crohn's disease [CD] at rs2240751 on 19p13 [pcombined = 3.03 × 10-8] and rs6936629 on 6q22 [pcombined = 3.63 × 10-8]. Pathway-based analysis of GWAS data using MAGMA showed that the MHC and antigenic stimulus-related pathways were more significant in Korean CD, whereas cytokine and transcription factor-related pathways were more significant in European CD. Phenotype variance explained by the polygenic risk scores derived from Korean data explained up to 14% of the variance of CD whereas those derived from European data explained 10%, emphasizing the need for large-scale genetic studies in this population. CONCLUSIONS The identification of novel loci not previously associated with IBD suggests the importance of studying IBD genetics in diverse populations.
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Affiliation(s)
- Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Gyeonghoon Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Dohoon Park
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Jianjun Liu
- Human Genetics Group, Genome Institute of Singapore, Singapore
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
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18
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Coronel L, Riege K, Schwab K, Förste S, Häckes D, Semerau L, Bernhart SH, Siebert R, Hoffmann S, Fischer M. Transcription factor RFX7 governs a tumor suppressor network in response to p53 and stress. Nucleic Acids Res 2021; 49:7437-7456. [PMID: 34197623 PMCID: PMC8287911 DOI: 10.1093/nar/gkab575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/25/2021] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
Despite its prominence, the mechanisms through which the tumor suppressor p53 regulates most genes remain unclear. Recently, the regulatory factor X 7 (RFX7) emerged as a suppressor of lymphoid neoplasms, but its regulation and target genes mediating tumor suppression remain unknown. Here, we identify a novel p53-RFX7 signaling axis. Integrative analysis of the RFX7 DNA binding landscape and the RFX7-regulated transcriptome in three distinct cell systems reveals that RFX7 directly controls multiple established tumor suppressors, including PDCD4, PIK3IP1, MXD4, and PNRC1, across cell types and is the missing link for their activation in response to p53 and stress. RFX7 target gene expression correlates with cell differentiation and better prognosis in numerous cancer types. Interestingly, we find that RFX7 sensitizes cells to Doxorubicin by promoting apoptosis. Together, our work establishes RFX7’s role as a ubiquitous regulator of cell growth and fate determination and a key node in the p53 transcriptional program.
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Affiliation(s)
- Luis Coronel
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Katjana Schwab
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Silke Förste
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - David Häckes
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Lena Semerau
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
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19
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Issac J, Raveendran PS, Das AV. RFX1: a promising therapeutic arsenal against cancer. Cancer Cell Int 2021; 21:253. [PMID: 33964962 PMCID: PMC8106159 DOI: 10.1186/s12935-021-01952-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 04/26/2021] [Indexed: 02/08/2023] Open
Abstract
Regulatory factor X1 (RFX1) is an evolutionary conserved transcriptional factor that influences a wide range of cellular processes such as cell cycle, cell proliferation, differentiation, and apoptosis, by regulating a number of target genes that are involved in such processes. On a closer look, these target genes also play a key role in tumorigenesis and associated events. Such observations paved the way for further studies evaluating the role of RFX1 in cancer. These studies were indispensable due to the failure of conventional chemotherapeutic drugs to target key cellular hallmarks such as cancer stemness, cellular plasticity, enhanced drug efflux, de-regulated DNA repair machinery, and altered pathways evading apoptosis. In this review, we compile significant evidence for the tumor-suppressive activities of RFX1 while also analyzing its oncogenic potential in some cancers. RFX1 induction decreased cellular proliferation, modulated the immune system, induced apoptosis, reduced chemoresistance, and sensitized cancer stem cells for chemotherapy. Thus, our review discusses the pleiotropic function of RFX1 in multitudinous gene regulations, decisive protein–protein interactions, and also its role in regulating key cell signaling events in cancer. Elucidation of these regulatory mechanisms can be further utilized for RFX1 targeted therapy.
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Affiliation(s)
- Joby Issac
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud.P.O, Thiruvananthapuram, 695014, Kerala, India
| | - Pooja S Raveendran
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud.P.O, Thiruvananthapuram, 695014, Kerala, India
| | - Ani V Das
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud.P.O, Thiruvananthapuram, 695014, Kerala, India.
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20
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Sanchez Caballero L, Gorgogietas V, Arroyo MN, Igoillo-Esteve M. Molecular mechanisms of β-cell dysfunction and death in monogenic forms of diabetes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 359:139-256. [PMID: 33832649 DOI: 10.1016/bs.ircmb.2021.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Monogenetic forms of diabetes represent 1%-5% of all diabetes cases and are caused by mutations in a single gene. These mutations, that affect genes involved in pancreatic β-cell development, function and survival, or insulin regulation, may be dominant or recessive, inherited or de novo. Most patients with monogenic diabetes are very commonly misdiagnosed as having type 1 or type 2 diabetes. The severity of their symptoms depends on the nature of the mutation, the function of the affected gene and, in some cases, the influence of additional genetic or environmental factors that modulate severity and penetrance. In some patients, diabetes is accompanied by other syndromic features such as deafness, blindness, microcephaly, liver and intestinal defects, among others. The age of diabetes onset may also vary from neonatal until early adulthood manifestations. Since the different mutations result in diverse clinical presentations, patients usually need different treatments that range from just diet and exercise, to the requirement of exogenous insulin or other hypoglycemic drugs, e.g., sulfonylureas or glucagon-like peptide 1 analogs to control their glycemia. As a consequence, awareness and correct diagnosis are crucial for the proper management and treatment of monogenic diabetes patients. In this chapter, we describe mutations causing different monogenic forms of diabetes associated with inadequate pancreas development or impaired β-cell function and survival, and discuss the molecular mechanisms involved in β-cell demise.
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Affiliation(s)
- Laura Sanchez Caballero
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/
| | - Vyron Gorgogietas
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/
| | - Maria Nicol Arroyo
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/
| | - Mariana Igoillo-Esteve
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/.
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21
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Chinniah R, Sevak V, Pandi S, Ravi PM, Vijayan M, Kannan A, Karuppiah B. HLA-DRB1 genes and the expression dynamics of HLA CIITA determine the susceptibility to T2DM. Immunogenetics 2021; 73:291-305. [PMID: 33754173 DOI: 10.1007/s00251-021-01212-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/01/2021] [Indexed: 12/18/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is a disease with polygenic inheritance. The expression of major histocompatibility complex class II genes are regulated by several trans-activators. We have studied the expression of HLA-DRB1, RFX, CIITA-P1, PIV transactivators, immunophenotyping of cells, SNPs in CIITA-168 (A/G) and IFN-γ + 874 (T/A) in T2DM patients and controls (n = 201 each). We observed increased frequencies of DRB1*03, DRB1*04 and DRB1*07 and decreased frequencies of DRB1*10, DRB1*14, and DRB1*15 alleles among patients. Significant up-regulations of HLA-DRB1 genes were observed in patients (p < 0.0001). Down-regulated expressions were documented in DRB1*03-homo (p < 0.002) and DRB1*04-homo (p < 0.009) patients. No significant differences were observed for CIITA-P1 expression except DRB1*04-pooled (p < 0.0113). The CIITA-PIV was up-regulated in overall (p < 0.0001), DRB1*03-pooled (p < 0.0006), DRB1*03-hetero (p < 0.0006) and DRB1*03-homo (p < 0.001) T2DM patients. However, significant down-regulations were documented for DRB1*04-pooled (p < 0.040), DRB1*04-hetero (p < 0.060), and DRB1*04-homo (p < 0.027) combinations. Further, significant down-regulations of RFX5 were observed in overall (p < 0.0006), DRB1*04-pooled (p < 0.0022), and DRB1*04-hetero (p < 0.0004) combinations. Immunophenotyping studies revealed significant increase of CD45+ CD14-, CD19+, CD14- and CD8 cells and elevated level of expression of IFN-γ (p < 0.0001) in patients. A significant increase of TT (p < 3.35 × 10-6) and decrease of TA (p < 4.57 × 10-4) genotypes of IFN-γ + 874 (T/A) and an increase of GG (p < 0.001) and decrease of AG (p < 8.24 × 10-5) genotypes of CIITA-168 A/G SNPs were observed. The combinatorial analysis revealed susceptible associations for DRB1*03 + AA, *03 + AG, *03 + GG and *04 + GG and protective associations for DRB1*10 + AG, *10 + GG, *15 + AG, and *14 + GG combinations. Thus, the present study corroborated the effect of differential expressions of promoters of risk alleles in the pathogenesis of T2DM.
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Affiliation(s)
- Rathika Chinniah
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu, 625021, India
| | - Vandit Sevak
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu, 625021, India
| | - Sasiharan Pandi
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu, 625021, India
| | - Padma Malini Ravi
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu, 625021, India
| | - Murali Vijayan
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Arun Kannan
- The Madurai Institute of Diabetes and Endocrine Practice Research, Madurai, Tamil Nadu, 625 001, India
| | - Balakrishnan Karuppiah
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu, 625021, India.
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Lee J, Park JE, Lee C, Kim AR, Kim BJ, Park WY, Ki CS, Lee J. Genomic Analysis of Korean Patient With Microcephaly. Front Genet 2021; 11:543528. [PMID: 33584783 PMCID: PMC7876370 DOI: 10.3389/fgene.2020.543528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022] Open
Abstract
Microcephaly is a prevalent phenotype in patients with neurodevelopmental problems, often with genetic causes. We comprehensively investigated the clinical phenotypes and genetic background of microcephaly in 40 Korean patients. We analyzed their clinical phenotypes and radiologic images and conducted whole exome sequencing (WES) and analysis of copy number variation (CNV). Infantile hypotonia and developmental delay were present in all patients. Thirty-four patients (85%) showed primary microcephaly. The diagnostic yield from the WES and CNV analyses was 47.5%. With WES, we detected pathogenic or likely pathogenic variants that were previously associated with microcephaly in 12 patients (30%); nine of these were de novo variants with autosomal dominant inheritance. Two unrelated patients had mutations in the KMT2A gene. In 10 other patients, we found mutations in the GNB1, GNAO1, TCF4, ASXL1, SMC1A, VPS13B, ACTG1, EP300, and KMT2D genes. Seven patients (17.5%) were diagnosed with pathogenic CNVs. Korean patients with microcephaly show a genetic spectrum that is different from that of patients with microcephaly of other ethnicities. WES along with CNV analysis represents an effective approach for diagnosis of the underlying causes of microcephaly.
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Affiliation(s)
- Jiwon Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jong Eun Park
- Department of Laboratory Medicine and Genetics, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Chung Lee
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ah Reum Kim
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Joon Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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23
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Hou T, Ye L, Wu S. Knockdown of LINC00504 Inhibits the Proliferation and Invasion of Breast Cancer via the Downregulation of miR-140-5p. Onco Targets Ther 2021; 14:3991-4003. [PMID: 34239305 PMCID: PMC8259944 DOI: 10.2147/ott.s294965] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/12/2021] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Breast cancer is one of the most common cancers in the world. Long noncoding RNA 00504 (LINC00504) was reported to be a functional gene in some tumours but not breast. Accordingly, the purpose of this article is to study the function of LINC00504 in breast cancer. METHODS qPCR assay was used to detect the expression of LINC00504 in tissue and cell lines. The online database and chromatin immunoprecipitation assay (ChIP) were employed to confirm the transcription factor of LINC00504. Cell function assays including cell proliferation, migration and invasion were designed to detect the function of LINC00504 in vitro and in vivo. Luciferase reporter assay and RNA immunoprecipitation (RIP) assay were used to confirm the relationship between LINC00504 and miR-140-5p. And Western blot assay was employed for testing the key protein. RESULTS We found that LINC00504 is upregulated in breast cancer. In addition, we found that the transcription factor regulatory factor X5 (RFX5) can strongly bind to the LINC00504 promoter region and subsequently increase its transcriptional activity. We also found that the manipulation of RFX5 expression can significantly affect LINC00504 expression, which suggested that RFX5 can transcriptionally activate LINC00504 in breast cancer (BC). Knockdown of LINC00504 inhibits cell proliferation, migration and invasion in vitro and in vivo. We further found that LINCOO504 inhibits miR-140-5p, which decreases the levels of VEGFA. The further results showed that miR-140-5p was one of the target gene of LINC00504. The WB assay demonstrated that the E-cadherin was increased and Vimentin was decreased when knocking down of LINC00504 and they can be rescued while adding the inhibitors of miR-140-5p. DISCUSSION Our results demonstrated the mechanism by which the LINC00504-miR-140-5p-VEGFA axis participates in breast cancer cell proliferation and invasion and may lead to new lncRNA-based diagnostic or therapeutic strategies for breast cancer.
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Affiliation(s)
- Tieying Hou
- Ph.D. Program of Immunology, Shantou University Medical College, Shantou, Guangdong Province, 515041, People’s Republic of China
- Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510000, People’s Republic of China
| | - Long Ye
- Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510000, People’s Republic of China
| | - Shulin Wu
- Ph.D. Program of Immunology, Shantou University Medical College, Shantou, Guangdong Province, 515041, People’s Republic of China
- Correspondence: Shulin Wu Ph.D. Program of Immunology, Shantou University Medical College, No. 22 Xinling Road, Shantou, Guangdong Province, 515041, People’s Republic of ChinaTel +86-754-88550917Fax +86-754-88550917 Email
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24
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Trott J, Alpagu Y, Tan EK, Shboul M, Dawood Y, Elsy M, Wollmann H, Tano V, Bonnard C, Eng S, Narayanan G, Junnarkar S, Wearne S, Strutt J, Kumar A, Tomaz LB, Goy PA, Mzoughi S, Jennings R, Hagoort J, Eskin A, Lee H, Nelson SF, Al-Kazaleh F, El-Khateeb M, Fathallah R, Shah H, Goeke J, Langley SR, Guccione E, Hanley N, De Bakker BS, Reversade B, Dunn NR. Mitchell-Riley syndrome iPSCs exhibit reduced pancreatic endoderm differentiation due to a mutation in RFX6. Development 2020; 147:dev194878. [PMID: 33033118 DOI: 10.1242/dev.194878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022]
Abstract
Mitchell-Riley syndrome (MRS) is caused by recessive mutations in the regulatory factor X6 gene (RFX6) and is characterised by pancreatic hypoplasia and neonatal diabetes. To determine why individuals with MRS specifically lack pancreatic endocrine cells, we micro-CT imaged a 12-week-old foetus homozygous for the nonsense mutation RFX6 c.1129C>T, which revealed loss of the pancreas body and tail. From this foetus, we derived iPSCs and show that differentiation of these cells in vitro proceeds normally until generation of pancreatic endoderm, which is significantly reduced. We additionally generated an RFX6HA reporter allele by gene targeting in wild-type H9 cells to precisely define RFX6 expression and in parallel performed in situ hybridisation for RFX6 in the dorsal pancreatic bud of a Carnegie stage 14 human embryo. Both in vitro and in vivo, we find that RFX6 specifically labels a subset of PDX1-expressing pancreatic endoderm. In summary, RFX6 is essential for efficient differentiation of pancreatic endoderm, and its absence in individuals with MRS specifically impairs formation of endocrine cells of the pancreas head and tail.
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Affiliation(s)
- Jamie Trott
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Yunus Alpagu
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Ee Kim Tan
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Mohammad Shboul
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 2210, Jordan
| | - Yousif Dawood
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Department of Obstetrics and Gynaecology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Michael Elsy
- Faculty of Biology, Medicine & Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Heike Wollmann
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Vincent Tano
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Carine Bonnard
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Shermaine Eng
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Gunaseelan Narayanan
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Seetanshu Junnarkar
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Stephen Wearne
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - James Strutt
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Aakash Kumar
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Lucian B Tomaz
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Pierre-Alexis Goy
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Slim Mzoughi
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Rachel Jennings
- Faculty of Biology, Medicine & Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Endocrinology Department, Manchester University NHS Foundation Trust, Grafton Street, Manchester M13 9WU, UK
| | - Jaco Hagoort
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Ascia Eskin
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Hane Lee
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Department of Pediatrics, UCLA Mattel Children's Hospital, Los Angeles, CA 90095, USA
| | - Fawaz Al-Kazaleh
- Department of Obstetrics and Gynecology, University of Jordan, Amman 19241, Jordan
| | - Mohammad El-Khateeb
- National Center for Diabetes, Endocrinology and Genetics, Amman 19241, Jordan
| | - Rajaa Fathallah
- National Center for Diabetes, Endocrinology and Genetics, Amman 19241, Jordan
| | - Harsha Shah
- Department of Obstetrics and Gynaecology, Queen Charlotte's & Chelsea Hospital, Imperial College London, Du Cane Road, London W12 0HS, UK
| | - Jonathan Goeke
- Genome Institute of Singapore, Agency for Science Technology and Research (A*STAR), 60 Biopolis Street, 138672, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Ernesto Guccione
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Neil Hanley
- Faculty of Biology, Medicine & Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Endocrinology Department, Manchester University NHS Foundation Trust, Grafton Street, Manchester M13 9WU, UK
| | - Bernadette S De Bakker
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bruno Reversade
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
- Department of Paediatrics, National University of Singapore, Yong Loo Lin School of Medicine, 1E Kent Ridge Road, NUHS Tower Block, Level 12, 119228, Singapore
- Koç University School of Medicine, Medical Genetics Department, Istanbul 34450, Turkey
| | - N Ray Dunn
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
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25
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Identifying Cattle Breed-Specific Partner Choice of Transcription Factors during the African Trypanosomiasis Disease Progression Using Bioinformatics Analysis. Vaccines (Basel) 2020; 8:vaccines8020246. [PMID: 32456126 PMCID: PMC7350023 DOI: 10.3390/vaccines8020246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 12/18/2022] Open
Abstract
African Animal Trypanosomiasis (AAT) is a disease caused by pathogenic trypanosomes which affects millions of livestock every year causing huge economic losses in agricultural production especially in sub-Saharan Africa. The disease is spread by the tsetse fly which carries the parasite in its saliva. During the disease progression, the cattle are prominently subjected to anaemia, weight loss, intermittent fever, chills, neuronal degeneration, congestive heart failure, and finally death. According to their different genetic programs governing the level of tolerance to AAT, cattle breeds are classified as either resistant or susceptible. In this study, we focus on the cattle breeds N’Dama and Boran which are known to be resistant and susceptible to trypanosomiasis, respectively. Despite the rich literature on both breeds, the gene regulatory mechanisms of the underlying biological processes for their resistance and susceptibility have not been extensively studied. To address the limited knowledge about the tissue-specific transcription factor (TF) cooperations associated with trypanosomiasis, we investigated gene expression data from these cattle breeds computationally. Consequently, we identified significant cooperative TF pairs (especially DBP−PPARA and DBP−THAP1 in N’Dama and DBP−PAX8 in Boran liver tissue) which could help understand the underlying AAT tolerance/susceptibility mechanism in both cattle breeds.
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Gao J, Xu C. Structural basis for the recognition of RFX7 by ANKRA2 and RFXANK. Biochem Biophys Res Commun 2020; 523:263-266. [DOI: 10.1016/j.bbrc.2019.12.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 10/25/2022]
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Umeda S, Kanda M, Kodera Y. Recent advances in molecular biomarkers for patients with hepatocellular carcinoma. Expert Rev Mol Diagn 2019; 19:725-738. [PMID: 31248309 DOI: 10.1080/14737159.2019.1638254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Hepatocellular carcinoma (HCC) is a leading cause of cancer death worldwide and recurrence rate after curative resection remains high. To improve HCC prognosis, novel sensitive biomarkers and targeted molecular therapies are needed. Accumulation of multiple genetic aberrations caused by pathologically derived liver damage results in HCC carcinogenesis. Elucidating the genes associated with tumorigenesis and progression of HCC may lead to the development of early detection and prognosis markers and to the identification of therapeutic targets. Areas covered: We review recently reported (January 2017-March 2019) HCC-associated molecules, including protein-coding genes, microRNAs, long non-coding RNAs, and methylated gene promoters. Expert opinion: The molecules reviewed have the potential to be clinical biomarkers and therapeutic targets for HCC. The accumulation and understanding of genetic and epigenetic data are essential to improve the management of HCC patients.
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Affiliation(s)
- Shinichi Umeda
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Mitsuro Kanda
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine , Nagoya , Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine , Nagoya , Japan
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López C, Kleinheinz K, Aukema SM, Rohde M, Bernhart SH, Hübschmann D, Wagener R, Toprak UH, Raimondi F, Kreuz M, Waszak SM, Huang Z, Sieverling L, Paramasivam N, Seufert J, Sungalee S, Russell RB, Bausinger J, Kretzmer H, Ammerpohl O, Bergmann AK, Binder H, Borkhardt A, Brors B, Claviez A, Doose G, Feuerbach L, Haake A, Hansmann ML, Hoell J, Hummel M, Korbel JO, Lawerenz C, Lenze D, Radlwimmer B, Richter J, Rosenstiel P, Rosenwald A, Schilhabel MB, Stein H, Stilgenbauer S, Stadler PF, Szczepanowski M, Weniger MA, Zapatka M, Eils R, Lichter P, Loeffler M, Möller P, Trümper L, Klapper W, Hoffmann S, Küppers R, Burkhardt B, Schlesner M, Siebert R. Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma. Nat Commun 2019; 10:1459. [PMID: 30926794 PMCID: PMC6440956 DOI: 10.1038/s41467-019-08578-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/18/2019] [Indexed: 12/17/2022] Open
Abstract
Burkitt lymphoma (BL) is the most common B-cell lymphoma in children. Within the International Cancer Genome Consortium (ICGC), we performed whole genome and transcriptome sequencing of 39 sporadic BL. Here, we unravel interaction of structural, mutational, and transcriptional changes, which contribute to MYC oncogene dysregulation together with the pathognomonic IG-MYC translocation. Moreover, by mapping IGH translocation breakpoints, we provide evidence that the precursor of at least a subset of BL is a B-cell poised to express IGHA. We describe the landscape of mutations, structural variants, and mutational processes, and identified a series of driver genes in the pathogenesis of BL, which can be targeted by various mechanisms, including IG-non MYC translocations, germline and somatic mutations, fusion transcripts, and alternative splicing. Burkitt lymphoma (BL) is the most common pediatric B-cell lymphoma. Here, within the International Cancer Genome Consortium, the authors performed whole genome and transcriptome sequencing of 39 sporadic BL, describing the landscape of mutations, structural variants, and mutational processes that underpin this disease how alterations on different cellular levels cooperate in deregulating key pathways and complexes.
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Affiliation(s)
- Cristina López
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, 69120, Heidelberg, Germany
| | - Sietse M Aukema
- Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany.,Hematopathology Section, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Marius Rohde
- Pediatric Hematology and Oncology, University Hospital Giessen, 35392, Giessen, Germany
| | - Stephan H Bernhart
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany.,Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany.,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, 04107, Leipzig, Germany
| | - Daniel Hübschmann
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Pediatric Immunology, Hematology and Oncology, University Hospital, 69120, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Division of Stem Cells and Cancer, Heidelberg, Germany and Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Umut H Toprak
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Francesco Raimondi
- Cell Networks, Bioquant and Biochemistry CenterBiochemie Zentrum Heidelberg (BZH), University of Heidelberg, 69120, Heidelberg, Germany
| | - Markus Kreuz
- Institute for Medical Informatics Statistics and Epidemiology, 04107, Leipzig, Germany
| | | | - Zhiqin Huang
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Lina Sieverling
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany.,Division of Applied Bioinformatics (G200), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Medical Faculty Heidelberg, Heidelberg University, 69120, Heidelber, Germany
| | - Julian Seufert
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | | | - Robert B Russell
- Cell Networks, Bioquant and Biochemistry CenterBiochemie Zentrum Heidelberg (BZH), University of Heidelberg, 69120, Heidelberg, Germany
| | - Julia Bausinger
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Helene Kretzmer
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany.,Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany.,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, 04107, Leipzig, Germany.,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anke K Bergmann
- Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany.,Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Hans Binder
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany.,Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany
| | - Arndt Borkhardt
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics (G200), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Alexander Claviez
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Gero Doose
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany.,Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany.,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, 04107, Leipzig, Germany
| | - Lars Feuerbach
- Division of Applied Bioinformatics (G200), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Andrea Haake
- Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Martin-Leo Hansmann
- Senckenberg Institute of Pathology, University of Frankfurt Medical School, 60590, Frankfurt am Main, Germany
| | - Jessica Hoell
- Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Michael Hummel
- Institute of Pathology, Charité - University Medicine Berlin, 10117, Berlin, Germany
| | - Jan O Korbel
- Genome Biology Unit, EMBL Heidelberg, 69117, Heidelberg, Germany
| | - Chris Lawerenz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Dido Lenze
- Institute of Pathology, Charité - University Medicine Berlin, 10117, Berlin, Germany
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Julia Richter
- Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany.,Hematopathology Section, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Andreas Rosenwald
- Institute of Pathology, Comprehensive Cancer Center Mainfranken, University of Würzburg, 97080, Würzburg, Germany
| | - Markus B Schilhabel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | | | | | - Peter F Stadler
- Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany
| | | | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, 45147, Essen, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, 69120, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Markus Loeffler
- Institute for Medical Informatics Statistics and Epidemiology, 04107, Leipzig, Germany
| | - Peter Möller
- Institute of Pathology, University of Ulm and University Hospital of Ulm, 89081, Ulm, Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August-University of Göttingen, 37075, Göttingen, Germany
| | - Wolfram Klapper
- Hematopathology Section, Christian-Albrechts-University, 24105, Kiel, Germany
| | | | - Steve Hoffmann
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany.,Bioinformatics Group, Department of Computer, University of Leipzig, 04107, Leipzig, Germany.,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, 04107, Leipzig, Germany.,Computational Biology, Leibniz Institute on Ageing-Fritz Lipmann Institut (FLI), 07745, Jena, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, 45147, Essen, Germany
| | - Birgit Burkhardt
- University Hospital Münster - Pediatric Hematology and Oncology, 48149, Münster, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. .,Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany. .,Institute of Human Genetics, Christian-Albrechts-University, 24105, Kiel, Germany.
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Mahmoud IS, Homsi A, Al-Ameer HJ, Alzyoud J, Darras M, Shhab MA, Zihlif M, Hatmal MM, Alshaer W. Screening the RFX6-DNA binding domain for potential genetic variants in patients with type 2 diabetes. World J Diabetes 2019; 10:181-188. [PMID: 30891153 PMCID: PMC6422854 DOI: 10.4239/wjd.v10.i3.181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The regulatory factor X6 (RFX6), a member of regulatory factor X family, is known to play a key role in the development and differentiation of pancreatic beta cells as well as insulin production and secretion. However, the potential role of RFX6 in type 2 diabetes (T2D) is still unclear.
AIM Recent studies have indicated that RFX6 binding to DNA could be disrupted in diabetes. Therefore, in this study we investigated whether genetic mutations are present in the DNA binding domain of RFX6 gene that could abrogate its function in T2D.
METHODS A cohort of T2D patients was enrolled in this study, and the gene encoding the DNA binding domain of RFX6 was amplified by polymerase chain reaction and then analysed by direct DNA sequencing.
RESULTS The DNA sequence analysis revealed the absence of any exonic mutation. However, we have identified a new heterozygous single nucleotide polymorphism (IVS6+31 C>T) in the intronic region of DNA binding domain gene that is present in 9.2% and 8.5% of diabetic and control people, respectively (P = 0.97).
CONCLUSION We report the absence of any significant genetic variant that could affect the function of RFX6-DNA binding domain in T2D.
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Affiliation(s)
- Ismail S Mahmoud
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, The Hashemite University, Zarqa 13133, Jordan
| | - Ayat Homsi
- Cell Therapy Centre, The University of Jordan, Amman 11942, Jordan
| | - Hamzeh J Al-Ameer
- Department of Pharmacology, Faculty of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Jihad Alzyoud
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, The Hashemite University, Zarqa 13133, Jordan
| | - Mais Darras
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, The Hashemite University, Zarqa 13133, Jordan
| | - Mohammad Al Shhab
- Department of Pharmacology, Faculty of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Malek Zihlif
- Department of Pharmacology, Faculty of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Ma’mon M Hatmal
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, The Hashemite University, Zarqa 13133, Jordan
| | - Walhan Alshaer
- Cell Therapy Centre, The University of Jordan, Amman 11942, Jordan
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30
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Du P, Gao K, Cao Y, Yang S, Wang Y, Guo R, Zhao M, Jia S. RFX1 downregulation contributes to TLR4 overexpression in CD14 + monocytes via epigenetic mechanisms in coronary artery disease. Clin Epigenetics 2019; 11:44. [PMID: 30857550 PMCID: PMC6413463 DOI: 10.1186/s13148-019-0646-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/01/2019] [Indexed: 02/07/2023] Open
Abstract
Background Toll-like receptor 4 (TLR4) expression is increased in activated monocytes, which play a critical role in the pathogenesis of coronary artery disease (CAD). However, the mechanism remains unclear. Regulatory factor X1 (RFX1) is a critical transcription factor regulating epigenetic modifications. In this study, we investigated whether RFX1 and epigenetic modifications mediated by RFX1 contributed to the overexpression of TLR4 in activated monocytes. Results Compared with those of the controls, the mRNA and protein expression of RFX1 were downregulated and the mRNA expression of TLR4 was upregulated in CD14+ monocytes obtained from CAD patients and CD14+ monocytes obtained from healthy controls treated with low-density lipoprotein (LDL). The mRNA expression of RFX1 was negatively correlated with the mRNA expression of TLR4 in CD14+ monocytes. RFX1 knockdown led to the overexpression of TLR4 and the activation of CD14+ monocytes. In contrast, the overexpression of RFX1 inhibited TLR4 expression and the activation of CD14+ monocytes stimulated with LDL. Moreover, TLR4 was identified as a target gene of RFX1. The results indicated that RFX1 downregulation contributed to the decreased DNA methylation and histone H3 lysine 9 trimethylation and the increased H3 and H4 acetylation in the TLR4 promoter via the lack of recruitments of DNA methyltransferase 1 (DNMT1), histone deacetylase 1 (HDAC1), and histone-lysine N-methyltransferase SUV39H1 (SUV39H1), which were observed in CD14+ monocytes of CAD patients. Conclusions Our results show that RFX1 expression deficiency leads to the overexpression of TLR4 and the activation of CD14+ monocytes in CAD patients by regulating DNA methylation and histone modifications, which highlights the vital role of RFX1 in the pathogenesis of CAD. Electronic supplementary material The online version of this article (10.1186/s13148-019-0646-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pei Du
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Keqin Gao
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Pharmacy, Weifang People's Hospital, Weifang, China
| | - Yu Cao
- Department of Cardiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Shuang Yang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yang Wang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ren Guo
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ming Zhao
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, China.
| | - Sujie Jia
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China. .,Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China.
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31
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Chen B, Niu J, Kreuzer J, Zheng B, Jarugumilli GK, Haas W, Wu X. Auto-fatty acylation of transcription factor RFX3 regulates ciliogenesis. Proc Natl Acad Sci U S A 2018; 115:E8403-E8412. [PMID: 30127002 PMCID: PMC6130365 DOI: 10.1073/pnas.1800949115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Defects in cilia have been associated with an expanding human disease spectrum known as ciliopathies. Regulatory Factor X 3 (RFX3) is one of the major transcription factors required for ciliogenesis and cilia functions. In addition, RFX3 regulates pancreatic islet cell differentiation and mature β-cell functions. However, how RFX3 protein is regulated at the posttranslational level remains poorly understood. Using chemical reporters of protein fatty acylation and mass spectrometry analysis, here we show that RFX3 transcriptional activity is regulated by S-fatty acylation at a highly conserved cysteine residue in the dimerization domain. Surprisingly, RFX3 undergoes enzyme-independent, "self-catalyzed" auto-fatty acylation and displays preferences for 18-carbon stearic acid and oleic acid. The fatty acylation-deficient mutant of RFX3 shows decreased homodimerization; fails to promote ciliary gene expression, ciliogenesis, and elongation; and impairs Hedgehog signaling. Our findings reveal a regulation of RFX3 transcription factor and link fatty acid metabolism and protein lipidation to the regulation of ciliogenesis.
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Affiliation(s)
- Baoen Chen
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Jixiao Niu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Johannes Kreuzer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129
- Department of Medicine, Harvard Medical School, Charlestown, MA 02129
| | - Baohui Zheng
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Gopala K Jarugumilli
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129
- Department of Medicine, Harvard Medical School, Charlestown, MA 02129
| | - Xu Wu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129;
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Castro W, Chelbi ST, Niogret C, Ramon-Barros C, Welten SPM, Osterheld K, Wang H, Rota G, Morgado L, Vivier E, Raeber ME, Boyman O, Delorenzi M, Barras D, Ho PC, Oxenius A, Guarda G. The transcription factor Rfx7 limits metabolism of NK cells and promotes their maintenance and immunity. Nat Immunol 2018; 19:809-820. [PMID: 29967452 DOI: 10.1038/s41590-018-0144-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 04/20/2018] [Indexed: 02/06/2023]
Abstract
Regulatory factor X 7 (Rfx7) is an uncharacterized transcription factor belonging to a family involved in ciliogenesis and immunity. Here, we found that deletion of Rfx7 leads to a decrease in natural killer (NK) cell maintenance and immunity in vivo. Genomic approaches showed that Rfx7 coordinated a transcriptional network controlling cell metabolism. Rfx7-/- NK lymphocytes presented increased size, granularity, proliferation, and energetic state, whereas genetic reduction of mTOR activity mitigated those defects. Notably, Rfx7-deficient NK lymphocytes were rescued by interleukin 15 through engagement of the Janus kinase (Jak) pathway, thus revealing the importance of this signaling for maintenance of such spontaneously activated NK cells. Rfx7 therefore emerges as a novel transcriptional regulator of NK cell homeostasis and metabolic quiescence.
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Affiliation(s)
- Wilson Castro
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Sonia T Chelbi
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland.,Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Charlène Niogret
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | | | | | - Kevin Osterheld
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Haiping Wang
- Ludwig Center for Cancer Research of the University of Lausanne, Epalinges, Switzerland.,Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland
| | - Giorgia Rota
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Leonor Morgado
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, Marseille, France.,Service d'Immunologie, Hôpital de la Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France.,Innate Pharma Research Labs., Innate Pharma, Marseille, France
| | - Miro E Raeber
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mauro Delorenzi
- Ludwig Center for Cancer Research of the University of Lausanne, Epalinges, Switzerland.,Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - David Barras
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Ping-Chih Ho
- Ludwig Center for Cancer Research of the University of Lausanne, Epalinges, Switzerland.,Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland
| | | | - Greta Guarda
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland. .,Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.
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Liu Y, Jiang P, Wang G, Liu X, Luo S. Downregulation of RFX1 predicts poor prognosis of patients with small hepatocellular carcinoma. Eur J Surg Oncol 2018; 44:1087-1093. [PMID: 29764705 DOI: 10.1016/j.ejso.2018.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/08/2018] [Accepted: 04/18/2018] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE Regulatory factor X1 (RFX1) deletion has been reported to be correlated with poor prognosis of some types of cancer. The present study aimed to investigate the prognostic value of RFX1 in HCC, especially in small hepatocellular carcinoma. METHODS Immunohistochemical assay was used to investigate RFX1 expression in 221 HCC tissues and another validation cohort of 71 small HCC samples. We also performed in vitro experiments to investigate if RFX1 regulated invasive capacity of HCC cells and expression of epithelial-mesenchymal transition (EMT) markers. RESULTS We found that RFX1 expression was significantly lower in HCC tissues compared to the corresponding non-tumor tissues. Further survival analysis suggested that the downregulation of RFX1 correlated with poor prognosis and a high recurrence risk in HCC patients, particularly in small HCC patients. Furthermore, another validation cohort of small HCC samples confirmed that downregulation of RFX1 in HCC tissues predicted high recurrence risk and poor prognosis for early stage HCC patients. In vitro studies suggested that knocking down RFX1 facilitated HCC cell invasion, while overexpression of RFX1 reduced the invasion of HCC cells. Western blot assays also indicated that RFX1 regulated expression of some EMT markers. Knocking down RFX1 decreased E-cadherin and increased vimentin expression, while RFX1 overexpression enhanced E-cadherin and decreased vimentin expression. CONCLUSIONS Our study demonstrated that RFX1 downregulation is a new predictive marker of high recurrence risk and poor prognosis of HCC; It has potential to help guide treatment for postoperative HCC patients, especially for small HCC patients.
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Affiliation(s)
- Yingjun Liu
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Peng Jiang
- Affiliated Tumor Hospital of Guangzhou Medical University, Guangzhou, China
| | - Gangcheng Wang
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Xiaonyong Liu
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Suxia Luo
- Department of Internal Medicine, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.
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34
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Chen YC, Tsai CL, Wei YH, Wu YT, Hsu WT, Lin HC, Hsu YC. ATOH1/RFX1/RFX3 transcription factors facilitate the differentiation and characterisation of inner ear hair cell-like cells from patient-specific induced pluripotent stem cells harbouring A8344G mutation of mitochondrial DNA. Cell Death Dis 2018; 9:437. [PMID: 29740017 PMCID: PMC5941227 DOI: 10.1038/s41419-018-0488-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 11/10/2022]
Abstract
Degeneration or loss of inner ear hair cells (HCs) is irreversible and results in sensorineural hearing loss (SHL). Human-induced pluripotent stem cells (hiPSCs) have been employed in disease modelling and cell therapy. Here, we propose a transcription factor (TF)-driven approach using ATOH1 and regulatory factor of x-box (RFX) genes to generate HC-like cells from hiPSCs. Our results suggest that ATOH1/RFX1/RFX3 could significantly increase the differentiation capacity of iPSCs into MYO7AmCherry-positive cells, upregulate the mRNA expression levels of HC-related genes and promote the differentiation of HCs with more mature stereociliary bundles. To model the molecular and stereociliary structural changes involved in HC dysfunction in SHL, we further used ATOH1/RFX1/RFX3 to differentiate HC-like cells from the iPSCs from patients with myoclonus epilepsy associated with ragged-red fibres (MERRF) syndrome, which is caused by A8344G mutation of mitochondrial DNA (mtDNA), and characterised by myoclonus epilepsy, ataxia and SHL. Compared with isogenic iPSCs, MERRF-iPSCs possessed ~42–44% mtDNA with A8344G mutation and exhibited significantly elevated reactive oxygen species (ROS) production and CAT gene expression. Furthermore, MERRF-iPSC-differentiated HC-like cells exhibited significantly elevated ROS levels and MnSOD and CAT gene expression. These MERRF-HCs that had more single cilia with a shorter length could be observed only by using a non-TF method, but those with fewer stereociliary bundle-like protrusions than isogenic iPSCs-differentiated-HC-like cells could be further observed using ATOH1/RFX1/RFX3 TFs. We further analysed and compared the whole transcriptome of M1ctrl-HCs and M1-HCs after treatment with ATOH1 or ATOH1/RFX1/RFX3. We revealed that the HC-related gene transcripts in M1ctrl-iPSCs had a significantly higher tendency to be activated by ATOH1/RFX1/RFX3 than M1-iPSCs. The ATOH1/RFX1/RFX3 TF-driven approach for the differentiation of HC-like cells from iPSCs is an efficient and promising strategy for the disease modelling of SHL and can be employed in future therapeutic strategies to treat SHL patients.
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Affiliation(s)
- Yen-Chun Chen
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Chia-Ling Tsai
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
| | - Yau-Huei Wei
- Center for Mitochondrial Medicine and Free Radical Research Changhua Christian Hospital, Changhua, Taiwan
| | - Yu-Ting Wu
- Center for Mitochondrial Medicine and Free Radical Research Changhua Christian Hospital, Changhua, Taiwan
| | - Wei-Ting Hsu
- Department of Audiology and Speech-Language Pathology, Mackay Medical College, New Taipei City, Taiwan
| | - Hung-Ching Lin
- Department of Audiology and Speech-Language Pathology, Mackay Medical College, New Taipei City, Taiwan.,Department of Otolaryngology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yi-Chao Hsu
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan.
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Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, Mathelier A, Lauter G, Misra S, Daub CO, Kere J, Swoboda P. Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC Genomics 2018; 19:181. [PMID: 29510665 PMCID: PMC5838959 DOI: 10.1186/s12864-018-4564-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1-8), their spatial and temporal expression profiles, potential upstream regulators and target genes. RESULTS We extracted all known human RFX1-8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology. RFX genes are broadly (RFX1-3, RFX5, RFX7) and specifically (RFX4, RFX6) expressed in different cell types, with high expression in four organ systems: immune system, gastrointestinal tract, reproductive system and nervous system. Tissue type specific expression profiles link defined RFX family members with the target gene batteries they regulate. We experimentally confirmed novel TSS locations and characterized the previously undescribed RFX8 to be lowly expressed. RFX tissue and cell type specificity arises mainly from differences in TSS architecture. RFX transcript isoforms lacking a DNA binding domain (DBD) open up new possibilities for combinatorial target gene regulation. Our results favor a new grouping of the RFX family based on protein domain composition. We uncovered and experimentally confirmed the TFs SP2 and ESR1 as upstream regulators of specific RFX genes. Using TF binding profiles from the JASPAR database, we determined relevant patterns of X-box motif positioning with respect to gene TSS locations of human RFX target genes. CONCLUSIONS The wealth of data we provide will serve as the basis for precisely determining the roles RFX TFs play in human development and disease.
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Affiliation(s)
| | - Morana Vitezic
- Department of Biology, Bioinformatics Centre, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark
| | - Eeva-Mari Jouhilahti
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, University of Oslo, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Sougat Misra
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King's College London, London, UK
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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De Stasio EA, Mueller KP, Bauer RJ, Hurlburt AJ, Bice SA, Scholtz SL, Phirke P, Sugiaman-Trapman D, Stinson LA, Olson HB, Vogel SL, Ek-Vazquez Z, Esemen Y, Korzynski J, Wolfe K, Arbuckle BN, Zhang H, Lombard-Knapp G, Piasecki BP, Swoboda P. An Expanded Role for the RFX Transcription Factor DAF-19, with Dual Functions in Ciliated and Nonciliated Neurons. Genetics 2018; 208:1083-1097. [PMID: 29301909 PMCID: PMC5844324 DOI: 10.1534/genetics.117.300571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/02/2017] [Indexed: 02/06/2023] Open
Abstract
Regulatory Factor X (RFX) transcription factors (TFs) are best known for activating genes required for ciliogenesis in both vertebrates and invertebrates. In humans, eight RFX TFs have a variety of tissue-specific functions, while in the worm Caenorhabditis elegans, the sole RFX gene, daf-19, encodes a set of nested isoforms. Null alleles of daf-19 confer pleiotropic effects including altered development with a dauer constitutive phenotype, complete absence of cilia and ciliary proteins, and defects in synaptic protein maintenance. We sought to identify RFX/daf-19 target genes associated with neuronal functions other than ciliogenesis using comparative transcriptome analyses at different life stages of the worm. Subsequent characterization of gene expression patterns revealed one set of genes activated in the presence of DAF-19 in ciliated sensory neurons, whose activation requires the daf-19c isoform, also required for ciliogenesis. A second set of genes is downregulated in the presence of DAF-19, primarily in nonsensory neurons. The human orthologs of some of these neuronal genes are associated with human diseases. We report the novel finding that daf-19a is directly or indirectly responsible for downregulation of these neuronal genes in C. elegans by characterizing a new mutation affecting the daf-19a isoform (tm5562) and not associated with ciliogenesis, but which confers synaptic and behavioral defects. Thus, we have identified a new regulatory role for RFX TFs in the nervous system. The new daf-19 candidate target genes we have identified by transcriptomics will serve to uncover the molecular underpinnings of the pleiotropic effects that daf-19 exerts on nervous system function.
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Affiliation(s)
| | | | - Rosemary J Bauer
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | | | - Sophie A Bice
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Sophie L Scholtz
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Prasad Phirke
- Department of Biosciences and Nutrition, Karolinska Institute, 141 83 Huddinge, Sweden
| | | | - Loraina A Stinson
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Haili B Olson
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Savannah L Vogel
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | | | - Yagmur Esemen
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Jessica Korzynski
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Kelsey Wolfe
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Bonnie N Arbuckle
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - He Zhang
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | | | - Brian P Piasecki
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, 141 83 Huddinge, Sweden
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Conditional ablation of the RFX4 isoform 1 transcription factor: Allele dosage effects on brain phenotype. PLoS One 2018; 13:e0190561. [PMID: 29298325 PMCID: PMC5752003 DOI: 10.1371/journal.pone.0190561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/21/2017] [Indexed: 11/25/2022] Open
Abstract
Regulatory factor X4 (RFX4) isoform 1 is a recently discovered isoform of the winged helix transcription factor RFX4, which can bind to X-box consensus sequences that are enriched in the promoters of cilia-related genes. Early insertional mutagenesis studies in mice first identified this isoform, and demonstrated that it was crucial for mouse brain development. RFX4 isoform 1 is the only RFX4 isoform significantly expressed in the mouse fetal and adult brain. In this study, we evaluated conditional knock-out (KO) mice in which one or two floxed alleles of Rfx4 were deleted early in development through the use of a Sox2-Cre transgene. Heterozygous deletion of Rfx4 resulted in severe, non-communicating congenital hydrocephalus associated with hypoplasia of the subcommissural organ. Homozygous deletion of Rfx4 resulted in formation of a single ventricle in the forebrain, and severe dorsoventral patterning defects in the telencephalon and midbrain at embryonic day 12.5, a collection of phenotypes that resembled human holoprosencephaly. No anatomical abnormalities were noted outside the brain in either case. At the molecular level, transcripts encoded by the cilia-related gene Foxj1 were significantly decreased, and Foxj1 was identified as a direct gene target of RFX4 isoform 1. The phenotypes were similar to those observed in the previous Rfx4 insertional mutagenesis studies. Thus, we provide a novel conditional KO animal model in which to investigate the downstream genes directly and/or indirectly regulated by RFX4 isoform 1. This model could provide new insights into the pathogenesis of obstructive hydrocephalus and holoprosencephaly in humans, both relatively common and disabling birth defects.
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Liao GY, Zhao S, Zhang T, Li CX, Liao LS, Zhang FF, Luo XM, Feng JX. The transcription factor TpRfx1 is an essential regulator of amylase and cellulase gene expression in Talaromyces pinophilus. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:276. [PMID: 30337955 PMCID: PMC6174557 DOI: 10.1186/s13068-018-1276-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/26/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Perfect and low cost of fungal amylolytic and cellulolytic enzymes are prerequisite for the industrialization of plant biomass biorefinergy to biofuels. Genetic engineering of fungal strains based on regulatory network of transcriptional factors (TFs) and their targets is an efficient strategy to achieve the above described aim. Talaromyces pinophilus produces integrative amylolytic and cellulolytic enzymes; however, the regulatory mechanism associated with the expression of amylase and cellulase genes in T. pinophilus remains unclear. In this study, we screened for and identified novel TFs regulating amylase and/or cellulase gene expression in T. pinophilus 1-95 through comparative transcriptomic and genetic analyses. RESULTS Comparative analysis of the transcriptomes from T. pinophilus 1-95 grown on media in the presence and absence of glucose or soluble starch as the sole carbon source screened 33 candidate TF-encoding genes that regulate amylase gene expression. Thirty of the 33 genes were successfully knocked out in the parental strain T. pinophilus ∆TpKu70, with seven of the deletion mutants firstly displaying significant changes in amylase production as compared with the parental strain. Among these, ∆TpRfx1 (TpRfx1: Talaromyces pinophilus Rfx1) showed the most significant decrease (81.5%) in amylase production, as well as a 57.7% reduction in filter paper cellulase production. Real-time quantitative reverse transcription PCR showed that TpRfx1 dynamically regulated the expression of major amylase and cellulase genes during cell growth, and in vitro electrophoretic mobility shift assay revealed that TpRfx1 bound the promoter regions of genes encoding α-amylase (TP04014/Amy13A), glucoamylase (TP09267/Amy15A), cellobiohydrolase (TP09412/cbh1), β-glucosidase (TP05820/bgl1), and endo-β-1,4-glucanase (TP08514/eg1). TpRfx1 protein containing a regulatory factor X (RFX) DNA-binding domain belongs to RFX family. CONCLUSION We identified a novel RFX protein TpRFX1 that directly regulates the expression of amylase and cellulase genes in T. pinophilus, which provides new insights into the regulatory mechanism of fungal amylase and cellulase gene expression.
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Affiliation(s)
- Gui-Yan Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Lu-Sheng Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Feng-Fei Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
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Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep 2017; 7:16196. [PMID: 29170422 PMCID: PMC5700937 DOI: 10.1038/s41598-017-16438-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022] Open
Abstract
Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.
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Exploring evidence of positive selection signatures in cattle breeds selected for different traits. Mamm Genome 2017; 28:528-541. [PMID: 28905131 DOI: 10.1007/s00335-017-9715-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 09/05/2017] [Indexed: 02/07/2023]
Abstract
Since domestication, the genome landscape of cattle has been changing due to natural and artificial selection forces resulting in several general and specialized cattle breeds of the world. Identifying genomic regions affected due to these forces in livestock gives an insight into the history of selection for economically important traits and genetic adaptation to specific environments of the populations under consideration. This study explores the genes/genomic regions under selection in relation to the phenotypes of Holstein, Hanwoo, and N'Dama cattle breeds using Tajima's D, XP-CLR, and XP-EHH population statistical methods. The whole genomes of 10 Holstein (South Korea), 11 Hanwoo (South Korea), and 10 N'Dama (West Africa-Guinea) cattle breeds re-sequenced to ~11x coverage and retained 37 million SNPs were used for the study. Selection signature analysis revealed 441, 512, and 461 genes under selection from Holstein, Hanwoo, and N'Dama cattle breeds, respectively. Among all these, seven genes including ARFGAP3, SNORA70, and other RNA genes were common between the breeds. From each of the gene lists, significant functional annotation cluster terms including milk protein and thyroid hormone signaling pathway (Holstein), histone acetyltransferase activity (Hanwoo), and renin secretion (N'Dama) were enriched. Genes that are related to the phenotypes of the respective breeds were also identified. Moreover, significant breed-specific missense variants were identified in CSN3, PAPPA2 (Holstein), C1orf116 (Hanwoo), and COMMD1 (N'Dama) genes. The genes identified from this study provide an insight into the biological mechanisms and pathways that are important in cattle breeds selected for different traits of economic significance.
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Kim D, Basile AO, Bang L, Horgusluoglu E, Lee S, Ritchie MD, Saykin AJ, Nho K. Knowledge-driven binning approach for rare variant association analysis: application to neuroimaging biomarkers in Alzheimer's disease. BMC Med Inform Decis Mak 2017; 17:61. [PMID: 28539126 PMCID: PMC5444041 DOI: 10.1186/s12911-017-0454-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Rapid advancement of next generation sequencing technologies such as whole genome sequencing (WGS) has facilitated the search for genetic factors that influence disease risk in the field of human genetics. To identify rare variants associated with human diseases or traits, an efficient genome-wide binning approach is needed. In this study we developed a novel biological knowledge-based binning approach for rare-variant association analysis and then applied the approach to structural neuroimaging endophenotypes related to late-onset Alzheimer’s disease (LOAD). Methods For rare-variant analysis, we used the knowledge-driven binning approach implemented in Bin-KAT, an automated tool, that provides 1) binning/collapsing methods for multi-level variant aggregation with a flexible, biologically informed binning strategy and 2) an option of performing unified collapsing and statistical rare variant analyses in one tool. A total of 750 non-Hispanic Caucasian participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort who had both WGS data and magnetic resonance imaging (MRI) scans were used in this study. Mean bilateral cortical thickness of the entorhinal cortex extracted from MRI scans was used as an AD-related neuroimaging endophenotype. SKAT was used for a genome-wide gene- and region-based association analysis of rare variants (MAF (minor allele frequency) < 0.05) and potential confounding factors (age, gender, years of education, intracranial volume (ICV) and MRI field strength) for entorhinal cortex thickness were used as covariates. Significant associations were determined using FDR adjustment for multiple comparisons. Results Our knowledge-driven binning approach identified 16 functional exonic rare variants in FANCC significantly associated with entorhinal cortex thickness (FDR-corrected p-value < 0.05). In addition, the approach identified 7 evolutionary conserved regions, which were mapped to FAF1, RFX7, LYPLAL1 and GOLGA3, significantly associated with entorhinal cortex thickness (FDR-corrected p-value < 0.05). In further analysis, the functional exonic rare variants in FANCC were also significantly associated with hippocampal volume and cerebrospinal fluid (CSF) Aβ1–42 (p-value < 0.05). Conclusions Our novel binning approach identified rare variants in FANCC as well as 7 evolutionary conserved regions significantly associated with a LOAD-related neuroimaging endophenotype. FANCC (fanconi anemia complementation group C) has been shown to modulate TLR and p38 MAPK-dependent expression of IL-1β in macrophages. Our results warrant further investigation in a larger independent cohort and demonstrate that the biological knowledge-driven binning approach is a powerful strategy to identify rare variants associated with AD and other complex disease.
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Affiliation(s)
- Dokyoon Kim
- Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA, USA.,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Anna O Basile
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Lisa Bang
- Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA, USA
| | - Emrin Horgusluoglu
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Seunggeun Lee
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Marylyn D Ritchie
- Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA, USA.,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA.
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Genetic regulatory signatures underlying islet gene expression and type 2 diabetes. Proc Natl Acad Sci U S A 2017; 114:2301-2306. [PMID: 28193859 DOI: 10.1073/pnas.1621192114] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified >100 independent SNPs that modulate the risk of type 2 diabetes (T2D) and related traits. However, the pathogenic mechanisms of most of these SNPs remain elusive. Here, we examined genomic, epigenomic, and transcriptomic profiles in human pancreatic islets to understand the links between genetic variation, chromatin landscape, and gene expression in the context of T2D. We first integrated genome and transcriptome variation across 112 islet samples to produce dense cis-expression quantitative trait loci (cis-eQTL) maps. Additional integration with chromatin-state maps for islets and other diverse tissue types revealed that cis-eQTLs for islet-specific genes are specifically and significantly enriched in islet stretch enhancers. High-resolution chromatin accessibility profiling using assay for transposase-accessible chromatin sequencing (ATAC-seq) in two islet samples enabled us to identify specific transcription factor (TF) footprints embedded in active regulatory elements, which are highly enriched for islet cis-eQTL. Aggregate allelic bias signatures in TF footprints enabled us de novo to reconstruct TF binding affinities genetically, which support the high-quality nature of the TF footprint predictions. Interestingly, we found that T2D GWAS loci were strikingly and specifically enriched in islet Regulatory Factor X (RFX) footprints. Remarkably, within and across independent loci, T2D risk alleles that overlap with RFX footprints uniformly disrupt the RFX motifs at high-information content positions. Together, these results suggest that common regulatory variations have shaped islet TF footprints and the transcriptome and that a confluent RFX regulatory grammar plays a significant role in the genetic component of T2D predisposition.
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Quigley IK, Kintner C. Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression. PLoS Genet 2017; 13:e1006538. [PMID: 28103240 PMCID: PMC5245798 DOI: 10.1371/journal.pgen.1006538] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/14/2016] [Indexed: 11/18/2022] Open
Abstract
Cooperative transcription factor binding at cis-regulatory sites in the genome drives robust eukaryotic gene expression, and many such sites must be coordinated to produce coherent transcriptional programs. The transcriptional program leading to motile cilia formation requires members of the DNA-binding forkhead (Fox) and Rfx transcription factor families and these factors co-localize to cilia gene promoters, but it is not clear how many cilia genes are regulated by these two factors, whether these factors act directly or indirectly, or how these factors act with specificity in the context of a 3-dimensional genome. Here, we use genome-wide approaches to show that cilia genes reside at the boundaries of topological domains and that these areas have low enhancer density. We show that the transcription factors Foxj1 and Rfx2 binding occurs in the promoters of more cilia genes than other known cilia transcription factors and that while Rfx2 binds directly to promoters and enhancers equally, Foxj1 prefers direct binding to enhancers and is stabilized at promoters by Rfx2. Finally, we show that Rfx2 and Foxj1 lie at the anchor endpoints of chromatin loops, suggesting that target genes are activated when Foxj1 bound at distal sites is recruited via a loop created by Rfx2 binding at both sites. We speculate that the primary function of Rfx2 is to stabilize distal enhancers with proximal promoters by operating as a scaffolding factor, bringing key regulatory domains bound by Foxj1 into close physical proximity and enabling coordinated cilia gene expression. The multiciliated cell extends hundreds of motile cilia to produce fluid flow in the airways and other organ systems. The formation of this specialized cell type requires the coordinated expression of hundreds of genes in order to produce all the protein parts motile cilia require. While a relatively small number of transcription factors has been identified that promote gene expression during multiciliate cell differentiation, it is not clear how they work together to coordinate the expression of genes required for multiple motile ciliation. Here, we show that two transcription factors known to drive cilia formation, Foxj1 and Rfx2, play complementary roles wherein Foxj1 activates target genes but tends not to bind near them in the genome, whereas Rfx2 can’t activate target genes by itself but instead acts as a scaffold by localizing Foxj1 to the proper targets. These results suggest not only a mechanism by which complex gene expression is coordinated in multiciliated cells, but also how transcriptional programs in general could be modular and deployed across different cellular contexts with the same basic promoter configuration.
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Affiliation(s)
- Ian K. Quigley
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies La Jolla, California, United States of America
- * E-mail:
| | - Chris Kintner
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies La Jolla, California, United States of America
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Pritchett EM, Lamont SJ, Schmidt CJ. Transcriptomic changes throughout post-hatch development in Gallus gallus pituitary. J Mol Endocrinol 2017; 58:43-55. [PMID: 27856505 PMCID: PMC5148799 DOI: 10.1530/jme-16-0186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 11/17/2016] [Indexed: 12/04/2022]
Abstract
The pituitary gland is a neuroendocrine organ that works closely with the hypothalamus to affect multiple processes within the body including the stress response, metabolism, growth and immune function. Relative tissue expression (rEx) is a transcriptome analysis method that compares the genes expressed in a particular tissue to the genes expressed in all other tissues with available data. Using rEx, the aim of this study was to identify genes that are uniquely or more abundantly expressed in the pituitary when compared to all other collected chicken tissues. We applied rEx to define genes enriched in the chicken pituitaries at days 21, 22 and 42 post-hatch. rEx analysis identified 25 genes shared between all time points, 295 genes shared between days 21 and 22 and 407 genes unique to day 42. The 25 genes shared by all time points are involved in morphogenesis and general nervous tissue development. The 295 shared genes between days 21 and 22 are involved in neurogenesis and nervous system development and differentiation. The 407 unique day 42 genes are involved in pituitary development, endocrine system development and other hormonally related gene ontology terms. Overall, rEx analysis indicates a focus on nervous system/tissue development at days 21 and 22. By day 42, in addition to nervous tissue development, there is expression of genes involved in the endocrine system, possibly for maturation and preparation for reproduction. This study defines the transcriptome of the chicken pituitary gland and aids in understanding the expressed genes critical to its function and maturation.
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Affiliation(s)
| | | | - Carl J Schmidt
- Animal and Food ScienceUniversity of Delaware, Newark, Delaware, USA
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Zhao Y, Xie X, Liao W, Zhang H, Cao H, Fei R, Wang X, Wei L, Shao Q, Chen H. The transcription factor RFX5 is a transcriptional activator of the TPP1 gene in hepatocellular carcinoma. Oncol Rep 2016; 37:289-296. [DOI: 10.3892/or.2016.5240] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/31/2016] [Indexed: 11/06/2022] Open
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Skopkova M, Ciljakova M, Havlicekova Z, Vojtkova J, Valentinova L, Danis D, Murgas D, Szepeova R, Stanik J, Banovcin P, Klimes I, Gasperikova D. Two novel RFX6 variants in siblings with Mitchell-Riley syndrome with later diabetes onset and heterotopic gastric mucosa. Eur J Med Genet 2016; 59:429-35. [PMID: 27523286 DOI: 10.1016/j.ejmg.2016.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 08/08/2016] [Accepted: 08/10/2016] [Indexed: 11/28/2022]
Abstract
Mitchell-Riley syndrome, an autosomal recessive disorder caused by mutations in the RFX6 gene, is defined as a combination of neonatal diabetes mellitus and serious congenital gastrointestinal defects. We describe Mitchell-Riley syndrome in two sisters with two novel compound heterozygous variants in the RFX6 gene: c.1154G > A, p.(Arg385Gln), and c.1316_1319delTCTA, p.(Ile439Thrfs*13). Both sisters present milder forms of the syndrome, likely due to possible residual activity of the p.Arg385Gln variant, which is localized in a dimerization domain of the RFX6 transcription factor. We propose that the prognosis is dependent on patient RFX6 genotype and possible residual activity of RFX6 transcription factor. Both sisters had atypical later onset of diabetes, at 2 years and 10 months and 2 years and 7 months, respectively. This supports the need of extending the definition of diabetes in Mitchell-Riley syndrome from neonatal to childhood onset and regular glyceamia check in patients with gastrointestinal tract malformations typical for Mitchell-Riley syndrome. The clinical course in both sisters improved significantly after surgical removal of parts of the small intestine with heterotopic gastric mucosa. We suggest that gastric mucosa heterotopy is an important actionable part of Mitchell-Riley syndrome and could have been responsible for the malabsorption, failure to thrive and severe anemia present in previously reported patients with Mitchell-Riley syndrome.
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Affiliation(s)
- Martina Skopkova
- Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miriam Ciljakova
- Department of Children and Adolescents, University Hospital in Martin, Comenius University Bratislava, Jessenius Faculty of Medicine, Martin, Slovakia.
| | - Zuzana Havlicekova
- Department of Children and Adolescents, University Hospital in Martin, Comenius University Bratislava, Jessenius Faculty of Medicine, Martin, Slovakia
| | - Jarmila Vojtkova
- Department of Children and Adolescents, University Hospital in Martin, Comenius University Bratislava, Jessenius Faculty of Medicine, Martin, Slovakia
| | - Lucia Valentinova
- Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Daniel Danis
- Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Dalibor Murgas
- Department of Pediatric Surgery, University Hospital in Martin, Comenius University Bratislava, Jessenius Faculty of Medicine, Martin, Slovakia
| | - Renata Szepeova
- Department of Children and Adolescents, University Hospital in Martin, Comenius University Bratislava, Jessenius Faculty of Medicine, Martin, Slovakia
| | - Juraj Stanik
- Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Banovcin
- Department of Children and Adolescents, University Hospital in Martin, Comenius University Bratislava, Jessenius Faculty of Medicine, Martin, Slovakia.
| | - Iwar Klimes
- Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Center, Slovak Academy of Sciences, Bratislava, Slovakia.
| | - Daniela Gasperikova
- Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Center, Slovak Academy of Sciences, Bratislava, Slovakia.
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Tammimies K, Bieder A, Lauter G, Sugiaman-Trapman D, Torchet R, Hokkanen ME, Burghoorn J, Castrén E, Kere J, Tapia-Páez I, Swoboda P. Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs. FASEB J 2016; 30:3578-3587. [PMID: 27451412 PMCID: PMC5024701 DOI: 10.1096/fj.201500124rr] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 07/05/2016] [Indexed: 11/11/2022]
Abstract
DYX1C1, DCDC2, and KIAA0319 are
three of the most replicated dyslexia candidate genes (DCGs). Recently, these DCGs
were implicated in functions at the cilium. Here, we investigate the regulation of
these DCGs by Regulatory Factor X transcription factors (RFX TFs), a gene family
known for transcriptionally regulating ciliary genes. We identify conserved X-box
motifs in the promoter regions of DYX1C1, DCDC2, and
KIAA0319 and demonstrate their functionality, as well as the
ability to recruit RFX TFs using reporter gene and electrophoretic mobility shift
assays. Furthermore, we uncover a complex regulation pattern between
RFX1, RFX2, and RFX3 and their
significant effect on modifying the endogenous expression of DYX1C1
and DCDC2 in a human retinal pigmented epithelial cell line
immortalized with hTERT (hTERT-RPE1). In addition, induction of ciliogenesis
increases the expression of RFX TFs and DCGs. At the protein level, we show that
endogenous DYX1C1 localizes to the base of the cilium, whereas DCDC2 localizes along
the entire axoneme of the cilium, thereby validating earlier localization studies
using overexpression models. Our results corroborate the emerging role of DCGs in
ciliary function and characterize functional noncoding elements, X-box promoter
motifs, in DCG promoter regions, which thus can be targeted for mutation screening in
dyslexia and ciliopathies associated with these genes.—Tammimies, K., Bieder,
A., Lauter, G., Sugiaman-Trapman, D., Torchet, R., Hokkanen, M.-E., Burghoorn, J.,
Castrén, E., Kere, J., Tapia-Páez, I., Swoboda, P. Ciliary dyslexia
candidate genes DYX1C1 and DCDC2 are regulated by
Regulatory Factor (RF) X transcription factors through X-box promoter motifs.
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Affiliation(s)
- Kristiina Tammimies
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Center of Neurodevelopmental Disorders (KIND), Pediatric Neuropsychiatry Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Andrea Bieder
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Rachel Torchet
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Jan Burghoorn
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Eero Castrén
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland; and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Isabel Tapia-Páez
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden;
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden;
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Wang B, Qi T, Chen SQ, Ye L, Huang ZS, Li H. RFX1 maintains testis cord integrity by regulating the expression of Itga6 in male mouse embryos. Mol Reprod Dev 2016; 83:606-14. [PMID: 27228460 DOI: 10.1002/mrd.22660] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/21/2016] [Indexed: 01/13/2023]
Abstract
Formation and maintenance of testis cords during embryogenesis are essential for establishing testicular structure and function in adults. At least five genes (Wt1, Dhh, Sox8/Sox9, and Dax1) appear to be required for the maintenance of testis cord integrity in mice. Here, we report that RFX1 is specifically expressed in fetal Sertoli cells. Mouse embryos conditionally deficient in Rfx1 (Rfx1(flox/flox) , Amh-Cre) possessed disrupted testis cords, as the basal lamina lining was fragmented or completely absent in some areas of the testes. Spermatogenesis was blocked, leading to complete infertility. Expression of integrin alpha-6 was significantly decreased in Rfx1-deficient testes compared to control testes; indeed, luciferase and chromatin immunoprecipitation assays indicated that RFX1 directly activates transcription of Itga6 (the gene coding for integrin alpha-6). Taken together, RFX1 transcriptionally targets Itga6 in Sertoli cells, thereby, helping maintain the integrity of the basal lamina during testis cord development. Mol. Reprod. Dev. 83: 606-614, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Bo Wang
- Department of Infertility and Sexual Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guang Zhou, China
| | - Tao Qi
- Department of Infertility and Sexual Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guang Zhou, China
| | - Shi-Qin Chen
- Assisted Reproductive Center, General Hospital of Guangzhou Military Command, Guangzhou, China
| | - Lei Ye
- Department of Infertility and Sexual Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guang Zhou, China
| | - Zhan-Sen Huang
- Department of Infertility and Sexual Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guang Zhou, China
| | - Hao Li
- Department of Infertility and Sexual Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guang Zhou, China
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Yamane S, Harada N, Inagaki N. Mechanisms of fat-induced gastric inhibitory polypeptide/glucose-dependent insulinotropic polypeptide secretion from K cells. J Diabetes Investig 2016; 7 Suppl 1:20-6. [PMID: 27186351 PMCID: PMC4854500 DOI: 10.1111/jdi.12467] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/09/2015] [Accepted: 12/21/2015] [Indexed: 12/19/2022] Open
Abstract
Gastric inhibitory polypeptide/glucose‐dependent insulinotropic polypeptide (GIP) is one of the incretins, which are gastrointestinal hormones released in response to nutrient ingestion and potentiate glucose‐stimulated insulin secretion. Single fat ingestion stimulates GIP secretion from enteroendocrine K cells; chronic high‐fat diet (HFD) loading enhances GIP secretion and induces obesity in mice in a GIP‐dependent manner. However, the mechanisms of GIP secretion from K cells in response to fat ingestion and GIP hypersecretion in HFD‐induced obesity are not well understood. We generated GIP‐green fluorescent protein knock‐in (GIPgfp/+) mice, in which K cells are labeled by enhanced GIP‐green fluorescent protein. Microarray analysis of isolated K cells from GIPgfp/+ mice showed that both fatty acid‐binding protein 5 and G protein‐coupled receptor 120 are highly expressed in K cells. Single oral administration of fat resulted in significant reduction of GIP secretion in both fatty acid‐binding protein 5‐ and G protein‐coupled receptor 120‐deficient mice, showing that fatty acid‐binding protein 5 and G protein‐coupled receptor 120 are involved in acute fat‐induced GIP secretion. Furthermore, the transcriptional factor, regulatory factor X6 (Rfx6), is highly expressed in K cells. In vitro experiments using the mouse enteroendocrine cell line, STC‐1, showed that GIP messenger ribonucleic acid levels are upregulated by Rfx6. Expression levels of Rfx6 messenger ribonucleic acid as well as that of GIP messenger ribonucleic acid were augmented in the K cells of HFD‐induced obese mice, in which GIP content in the small intestine is increased compared with that in lean mice fed a control diet. These results suggest that Rfx6 is involved in hypersecretion of GIP in HFD‐induced obese conditions by increasing GIP gene expression.
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Affiliation(s)
- Shunsuke Yamane
- Department of Diabetes, Endocrinology and Nutrition Graduate School of Medicine Kyoto University Kyoto Japan
| | - Norio Harada
- Department of Diabetes, Endocrinology and Nutrition Graduate School of Medicine Kyoto University Kyoto Japan
| | - Nobuya Inagaki
- Department of Diabetes, Endocrinology and Nutrition Graduate School of Medicine Kyoto University Kyoto Japan
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Abstract
Lineage tracing studies have revealed that transcription factors play a cardinal role in pancreatic development, differentiation and function. Three transitions define pancreatic organogenesis, differentiation and maturation. In the primary transition, when pancreatic organogenesis is initiated, there is active proliferation of pancreatic progenitor cells. During the secondary transition, defined by differentiation, there is growth, branching, differentiation and pancreatic cell lineage allocation. The tertiary transition is characterized by differentiated pancreatic cells that undergo further remodeling, including apoptosis, replication and neogenesis thereby establishing a mature organ. Transcription factors function at multiple levels and may regulate one another and auto-regulate. The interaction between extrinsic signals from non-pancreatic tissues and intrinsic transcription factors form a complex gene regulatory network ultimately culminating in the different cell lineages and tissue types in the developing pancreas. Mutations in these transcription factors clinically manifest as subtypes of diabetes mellitus. Current treatment for diabetes is not curative and thus, developmental biologists and stem cell researchers are utilizing knowledge of normal pancreatic development to explore novel therapeutic alternatives. This review summarizes current knowledge of transcription factors involved in pancreatic development and β-cell differentiation in rodents.
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Affiliation(s)
- Reshmi Dassaye
- a Discipline of Pharmaceutical Sciences; Nelson R. Mandela School of Medicine, University of KwaZulu-Natal , Durban , South Africa
| | - Strini Naidoo
- a Discipline of Pharmaceutical Sciences; Nelson R. Mandela School of Medicine, University of KwaZulu-Natal , Durban , South Africa
| | - Marlon E Cerf
- b Diabetes Discovery Platform, South African Medical Research Council , Cape Town , South Africa
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