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Lee SHT, Garske KM, Arasu UT, Kar A, Miao Z, Alvarez M, Koka A, Darci-Maher N, Benhammou JN, Pan DZ, Örd T, Kaminska D, Männistö V, Heinonen S, Wabitsch M, Laakso M, Agopian VG, Pisegna JR, Pietiläinen KH, Pihlajamäki J, Kaikkonen MU, Pajukanta P. Single nucleus RNA-sequencing integrated into risk variant colocalization discovers 17 cell-type-specific abdominal obesity genes for metabolic dysfunction-associated steatotic liver disease. EBioMedicine 2024; 106:105232. [PMID: 38991381 PMCID: PMC11663762 DOI: 10.1016/j.ebiom.2024.105232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Abdominal obesity increases the risk for non-alcoholic fatty liver disease (NAFLD), now known as metabolic dysfunction-associated steatotic liver disease (MASLD). METHODS To elucidate the directional cell-type level biological mechanisms underlying the association between abdominal obesity and MASLD, we integrated adipose and liver single nucleus RNA-sequencing and bulk cis-expression quantitative trait locus (eQTL) data with the UK Biobank genome-wide association study (GWAS) data using colocalization. Then we used colocalized cis-eQTL variants as instrumental variables in Mendelian randomization (MR) analyses, followed by functional validation experiments on the target genes of the cis-eQTL variants. FINDINGS We identified 17 colocalized abdominal obesity GWAS variants, regulating 17 adipose cell-type marker genes. Incorporating these 17 variants into MR discovers a putative tissue-of-origin, cell-type-aware causal effect of abdominal obesity on MASLD consistently with multiple MR methods without significant evidence for pleiotropy or heterogeneity. Single cell data confirm the adipocyte-enriched mean expression of the 17 genes. Our cellular experiments across human adipogenesis identify risk variant -specific epigenetic and transcriptional mechanisms. Knocking down two of the 17 genes, PPP2R5A and SH3PXD2B, shows a marked decrease in adipocyte lipidation and significantly alters adipocyte function and adipogenesis regulator genes, including DGAT2, LPL, ADIPOQ, PPARG, and SREBF1. Furthermore, the 17 genes capture a characteristic MASLD expression signature in subcutaneous adipose tissue. INTERPRETATION Overall, we discover a significant cell-type level effect of abdominal obesity on MASLD and trace its biological effect to adipogenesis. FUNDING NIH grants R01HG010505, R01DK132775, and R01HL170604; the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant No. 802825), Academy of Finland (Grants Nos. 333021), the Finnish Foundation for Cardiovascular Research the Sigrid Jusélius Foundation and the Jane and Aatos Erkko Foundation; American Association for the Study of Liver Diseases (AASLD) Advanced Transplant Hepatology award and NIH/NIDDK (P30DK41301) Pilot and Feasibility award; NIH/NIEHS F32 award (F32ES034668); Finnish Diabetes Research Foundation, Kuopio University Hospital Project grant (EVO/VTR grants 2005-2021), the Academy of Finland grant (Contract no. 138006); Academy of Finland (Grant Nos 335443, 314383, 272376 and 266286), Sigrid Jusélius Foundation, Finnish Medical Foundation, Finnish Diabetes Research Foundation, Novo Nordisk Foundation (#NNF20OC0060547, NNF17OC0027232, NNF10OC1013354) and Government Research Funds to Helsinki University Hospital; Orion Research Foundation, Maud Kuistila Foundation, Finish Medical Foundation, and University of Helsinki.
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Affiliation(s)
- Seung Hyuk T Lee
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Kristina M Garske
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Uma Thanigai Arasu
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Asha Kar
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - Zong Miao
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - Marcus Alvarez
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Amogha Koka
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Nicholas Darci-Maher
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jihane N Benhammou
- Vatche and Tamar Manoukian Division of Digestive Diseases and Gastroenterology, Hepatology and Parenteral Nutrition, David Geffen School of Medicine at UCLA and VA Greater Los Angeles HCS, Los Angeles, CA, USA
| | - David Z Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - Tiit Örd
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Dorota Kaminska
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Division of Cardiology, Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Ville Männistö
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland; Department of Internal Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Sini Heinonen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Martin Wabitsch
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University of Ulm, Ulm, Germany
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Vatche G Agopian
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Joseph R Pisegna
- Department of Medicine and Human Genetics, Division of Gastroenterology, Hepatology and Parenteral Nutrition, David Geffen School of Medicine at UCLA and VA Greater Los Angeles HCS, Los Angeles, CA, USA
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Healthy WeightHub, Endocrinology, Abdominal Center, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland; Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA; Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
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Kamimura R, Uchida D, Kanno SI, Shiraishi R, Hyodo T, Sawatani Y, Shimura M, Hasegawa T, Tsubura-Okubo M, Yaguchi E, Komiyama Y, Fukumoto C, Izumi S, Fujita A, Wakui T, Kawamata H. Identification of Binding Proteins for TSC22D1 Family Proteins Using Mass Spectrometry. Int J Mol Sci 2021; 22:ijms222010913. [PMID: 34681573 PMCID: PMC8536140 DOI: 10.3390/ijms222010913] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
TSC-22 (TGF-β stimulated clone-22) has been reported to induce differentiation, growth inhibition, and apoptosis in various cells. TSC-22 is a member of a family in which many proteins are produced from four different family genes. TSC-22 (corresponding to TSC22D1-2) is composed of 144 amino acids translated from a short variant mRNA of the TSC22D1 gene. In this study, we attempted to determine the intracellular localizations of the TSC22D1 family proteins (TSC22D1-1, TSC-22 (TSC22D1-2), and TSC22(86) (TSC22D1-3)) and identify the binding proteins for TSC22D1 family proteins by mass spectrometry. We determined that TSC22D1-1 was mostly localized in the nucleus, TSC-22 (TSC22D1-2) was localized in the cytoplasm, mainly in the mitochondria and translocated from the cytoplasm to the nucleus after DNA damage, and TSC22(86) (TSC22D1-3) was localized in both the cytoplasm and nucleus. We identified multiple candidates of binding proteins for TSC22D1 family proteins in in vitro pull-down assays and in vivo binding assays. Histone H1 bound to TSC-22 (TSC22D1-2) or TSC22(86) (TSC22D1-3) in the nucleus. Guanine nucleotide-binding protein-like 3 (GNL3), which is also known as nucleostemin, bound to TSC-22 (TSC22D1-2) in the nucleus. Further investigation of the interaction of the candidate binding proteins with TSC22D1 family proteins would clarify the biological roles of TSC22D1 family proteins in several cell systems.
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Affiliation(s)
- Ryouta Kamimura
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
| | - Daisuke Uchida
- Department of Oral and Maxillofacial Surgery, Ehime University Graduate School of Medicine, Shitsukawa, Toon 791-0295, Ehime, Japan;
| | - Shin-ichiro Kanno
- Division of Dynamic Proteome, Institute of Development, Aging, and Cancer, Tohoku University, 4-1 Seiryo-machi, Sendai 980-8575, Aobaku, Japan;
| | - Ryo Shiraishi
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
| | - Toshiki Hyodo
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
| | - Yuta Sawatani
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
- Section of Dentistry, Oral and Maxillofacial Surgery, Kamitsuga General Hospital, 1-1033 Shimoda-machi, Kanuma 322-8550, Tochigi, Japan
| | - Michiko Shimura
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
- Section of Dentistry and Oral and Maxillofacial Surgery, Sano Kosei General Hospital, 1728 Horigomecho, Sano 327-8511, Tochigi, Japan
| | - Tomonori Hasegawa
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
| | - Maki Tsubura-Okubo
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
- Section of Dentistry and Oral and Maxillofacial Surgery, Sano Kosei General Hospital, 1728 Horigomecho, Sano 327-8511, Tochigi, Japan
| | - Erika Yaguchi
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
| | - Yuske Komiyama
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
| | - Chonji Fukumoto
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
| | - Sayaka Izumi
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
| | - Atsushi Fujita
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
| | - Takahiro Wakui
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
| | - Hitoshi Kawamata
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, 880 Kita-kobayashi, Shimotsuga, Mibu 321-0293, Tochigi, Japan; (R.K.); (R.S.); (T.H.); (Y.S.); (M.S.); (T.H.); (M.T.-O.); (E.Y.); (Y.K.); (C.F.); (S.I.); (A.F.); (T.W.)
- Correspondence: ; Tel.: +81-282-87-2130; Fax: +81-282-86-1681
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Huang PS, Chung IH, Lin YH, Lin TK, Chen WJ, Lin KH. The Long Non-Coding RNA MIR503HG Enhances Proliferation of Human ALK-Negative Anaplastic Large-Cell Lymphoma. Int J Mol Sci 2018; 19:ijms19051463. [PMID: 29758012 PMCID: PMC5983830 DOI: 10.3390/ijms19051463] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/10/2018] [Accepted: 05/12/2018] [Indexed: 02/07/2023] Open
Abstract
Anaplastic lymphoma kinase (ALK)-negative anaplastic large-cell lymphoma (ALCL) is a rare type of highly malignant, non-Hodgkin lymphoma. Currently, only a few gene rearrangements have been linked to ALK-negative ALCL progression. However, the specific molecular mechanisms underlying the growth of ALK-negative ALCL tumors remain unclear. Here, we investigated aberrantly expressed, long non-coding RNAs (lncRNAs) in ALK-negative ALCL and assessed their potential biological function. MIR503HG (miR-503 host gene) was highly expressed in ALK-negative cell lines and was significantly upregulated in tumors in mice formed from ALK-negative ALCL cell lines. Depletion of MIR503HG suppressed tumor cell proliferation in vivo and in vitro; conversely, its overexpression enhanced tumor cell growth. MIR503HG-induced proliferation was mediated by the induction of microRNA-503 (miR-503) and suppression of Smurf2, resulting in stabilization of the tumor growth factor-β receptor (TGFBR) and enhanced tumor cell growth. Collectively, these findings support a potential role for MIR503HG in cancer cell proliferation through the miR-503/Smurf2/TGFBR axis and indicate that MIR503HG is a potential marker in ALK-negative ALCL.
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MESH Headings
- Anaplastic Lymphoma Kinase
- Animals
- Cell Line, Tumor
- Cell Proliferation
- Disease Models, Animal
- Gene Expression Regulation, Neoplastic
- Heterografts
- Humans
- Lymphoma, Large-Cell, Anaplastic/genetics
- Lymphoma, Large-Cell, Anaplastic/metabolism
- Lymphoma, Large-Cell, Anaplastic/pathology
- Mice
- MicroRNAs/genetics
- RNA Interference
- RNA, Long Noncoding/genetics
- Receptor Protein-Tyrosine Kinases/deficiency
- Receptors, Transforming Growth Factor beta
- Ubiquitin-Protein Ligases/genetics
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Affiliation(s)
- Po-Shuan Huang
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan.
| | - I-Hsiao Chung
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan.
| | - Yang-Hsiang Lin
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan.
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan.
| | - Tzu-Kang Lin
- Neurosurgery, Fu Jen Catholic University Hospital and School of Medicine, Fu Jen Catholic University, New Taipei City 24250, Taiwan.
| | - Wei-Jan Chen
- Cardiovascular Division, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 333, Taiwan.
| | - Kwang-Huei Lin
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan.
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan.
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan.
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