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Dai D, Sari EM, Si J, Ashari H, Dagong MIA, Pauciullo A, Lenstra JA, Han J, Zhang Y. Genomic analysis reveals the association of KIT and MITF variants with the white spotting in swamp buffaloes. BMC Genomics 2024; 25:713. [PMID: 39048931 PMCID: PMC11267946 DOI: 10.1186/s12864-024-10634-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Swamp-type buffaloes with varying degrees of white spotting are found exclusively in Tana Toraja, South Sulawesi, Indonesia, where spotted buffalo bulls are highly valued in accordance with the Torajan customs. The white spotting depigmentation is caused by the absence of melanocytes. However, the genetic variants that cause this phenotype have not been fully characterized. The objective of this study was to identify the genomic regions and variants responsible for this unique coat-color pattern. RESULTS Genome-wide association study (GWAS) and selection signature analysis identified MITF as a key gene based on the whole-genome sequencing data of 28 solid and 39 spotted buffaloes, while KIT was also found to be involved in the development of this phenotype by a candidate gene approach. Alternative candidate mutations included, in addition to the previously reported nonsense mutation c.649 C > T (p.Arg217*) and splice donor mutation c.1179 + 2T > A in MITF, a nonsense mutation c.2028T > A (p.Tyr676*) in KIT. All these three mutations were located in the genomic regions that were highly conserved exclusively in Indonesian swamp buffaloes and they accounted largely (95%) for the manifestation of white spotting. Last but not the least, ADAMTS20 and TWIST2 may also contribute to the diversification of this coat-color pattern. CONCLUSIONS The alternative mutations identified in this study affect, at least partially and independently, the development of melanocytes. The presence and persistence of such mutations may be explained by significant financial and social value of spotted buffaloes used in historical Rambu Solo ceremony in Tana Toraja, Indonesia. Several de novo spontaneous mutations have therefore been favored by traditional breeding for the spotted buffaloes.
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Affiliation(s)
- Dongmei Dai
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Eka Meutia Sari
- Department of Animal Science, Agriculture Faculty, Universitas Syiah Kuala (USK), Banda Aceh, 23111, Indonesia.
| | - Jingfang Si
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hidayat Ashari
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Muhammad Ihsan Andi Dagong
- Animal Production Department, Faculty of Animal Science, Hasanuddin University, Makassar, 90245, Indonesia
| | - Alfredo Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco (TO), 10095, Italy
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM, Utrecht, The Netherlands
| | - Jianlin Han
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Yi Zhang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Zekavat SM, Raghu VK, Trinder M, Ye Y, Koyama S, Honigberg MC, Yu Z, Pampana A, Urbut S, Haidermota S, O’Regan DP, Zhao H, Ellinor PT, Segrè AV, Elze T, Wiggs JL, Martone J, Adelman RA, Zebardast N, Del Priore L, Wang JC, Natarajan P. Deep Learning of the Retina Enables Phenome- and Genome-Wide Analyses of the Microvasculature. Circulation 2022; 145:134-150. [PMID: 34743558 PMCID: PMC8746912 DOI: 10.1161/circulationaha.121.057709] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND The microvasculature, the smallest blood vessels in the body, has key roles in maintenance of organ health and tumorigenesis. The retinal fundus is a window for human in vivo noninvasive assessment of the microvasculature. Large-scale complementary machine learning-based assessment of the retinal vasculature with phenome-wide and genome-wide analyses may yield new insights into human health and disease. METHODS We used 97 895 retinal fundus images from 54 813 UK Biobank participants. Using convolutional neural networks to segment the retinal microvasculature, we calculated vascular density and fractal dimension as a measure of vascular branching complexity. We associated these indices with 1866 incident International Classification of Diseases-based conditions (median 10-year follow-up) and 88 quantitative traits, adjusting for age, sex, smoking status, and ethnicity. RESULTS Low retinal vascular fractal dimension and density were significantly associated with higher risks for incident mortality, hypertension, congestive heart failure, renal failure, type 2 diabetes, sleep apnea, anemia, and multiple ocular conditions, as well as corresponding quantitative traits. Genome-wide association of vascular fractal dimension and density identified 7 and 13 novel loci, respectively, that were enriched for pathways linked to angiogenesis (eg, vascular endothelial growth factor, platelet-derived growth factor receptor, angiopoietin, and WNT signaling pathways) and inflammation (eg, interleukin, cytokine signaling). CONCLUSIONS Our results indicate that the retinal vasculature may serve as a biomarker for future cardiometabolic and ocular disease and provide insights into genes and biological pathways influencing microvascular indices. Moreover, such a framework highlights how deep learning of images can quantify an interpretable phenotype for integration with electronic health record, biomarker, and genetic data to inform risk prediction and risk modification.
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Affiliation(s)
- Seyedeh Maryam Zekavat
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT (S.M.Z., J.M., R.A.A., L.D.P., J.C.W.)
- Computational Biology & Bioinformatics Program (S.M.Z., Y.Y., H.Z.), Yale University, New Haven, CT
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
| | - Vineet K. Raghu
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
- Cardiovascular Imaging Research Center (V.K.R.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Mark Trinder
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada (M.T.)
| | - Yixuan Ye
- Computational Biology & Bioinformatics Program (S.M.Z., Y.Y., H.Z.), Yale University, New Haven, CT
| | - Satoshi Koyama
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
| | - Michael C. Honigberg
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Zhi Yu
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
| | - Akhil Pampana
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
| | - Sarah Urbut
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Sara Haidermota
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Declan P. O’Regan
- MRC London Institute of Medical Sciences, Imperial College London, UK (D.P.O.)
| | - Hongyu Zhao
- Computational Biology & Bioinformatics Program (S.M.Z., Y.Y., H.Z.), Yale University, New Haven, CT
- School of Public Health (H.Z.), Yale University, New Haven, CT
| | - Patrick T. Ellinor
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Ayellet V. Segrè
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston (A.V.S., T.E., J.L.W., N.Z.)
| | - Tobias Elze
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston (A.V.S., T.E., J.L.W., N.Z.)
| | - Janey L. Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston (A.V.S., T.E., J.L.W., N.Z.)
| | - James Martone
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT (S.M.Z., J.M., R.A.A., L.D.P., J.C.W.)
| | - Ron A. Adelman
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT (S.M.Z., J.M., R.A.A., L.D.P., J.C.W.)
| | - Nazlee Zebardast
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston (A.V.S., T.E., J.L.W., N.Z.)
| | - Lucian Del Priore
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT (S.M.Z., J.M., R.A.A., L.D.P., J.C.W.)
| | - Jay C. Wang
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT (S.M.Z., J.M., R.A.A., L.D.P., J.C.W.)
| | - Pradeep Natarajan
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
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Albarry MA, Latif M, Alreheli AQ, Awadh MA, Almatrafi AM, Albalawi AM, Basit S. Frameshift variant in MITF gene in a large family with Waardenburg syndrome type II and a co-segregation of a C2orf74 variant. PLoS One 2021; 16:e0246607. [PMID: 33571247 PMCID: PMC7877624 DOI: 10.1371/journal.pone.0246607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/21/2021] [Indexed: 11/30/2022] Open
Abstract
Waardenburg syndrome (WS) is a hereditary disorder affecting the auditory system and pigmentation of hair, eyes, and skin. Different variants of the disease exist with the involvement of mutation in six genes. The aim of the study is to identify the genetic defects underlying Waardenburg syndrome in a large family with multiple affected individuals. Here, in this study, we recruited a large family with eleven affected individuals segregating WS type 2. We performed whole genome SNP genotyping, whole exome sequencing and segregation analysis using Sanger approach. Whole genome SNP genotyping, whole exome sequencing followed by Sanger validation of variants of interest identified a novel single nucleotide deletion mutation (c.965delA) in the MITF gene. Moreover, a rare heterozygous, missense damaging variant (c.101T>G; p.Val34Gly) in the C2orf74 has also been identified. The C2orf74 is an uncharacterized gene present in the linked region detected by DominantMapper. Variants in MITF and C2orf74 follows autosomal dominant segregation with the phenotype, however, the variant in C2orf74 is incompletely penetrant. We proposed a digenic inheritance of variants as an underlying cause of WS2 in this family.
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Affiliation(s)
- Maan Abdullah Albarry
- Department of Ophthalmology, College of Medicine, Taibah University, Almadinah, Saudi Arabia
| | - Muhammad Latif
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah, Saudi Arabia
| | - Ahdab Qasem Alreheli
- Department of Ophthalmology, College of Medicine, Taibah University, Almadinah, Saudi Arabia
| | - Mohammed A. Awadh
- College of Applied Medical Sciences, Taibah University, Almadinah, Saudi Arabia
| | - Ahmad M. Almatrafi
- Department of Biology, College of Science, Taibah University, Almadinah, Saudi Arabia
| | - Alia M. Albalawi
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah, Saudi Arabia
- Department of Biology, College of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah, Saudi Arabia
- * E-mail:
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Li S, Lu G, Wang D, He JL, Zuo L, Wang H, Gu ZT, Zhou JS, Yan FL, Deng QW. MicroRNA-4443 regulates monocyte activation by targeting tumor necrosis factor receptor associated factor 4 in stroke-induced immunosuppression. Eur J Neurol 2020; 27:1625-1637. [PMID: 32337817 DOI: 10.1111/ene.14282] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND AND PURPOSE MicroRNAs (miRNAs) have been demonstrated to play crucial roles in the early stage of acute ischaemic stroke (AIS). The purpose of this study was to investigate the expression patterns of miRNAs in peripheral blood mononuclear cells (PBMCs) from AIS patients and further explore related molecular mechanisms in stroke-induced immunodeficiency syndrome (SIDS). METHODS The miRNA expression patterns of PBMCs were detected by miRNA microarray and validated by quantitative real-time polymerase chain reaction (qRT-PCR) in AIS patients and healthy controls. Bioinformatics methods and luciferase reporter assays were used to detect the downstream target genes. Following stimulation with lipopolysaccharide and interleukin-4, the expression of miR-4443, tumor necrosis factor receptor associated factor 4 (TRAF4) and the nuclear factor kappa B (NF-κB) pathway were evaluated. Furthermore, transfection with miR-4443 mimic or inhibitor in the monocytes was carried out to gain insight into the mechanisms in SIDS. RESULTS Interleukin-10 in AIS patients was significantly higher than that of healthy controls. The miRNA microarray analysis and qRTPCR validation showed that only miR-4443 was upregulated expressed in PBMCs from AIS patients, especially in monocytes. miR-4443 was shown to directly interact with the 3' untranslated regions of TRAF4, resulting in suppression of TRAF4 protein expression. Furthermore, the expression of miR-4443 and TRAF4 was regulated by stimulation with lipopolysaccharide or interleukin-4. Additionally, overexpression of miR-4443 suppressed the TRAF4/Iκα/NF-κB signaling pathway to activate the expression of anti-inflammatory cytokines in monocytes. CONCLUSIONS The increased expression of miR-4443 induced monocyte dysfunction by targeting TRAF4, which may function as a crucial mediator in SIDS.
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Affiliation(s)
- S Li
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, China
| | - G Lu
- Department of Neurology, Dezhou People's Hospital, Dezhou, China
| | - D Wang
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, China
| | - J L He
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, China
| | - L Zuo
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, China
| | - H Wang
- Department of Respiratory, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Z T Gu
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, China
| | - J S Zhou
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - F L Yan
- Department of Neurology, Affiliated ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Q W Deng
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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