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da Silva Santos R, Pascoalino Pinheiro D, Gustavo Hirth C, Barbosa Bezerra MJ, Joyce de Lima Silva-Fernandes I, Andréa da Silva Oliveira F, Viana de Holanda Barros M, Silveira Ramos E, A. Moura A, Filho ODMM, Pessoa C, Miranda Furtado CL. Hypomethylation at H19DMR in penile squamous cell carcinoma is not related to HPV infection. Epigenetics 2024; 19:2305081. [PMID: 38245880 PMCID: PMC10802203 DOI: 10.1080/15592294.2024.2305081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Penile squamous cell carcinoma (SCC) is a rare and aggressive tumour mainly related to lifestyle behaviour and human papillomavirus (HPV) infection. Environmentally induced loss of imprinting (LOI) at the H19 differentially methylated region (H19DMR) is associated with many cancers in the early events of tumorigenesis and may be involved in the pathogenesis of penile SCC. We sought to evaluate the DNA methylation pattern at H19DMR and its association with HPV infection in men with penile SCC by bisulfite sequencing (bis-seq). We observed an average methylation of 32.2% ± 11.6% at the H19DMR of penile SCC and did not observe an association between the p16INK4a+ (p = 0.59) and high-risk HPV+ (p = 0.338) markers with methylation level. The average methylation did not change according to HPV positive for p16INK4a+ or hrHPV+ (35.4% ± 10%) and negative for both markers (32.4% ± 10.1%) groups. As the region analysed has a binding site for the CTCF protein, the hypomethylation at the surrounding CpG sites might alter its insulator function. In addition, there was a positive correlation between intense polymorphonuclear cell infiltration and hypomethylation at H19DMR (p = 0.035). Here, we report that hypomethylation at H19DMR in penile SCC might contribute to tumour progression and aggressiveness regardless of HPV infection.
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Affiliation(s)
- Renan da Silva Santos
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | | | | | | | | | - Maisa Viana de Holanda Barros
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Ester Silveira Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Arlindo A. Moura
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Animal Science, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Odorico de Moraes Manoel Filho
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Claudia Pessoa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Cristiana Libardi Miranda Furtado
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Experimental Biology Center, University of Fortaleza, Fortaleza, Ceará, Brazil
- Graduate Program in Medical Sciences, Universidade de Fortaleza, Fortaleza, Ceará, Brazil
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Bursakov SA, Kovaleva AV, Brigida AV, Zaripov OG. Functional analysis of the GPAT4 gene mutation predicted to affect splicing. Anim Biotechnol 2024; 35:2269210. [PMID: 37906284 DOI: 10.1080/10495398.2023.2269210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The GPAT4 gene is considered as a potential functional candidate for single nucleotide polymorphism (SNP) studies in dairy cattle breeding due to its association with dairy performance in cattle by encoding an enzyme responsible for the presence of diacylglycerols and triacylglycerols in milk. Using the example of the GPAT4 gene, we applied the minigene splicing assay to analyze the functional consequences of its variant that was predicted to affect normal splicing. The results of functional analysis revealed the sequence variations (rs442541537), transfection experiments in a wild type and mutant cell line model system demonstrated that the investigated mutation in the second intron of the GPAT4 gene was responsible for the presence of a second exon in mature messenger RNA (mRNA). The cases of its absence in the spliced mature mRNA transcript resulted in a truncated dysfunctional protein due to the appearance of a stop codon. Thus, the discovered SNP led to alternative splicing in pre-mRNA by the 'cassette exon' ('exon skipping') mechanism. The studied mutation can potentially be a molecular genetic marker for alternative splicing for the GPAT4 gene and, therefore contributes to economic benefits in cattle breeding programs.
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Affiliation(s)
- Sergey A Bursakov
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
- Federal State Budgetary Scientific Institution "All-Russia Research Institute of Agricultural Biotechnology", Moscow, Russia
| | - Anastasia V Kovaleva
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
| | - Artyom V Brigida
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
| | - Oleg G Zaripov
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
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Kaye RA, Peto T, Hogg R, Griffiths H, Sivaprasad S, Lotery AJ. CHOROIDAL VASCULARITY IN CHRONIC CENTRAL SEROUS CHORIORETINOPATHY AND ITS ASSOCIATION WITH RISK SINGLE-NUCLEOTIDE POLYMORPHISMS. Retina 2024; 44:837-843. [PMID: 38109714 PMCID: PMC11027981 DOI: 10.1097/iae.0000000000004024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
PURPOSE To analyze the choroidal parameters of patients with chronic central serous chorioretinopathy (cCSC) and the association with central serous chorioretinopathy susceptibility genes. METHODS The choroidal vascular index (CVI) was obtained by binarizing spectral domain optical coherence tomography enhanced depth images of patients with cCSC and healthy age-matched controls. Patients with cCSC were genotyped for three central serous chorioretinopathy susceptibility single-nucleotide polymorphisms: rs4844392 ( mir-29b-2/CD46 ), rs1329428 ( CFH ), and rs2379120 (upstream GATA5 ). RESULTS One hundred three eyes with cCSC and 53 control eyes were included. There was a significant increase in the subfoveal choroidal area in both the affected (2.4 ± 0.6 mm 2 ) and fellow (2.2 ± 0.6 mm 2 ) eyes of patients with cCSC compared with controls (1.8 ± 0.5 mm 2 , P < 0.0001 and P < 0.0001). The CVI was reduced in patients with cCSC 63.5% ± 3.1% compared with controls 65.4% ± 2.3% ( P < 0.001) and also in the affected compared with the fellow eyes 64.6% ± 2.9% ( P < 0.01). There was a significant association between CVI in the cCSC group and presence of the risk single-nucleotide polymorphisms rs2379120 at GATA5 ( P < 0.01). CONCLUSION The relative reduction of CVI in patients with cCSC may suggest a persistence of vessel hyperpermeability over dilation in chronic disease. GATA5 is associated with CVI in patients with cCSC and therefore may have a role in choroidal vascularity.
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Affiliation(s)
- Rebecca A. Kaye
- Department of Ophthalmology, University Hospital Southampton, Southampton, United Kingdom
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Tunde Peto
- School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, United Kingdom
- The VICI Trial, ISRCTN92746680
| | - Ruth Hogg
- School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, United Kingdom
| | - Helen Griffiths
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sobha Sivaprasad
- University College London Institute of Ophthalmology, London, United Kingdom; and
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
| | - Andrew J. Lotery
- Department of Ophthalmology, University Hospital Southampton, Southampton, United Kingdom
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- The VICI Trial, ISRCTN92746680
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Boldinova EO, Baranovskiy AG, Filina YV, Miftakhova RR, Shamsutdinova YF, Tahirov TH, Makarova AV. PrimPol Variant V102A with Altered Primase and Polymerase Activities. J Mol Biol 2024; 436:168542. [PMID: 38492718 DOI: 10.1016/j.jmb.2024.168542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
PrimPol is a human DNA primase-polymerase which restarts DNA synthesis beyond DNA lesions and non-B DNA structures blocking replication. Disfunction of PrimPol in cells leads to slowing of DNA replication rates in mitochondria and nucleus, accumulation of chromosome aberrations, cell cycle delay, and elevated sensitivity to DNA-damaging agents. A defective PrimPol has been suggested to be associated with the development of ophthalmic diseases, elevated mitochondrial toxicity of antiviral drugs and increased cell resistance to chemotherapy. Here, we describe a rare missense PrimPol variant V102A with altered biochemical properties identified in patients suffering from ovarian and cervical cancer. The Val102 to Ala substitution dramatically reduced both the primase and DNA polymerase activities of PrimPol as well as specifically decreased its ability to incorporate ribonucleotides. Structural analysis indicates that the V102A substitution can destabilize the hydrophobic pocket adjacent to the active site, affecting dNTP binding and catalysis.
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Affiliation(s)
- Elizaveta O Boldinova
- National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Vavilova 34 / 5, 119334 Moscow, Russia
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Yulia V Filina
- "Translational Oncology" Research Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
| | - Regina R Miftakhova
- "Translational Oncology" Research Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
| | - Yana F Shamsutdinova
- Chemotherapy Department №1, Republican Clinical Oncology Dispensary of the Ministry of Health of the Republic of Tatarstan Named After Prof. M.Z. Sigal, Sibirskiy trakt 29, 420029 Kazan, Russia
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Alena V Makarova
- National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Vavilova 34 / 5, 119334 Moscow, Russia.
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Ji Y, Guo N, Lu C, Zhang M, Wang S, Yang L, Li Q, Lv M, Yang Y, Gao Y. Association between mtDNA haplogroups and skeletal fluorosis in Han population residing in drinking water endemic fluorosis area of northern China. Int J Environ Health Res 2024; 34:2397-2406. [PMID: 37660259 DOI: 10.1080/09603123.2023.2253161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
To investigate the association between mtDNA genetic information and the risk of SF, individuals were conducted in the drinking water endemic fluorosis area in northern China, sequenced the whole genome of mtDNA, identified the SNPs and SNVs, analyzed the haplogroups, and diagnosed SF, and then, the effect of mtDNA genetic information on the risk of SF was evaluated. We find that, D5 haplogroup and its specific SNPs reduced the risk, while the D4 haplogroup and its specific SNPs increased the risk of SF. The number of SNVs in coding regions of mitochondrial respiratory chain (MRC) is different between the controls and cases. This suggests that D5 haplogroup may play a protective role in the risk of SF, while the opposite is observed for the D4 haplogroup, this may relate to their specific SNPs. And SNVs that encode the MRC complex may also be associated with the risk of SF.
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Affiliation(s)
- Yi Ji
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Ning Guo
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Chunqing Lu
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Meichen Zhang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Sa Wang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Liu Yang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Qiao Li
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Man Lv
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yanmei Yang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yanhui Gao
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health of P. R. China, Harbin Medical University, Harbin, Heilongjiang Province, China
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Pant S, Bhati T, Dimri A, Arora R, Siraj F, Rastogi S. Screening of single nucleotide polymorphism in matrix metalloproteinase-2 (MMP2) and tetraspanin CD63 genes in Chlamydia trachomatis-infected tubal ectopic pregnancy patients. Int J Gynaecol Obstet 2024. [PMID: 38650387 DOI: 10.1002/ijgo.15547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/04/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024]
Abstract
OBJECTIVE Tubal ectopic pregnancy (EP) is a leading cause of maternal morbidity and mortality. Studies have suggested that infection-induced inflammatory responses are major risk factors for EP. The aim of the present study was to find an association between MMP2 and CD63 gene variants and risk of EP during Chlamydia trachomatis infection in an Indian population. METHODS Fallopian tube samples of 120 EP and 120 tubal ligation women were collected. C. trachomatis was detected by PCR. The genotyping of MMP2 (rs17859882 G/T, rs7201A/C) and CD63(rs2231464 C/T, rs376086542 A/G) gene variants was done by qualitative real-time PCR using allelic discrimination method (VIC- and FAM-labeled). RESULTS The frequency of GG or GT genotype of MMP2 G/T polymorphism (rs17859882) was 66.6% in infected EP and 36.7% in uninfected EP and 22% in tubal ligation controls (P < 0.0001), while the frequency of AC or CC genotype of MMP2 A/C polymorphism (rs7201) was 66.6% in infected EP and 20.6% in uninfected EP and 13.5% in tubal ligation controls (P < 0.0001). The frequency of CT or TT genotype of CD63 C/T polymorphism (rs2231464) was 74% in infected EP and 21.8% in uninfected EP and 11.8% tubal ligation controls (P < 0.0001), while the frequency of AG or GG genotype of CD63 A/G polymorphism (rs376086542) was 48.1% in infected EP and 41.3% in uninfected EP and 18.6% tubal ligation controls (P < 0.0001). CONCLUSIONS The present study revealed a strong association between the presence of gene variants MMP2 (rs17859882 G/T, rs7201A/C) and CD63 (rs2231464 C/T, rs376086542 A/G) and risk of tubal EP during C. trachomatis infection.
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Affiliation(s)
- Shipra Pant
- Molecular Microbiology Laboratory, ICMR-National Institute of Pathology, Sriramachari Bhawan, Safdarjung Hospital Campus, New Delhi, India
| | - Tanu Bhati
- Molecular Microbiology Laboratory, ICMR-National Institute of Pathology, Sriramachari Bhawan, Safdarjung Hospital Campus, New Delhi, India
| | - Astha Dimri
- Molecular Microbiology Laboratory, ICMR-National Institute of Pathology, Sriramachari Bhawan, Safdarjung Hospital Campus, New Delhi, India
| | - Renu Arora
- Department of Obstetrics and Gynecology, Vardhman Mahavir Medical College (VMMC) and Safdarjung Hospital, New Delhi, India
| | - Fouzia Siraj
- Pathology Laboratory, ICMR-National Institute of Pathology, Sriramachari Bhawan, Safdarjung Hospital Campus, New Delhi, India
| | - Sangita Rastogi
- Molecular Microbiology Laboratory, ICMR-National Institute of Pathology, Sriramachari Bhawan, Safdarjung Hospital Campus, New Delhi, India
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Quiniou G, Andromaque L, Duclaux-Loras R, Dinet O, Cervantes O, Verdet M, Meunier C, Boschetti G, Viret C, Nancey S, Faure M, Rozières A. Impaired reprogramming of the autophagy flux in maturing dendritic cells from crohn disease patients with core autophagy gene-related polymorphisms. Autophagy 2024:1-17. [PMID: 38615686 DOI: 10.1080/15548627.2024.2338574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/29/2024] [Indexed: 04/16/2024] Open
Abstract
Crohn disease (CD) is an inflammatory bowel disease whose pathogenesis involves inappropriate immune responses toward gut microbiota on genetically predisposed backgrounds. Notably, CD is associated with single-nucleotide polymorphisms affecting several genes involved in macroautophagy/autophagy, the catabolic process that ensures the degradation and recycling of cytosolic components and microorganisms. In a clinical translation perspective, monitoring the autophagic activity of CD patients will require some knowledge on the intrinsic functional status of autophagy. Here, we focused on monocyte-derived dendritic cells (DCs) to characterize the intrinsic quantitative features of the autophagy flux. Starting with DCs from healthy donors, we documented a reprogramming of the steady state flux during the transition from the immature to mature status: both the autophagosome pool size and the flux were diminished at the mature stage while the autophagosome turnover remained stable. At the cohort level, DCs from CD patients were comparable to control in term of autophagy flux reprogramming capacity. However, the homozygous presence of ATG16L1 rs2241880 A>G (T300A) and ULK1 rs12303764 (G/T) polymorphisms abolished the capacity of CD patient DCs to reprogram their autophagy flux during maturation. This effect was not seen in the case of CD patients heterozygous for these polymorphisms, revealing a gene dose dependency effect. In contrast, the NOD2 rs2066844 c.2104C>T (R702W) polymorphism did not alter the flux reprogramming capacity of DCs. The data, opening new clinical translation perspectives, indicate that polymorphisms affecting autophagy-related genes can differentially influence the capacity of DCs to reprogram their steady state autophagy flux when exposed to proinflammatory challenges.Abbreviation: BAFA1: bafilomycin A1, CD: Crohn disease; DC: dendritic cells; HD: healthy donor; iDCs: immature DCs; IL: interleukin; J: autophagosome flux; LPS: lipopolysaccharide; MHC: major histocompatibility complex; nA: autophagosome pool size; SNPs: single-nucleotide polymorphisms; PCA: principal component analysis; TLR: toll like receptor; τ: transition time; TNF: tumor necrosis factor.
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Affiliation(s)
- Gaëlle Quiniou
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Leslie Andromaque
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Rémi Duclaux-Loras
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
- Department of Pediatric Hepatology, Gastroenterology and Nutrition, Femme-Mère-Enfant Hospital, Hospices Civils de Lyon, Bron, France
| | - Océane Dinet
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Ornella Cervantes
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Mallorie Verdet
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Camille Meunier
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
- Department of Gastroenterology, Lyon-Sud university hospital, Lyon, France
| | - Gilles Boschetti
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
- Department of Gastroenterology, Lyon-Sud university hospital, Lyon, France
| | - Christophe Viret
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Stéphane Nancey
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
- Department of Gastroenterology, Lyon-Sud university hospital, Lyon, France
| | - Mathias Faure
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
- Equipe Labellisée par la Fondation pour la Recherche Médicale, FRM, France
| | - Aurore Rozières
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
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Wu H, Wang H, Sun L, Liu M, Wang H, Sun X, Zhang W. Association Between rs2278426 Polymorphism of the ANGPTL8 Gene and Polycystic Ovary Syndrome. Diabetes Metab Syndr Obes 2024; 17:1749-1760. [PMID: 38645655 PMCID: PMC11032162 DOI: 10.2147/dmso.s455274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024] Open
Abstract
Purpose To study the relationship between the single nucleotide polymorphism (SNP) rs2278426 in the angiopoietin-like protein 8 gene (ANGPTL8) and polycystic ovary syndrome (PCOS). Patients and methods A total of 122 patients with PCOS and 108 controls were recruited for comparison of glucose, lipid, insulin, sex hormone, and ANGPTL8 levels. Polymerase chain reaction (PCR) and gene sequencing were performed for comparison of the frequency of the CC, CT, and TT rs2278426 genotypes and the rs2278426 allele distributions between the PCOS and control groups and between the obese and non-obese subgroups of the PCOS and control groups. Results The frequency of the T allele was significantly higher in the PCOS group than that in the controls (P = 0.037). In the dominant genetic model, the proportion of the CT+TT genotype in the PCOS group was significantly higher than that in the controls (P = 0.047). Subgroup analysis demonstrated that the T allele proportion was significantly higher in obese PCOS group than obese control group (P = 0.027). PCOS with the CT+TT genotype had significantly higher body mass index (BMI; P = 0.001), triglyceride (TG; P = 0.005), homeostasis model assessment of insulin resistance (HOMA-IR; P = 0.035), testosterone (P = 0.041), and ANGPTL8 (P = 0.037) levels and significantly lower high-density lipoprotein (HDL) levels (P = 0.025) than PCOS with the CC genotype. Obese PCOS group with the CT+TT genotype had significantly higher TG (P = 0.015), luteinizing hormone (LH; P = 0.030), fasting insulin (FINS; P = 0.039), HOMA-IR (P = 0.018), and ANGPTL8 (P = 0.049) levels than obese PCOS group with the CC genotype. Conclusion Polymorphisms of rs2278426 may induce glycolipid metabolic disorders by affecting ANGPTL8 levels and functions in Han Chinese females with obesity from the Shandong region, increasing the risk of PCOS in this population.
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Affiliation(s)
- Han Wu
- Center for Reproductive Medicine, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, People’s Republic of China
| | - Hui Wang
- Gynecological Minimally Invasive Surgery Center, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, People’s Republic of China
| | - Lixia Sun
- Department of Hematology, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, People’s Republic of China
| | - Mengchen Liu
- Center for Reproductive Medicine, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, People’s Republic of China
| | - Haoran Wang
- Center for Reproductive Medicine, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, People’s Republic of China
| | - Xianchang Sun
- Department of Physiology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, People’s Republic of China
| | - Wenjuan Zhang
- Center for Reproductive Medicine, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, People’s Republic of China
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Jung JH, Lee SM, Oh SH. A genome-wide association study on growth traits of Korean commercial pig breeds using Bayesian methods. Anim Biosci 2024:ab.23.0443. [PMID: 38637973 DOI: 10.5713/ab.23.0443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024] Open
Abstract
Objective This study aims to identify the significant regions and candidate genes of growth-related traits (adjusted backfat thickness; ABF, average daily gain; ADG, and days to 90 kg body weight; DAYS90) in Korean commercial GGP pig (Duroc, Landrace, and Yorkshire) populations. Results Methods: A genome-wide association study was performed using single-nucleotide polymorphism (SNP) markers for imputation to Illumina PorcineSNP60. The BayesB method was applied to calculate thresholds for the significance of SNP markers. The identified windows were considered significant if they explained ≥ 1% genetic variance. Results A total of 28 window regions were related to genetic growth effects. Bayesian GWAS revealed 28 significant genetic regions including 52 informative SNPs associated with growth traits (ABF, ADG, DAYS90) in Duroc, Landrace, and Yorkshire pigs, with genetic variance ranging from 1.00% to 5.46%. Additionally, 14 candidate genes with previous functional validation were identified for these traits. Conclusion The results enhance our understanding of genetic architecture and our potential to genetically improve pigs. SNPs within the identified regions could prove valuable for future marker-assisted or genomic selection in pig breeding programs.
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Affiliation(s)
| | - Sang Min Lee
- National Institute of Animal Science, RDA, Cheonan 31000, Korea
| | - Sang Hyon Oh
- Division of Animal Science, Gyeongsang National University, Jinju 52725, Korea
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10
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Giaccherini M, Rende M, Gentiluomo M, Corradi C, Archibugi L, Ermini S, Maiello E, Morelli L, van Eijck CHJ, Cavestro GM, Schneider M, Mickevicius A, Adamonis K, Basso D, Hlavac V, Gioffreda D, Talar-Wojnarowska R, Schöttker B, Lovecek M, Vanella G, Gazouli M, Uno M, Malecka-Wojciesko E, Vodicka P, Goetz M, Bijlsma MF, Petrone MC, Bazzocchi F, Kiudelis M, Szentesi A, Carrara S, Nappo G, Brenner H, Milanetto AC, Soucek P, Katzke V, Peduzzi G, Rizzato C, Pasquali C, Chen X, Capurso G, Hackert T, Bueno-de-Mesquita B, Uzunoglu FGG, Hegyi P, Greenhalf W, Theodoropoulos GEE, Sperti C, Perri F, Oliverius M, Mambrini A, Tavano F, Farinella R, Arcidiacono PG, Lucchesi M, Bunduc S, Kupcinskas J, Di Franco G, Stocker S, Neoptolemos JP, Bambi F, Jamroziak K, Testoni SGG, Aoki MN, Mohelnikova-Duchonova B, Izbicki JR, Pezzilli R, Lawlor RT, Kauffmann EF, López de Maturana E, Malats N, Canzian F, Campa D. A pleiotropy scan to discover new susceptibility loci for pancreatic ductal adenocarcinoma. Mutagenesis 2024:geae012. [PMID: 38606763 DOI: 10.1093/mutage/geae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Indexed: 04/13/2024] Open
Abstract
Pleiotropic variants (i.e., genetic polymorphisms influencing more than one phenotype) are often associated with cancer risk. A scan of pleiotropic variants was successfully conducted ten years ago in relation to pancreatic ductal adenocarcinoma susceptibility. However, in the last decade, genetic association studies performed on several human traits have greatly increased the number of known pleiotropic variants. Based on the hypothesis that variants already associated with a least one trait have a higher probability of association with other traits, 61,052 variants reported to be associated by at least one genome wide association study (GWAS) with at least one human trait were tested in the present study consisting of two phases (discovery and validation), comprising a total of 16,055 pancreatic ductal adenocarcinoma (PDAC) cases and 212,149 controls. The meta-analysis of the two phases showed two loci (10q21.1-rs4948550 (P=6.52×10-5) and 7q36.3-rs288762 (P=3.03×10-5) potentially associated with PDAC risk. 10q21.1-rs4948550 shows a high degree of pleiotropy and it is also associated with colorectal cancer risk while 7q36.3-rs288762 is situated 28,558 base pairs upstream of the Sonic Hedgehog (SHH) gene, which is involved in the cell differentiation process and PDAC etiopathogenesis. In conclusion, none of the single nucleotide polymorphisms (SNPs) showed a formally statistically significant association after correction for multiple testing. However, given their pleiotropic nature and association with various human traits including colorectal cancer, the two SNPs showing the best associations with PDAC risk merit further investigation through fine mapping and ad hoc functional studies.
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Affiliation(s)
- M Giaccherini
- Department of Biology, University of Pisa, Pisa, Italy
| | - M Rende
- Department of Biology, University of Pisa, Pisa, Italy
| | - M Gentiluomo
- Department of Biology, University of Pisa, Pisa, Italy
| | - C Corradi
- Department of Biology, University of Pisa, Pisa, Italy
| | - L Archibugi
- Digestive and Liver Disease Unit, Sant'Andrea Hospital, Rome, Italy
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | - S Ermini
- Blood Transfusion Service, Azienda Ospedaliero Universitaria Meyer, Florence, Italy
| | - E Maiello
- Department of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - L Morelli
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - C H J van Eijck
- Department of Surgery, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - G M Cavestro
- Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele, Milan, Italy
| | - M Schneider
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - A Mickevicius
- Surgery Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - K Adamonis
- Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - D Basso
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padua, Italy
| | - V Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - D Gioffreda
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - R Talar-Wojnarowska
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - B Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research (NAR), Heidelberg University, Heidelberg, Germany
| | - M Lovecek
- Department of Surgery I, University Hospital Olomouc, Olomouc, Czech Republic
| | - G Vanella
- Digestive and Liver Disease Unit, Sant'Andrea Hospital, Rome, Italy
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | - M Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - M Uno
- Center for Translational Research in Oncology (LIM24), Instituto Do Câncer Do Estado de São Paulo, (ICESP), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil
| | - E Malecka-Wojciesko
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - P Vodicka
- Institute of Experimental Medicine, Czech Academy of Science, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University in Prague, Prague, Czech Republic
| | - M Goetz
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - M F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC and Cancer Center Amsterdam, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - M C Petrone
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | - F Bazzocchi
- Department of Surgery, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - M Kiudelis
- Surgery Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - A Szentesi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- János Szentágothai Research Center, University of Pécs, Pécs, Hungary
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Centre for Translational Medicine, Department of Medicine, University of Szeged, Szeged, Hungary
| | - S Carrara
- Digestive Endoscopy Unit, Division of Gastroenterology, Humanitas Clinical and Research Center IRCCS, Milan, Italy
| | - G Nappo
- Pancreatic Unit, Humanitas Clinical and Research Center IRCCS, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - H Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - A C Milanetto
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padua, Italy
| | - P Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - V Katzke
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - G Peduzzi
- Department of Biology, University of Pisa, Pisa, Italy
| | - C Rizzato
- Department of Biology, University of Pisa, Pisa, Italy
| | - C Pasquali
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padua, Italy
| | - X Chen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - G Capurso
- Digestive and Liver Disease Unit, Sant'Andrea Hospital, Rome, Italy
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | - T Hackert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - B Bueno-de-Mesquita
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - F G G Uzunoglu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - P Hegyi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- János Szentágothai Research Center, University of Pécs, Pécs, Hungary
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - W Greenhalf
- Institute for Health Research Liverpool Pancreas Biomedical Research Unit, University of Liverpool, Liverpool, United Kingdom
| | - G E E Theodoropoulos
- First Department of Propaedeutic Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - C Sperti
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padua, Italy
| | - F Perri
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - M Oliverius
- Surgery Clinic Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - A Mambrini
- Oncological Department Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - F Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - R Farinella
- Department of Biology, University of Pisa, Pisa, Italy
| | - P G Arcidiacono
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | - M Lucchesi
- Oncological Department Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - S Bunduc
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- Fundeni Clinical Institute, Bucharest, Romania
| | - J Kupcinskas
- Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - G Di Franco
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - S Stocker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research (NAR), Heidelberg University, Heidelberg, Germany
| | - J P Neoptolemos
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - F Bambi
- Blood Transfusion Service, Azienda Ospedaliero Universitaria Meyer, Florence, Italy
| | - K Jamroziak
- Department of Hematology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - S G G Testoni
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | - M N Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, Brazil
| | | | - J R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - R Pezzilli
- County Medical Association of Potenza, Potenza, Italy
| | - R T Lawlor
- ARC-NET: Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - E F Kauffmann
- Division of General and Transplant Surgery, Pisa University Hospital, Pisa, Italy
| | - E López de Maturana
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - N Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - F Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - D Campa
- Department of Biology, University of Pisa, Pisa, Italy
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11
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Liang R, Zhong W, Ze S, Qiao Y, Yuan L. Causal association between dried fruit intake and risk of osteoarthritis: A Mendelian randomization study. Medicine (Baltimore) 2024; 103:e37710. [PMID: 38579063 PMCID: PMC10994511 DOI: 10.1097/md.0000000000037710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024] Open
Abstract
This study aimed to examine whether dried fruit intake is causally associated with Osteoarthritis (OA). A two-sample Mendelian randomization (MR) analysis using the inverse-variance weighted (IVW), weighted median (WM), and MR-Egger regression methods was performed. We used the publicly available summary statistics data sets of genome-wide association studies (GWAS) meta-analyses for dried fruit intake in individuals included in the UK Biobank (n = 421,764; MRC-IEU consortium) as the exposure and a GWAS publicly available in PubMed for OA (total n = 484,598; case = 39,515, control = 445,083) as the outcome. We selected 41 single nucleotide polymorphisms at genome-wide significance from GWASs on dried fruit intake as the instrumental variables. The IVW method showed evidence to support a causal association between dried fruit intake and OA (beta = -0.020, SE = 0.009, P = .039). MR-Egger regression indicated no directional pleiotropy (intercept = 1E-05; P = .984), but it showed no causal association between dried fruit intake and OA (beta = -0.020, SE = 0.043, P = .610). However, the WM approach yielded evidence of a causal association between dried fruit intake and OA (beta = -0.026, SE = 0.012, P = .026). Cochran's Q test showed the existence of heterogeneity, but the statistics of I2 showed low heterogeneity. The results of MR analysis support that dried fruit intake may be causally associated with a decreased risk of OA.
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Affiliation(s)
- Ruiming Liang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Weixing Zhong
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Shuaidi Ze
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Yuxiang Qiao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Lixia Yuan
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
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12
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Zhao L, Yuan L, Li F, Zhang X, Tian H, Ma Z, Zhang D, Zhang Y, Zhao Y, Huang K, Li X, Cheng J, Xu D, Yang X, Han K, Weng X, Wang W. Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits. J Genet Genomics 2024:S1673-8527(24)00068-7. [PMID: 38582298 DOI: 10.1016/j.jgg.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/30/2024] [Accepted: 03/30/2024] [Indexed: 04/08/2024]
Abstract
The phenotypic diversity resulting from artificial or natural selection of sheep has made a significant contribution to human civilization. Hu sheep are a local sheep breed unique to China with high reproductive rates and rapid growth. Genome selection signatures have been widely used to investigate the genetic mechanisms underlying phenotypic variation in livestock. Here, we conduct whole-genome sequencing of 207 Hu sheep and compare them with the wild ancestors of domestic sheep (Asiatic mouflon) to investigate the genetic characteristics and selection signatures of Hu sheep. Based on six signatures of selection approaches, we detect genomic regions containing genes related to reproduction (BMPR1B, BMP2, PGFS, CYP19, CAMK4, GGT5, and GNAQ), vision (ALDH1A2, SAG, and PDE6B), nervous system (NAV1), and immune response (GPR35, SH2B2, PIK3R3, and HRAS). Association analysis with a population of 1299 Hu sheep reveal those missense mutations in the GPR35 (GPR35 g.952651 A>G; GPR35 g.952496 C>T) and NAV1 (NAV1 g.84216190 C>T; NAV1 g.84227412 G>A) genes are significantly associated (P < 0.05) with immune and growth traits in Hu sheep, respectively. This research offers unique insights into the selection characteristics of Hu sheep and facilitates further genetic improvement and molecular investigations.
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Affiliation(s)
- Liming Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Lvfeng Yuan
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Fadi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Huibin Tian
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Yukun Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Yuan Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Kai Huang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaolong Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Jiangbo Cheng
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Dan Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaobin Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Kunchao Han
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiuxiu Weng
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Weimin Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China.
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13
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Sonti S, Littleton SH, Pahl MC, Zimmerman AJ, Chesi A, Palermo J, Lasconi C, Brown EB, Pippin JA, Wells AD, Doldur-Balli F, Pack AI, Gehrman PR, Keene AC, Grant SFA. Perturbation of the insomnia WDR90 GWAS locus pinpoints rs3752495 as a causal variant influencing distal expression of neighboring gene, PIG-Q. Sleep 2024:zsae085. [PMID: 38571402 DOI: 10.1093/sleep/zsae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Indexed: 04/05/2024] Open
Abstract
Although genome wide association studies (GWAS) have identified loci for sleep-related traits, they do not directly uncover the underlying causal variants and corresponding effector genes. The majority of such variants reside in non-coding regions and are therefore presumed to impact cis-regulatory elements. Our previously reported 'variant-to-gene mapping' effort in human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs), combined with validation in both Drosophila and zebrafish, implicated PIG-Q as a functionally relevant gene at the insomnia 'WDR90' GWAS locus. However, importantly that effort did not characterize the corresponding underlying causal variant. Specifically, our previous 3D genomic datasets nominated a shortlist of three neighboring single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium within an intronic enhancer region of WDR90 that contacted the open PIG-Q promoter. We sought to investigate the influence of these SNPs collectively and then individually on PIG-Q modulation to pinpoint the causal "regulatory" variant. Starting with gross level perturbation, deletion of the entire region in NPCs via CRISPR-Cas9 editing and subsequent RNA sequencing revealed expression changes in specific PIG-Q transcripts. Results from individual luciferase reporter assays for each SNP in iPSCs revealed that the region with the rs3752495 risk allele induced a ~2.5-fold increase in luciferase expression. Importantly, rs3752495 also exhibited an allele specific effect, with the risk allele increasing the luciferase expression by ~2-fold versus the non-risk allele. In conclusion, our variant-to-function approach and in vitro validation implicates rs3752495 as a causal insomnia variant embedded within WDR90 while modulating the expression of the distally located PIG-Q.
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Affiliation(s)
- Shilpa Sonti
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sheridan H Littleton
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Amber J Zimmerman
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Justin Palermo
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Chiara Lasconi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Elizabeth B Brown
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Fusun Doldur-Balli
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Allan I Pack
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Phillip R Gehrman
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Division of Human Genetics and Endocrinology & Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
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14
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Rong Y, Ma R, Zhang Y, Guo Z. Melatonin's effect on hair follicles in a goat ( Capra hircus) animal model. Front Endocrinol (Lausanne) 2024; 15:1361100. [PMID: 38628581 PMCID: PMC11018883 DOI: 10.3389/fendo.2024.1361100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction Melatonin can treat androgenetic alopecia in males. Goats can be used as animal models to study melatonin treatment for human alopecia. In this study, a meta-analysis of melatonin's effects on goat hair follicles was pursued. Methods Literature from the last 20 years was searched in Scopus, Science Direct, Web of Science and PubMed. Melatonin's effect on goat hair follicles and litter size were performed through a traditional meta-analysis and trial sequential analysis. A network meta-analysis used data from oocyte development to blastocyst. The hair follicle genes regulated by melatonin performed KEGG and PPI. We hypothesized that there are differences in melatonin receptors between different goats, and therefore completed melatonin receptor 1A homology modelling and molecular docking. Results The results showed that melatonin did not affect goat primary follicle or litter size. However, there was a positive correlation with secondary follicle growth. The goat melatonin receptor 1A SNPs influence melatonin's functioning. The wild type gene defect MR1 is a very valuable animal model. Discussion Future studies should focus on the relationship between goat SNPs and the effect of embedded melatonin. This study will provide theoretical guidance for the cashmere industry and will be informative for human alopecia research.
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Affiliation(s)
- Youjun Rong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Rong Ma
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Northern Agriculture and Livestock Husbandry Technical Innovation Center, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zhenhua Guo
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, China
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15
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Qin L, Qiu M, Lin Q, Jiang B, Zhan S, Wei X, Wei J, Liu Y, Wen Q, Chen P, Jiang Y, Zhou Z, Liang X, Cao J, Gong Y, Wei Y, Wei X, Yu H. Association between novel genetic variants of Notch signaling pathway genes and survival of hepatitis B virus-related hepatocellular carcinoma. Cancer Med 2024; 13:e7040. [PMID: 38562021 PMCID: PMC10985410 DOI: 10.1002/cam4.7040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/22/2023] [Accepted: 02/08/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Although the Notch pathway plays an important role in formation and progression of hepatocellular carcinoma (HCC), few studies have reported the associations between functional genetic variants and the survival of hepatitis B virus (HBV)-related HCC. METHODS In the present study, we performed multivariable Cox proportional hazard regression analysis to evaluate associations between 36,101 SNPs in 264 Notch pathway-related genes and overall survival (OS) of 866 patients with HBV-related HCC. RESULTS It was found that three independent SNPs (NEURL1B rs4868192, CNTN1 rs444927 and FCER2 rs1990975) were significantly associated with the HBV-related HCC OS. The number of protective genotypes (NPGs) were significantly associated with better survival in a dose-response manner (ptrend <0.001). Compared with the model with sole clinical factors, the addition of protective genotypes to the predict models significantly increased the AUC, i.e., from 72.72% to 75.13% (p = 0.002) and from 72.04% to 74.76 (p = 0.004) for 3-year and 5-year OS, respectively. The expression quantitative trait loci (eQTL) analysis further revealed that the rs4868192 C allele was associated with lower mRNA expression levels of NEURL1B in the whole blood (p = 1.71 × 10-3), while the rs1990975 T allele was correlated with higher mRNA expression levels of FCER2 in the whole blood and normal liver tissues (p = 3.51 × 10-5 and 0.033, respectively). CONCLUSIONS Three potentially functional SNPs of NEURL1B, CNTN1 and FCER2 may serve as potential prognostic biomarkers for HBV-related HCC.
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Affiliation(s)
- Liming Qin
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Moqin Qiu
- Department of Respiratory OncologyGuangxi Medical University Cancer HospitalNanningChina
| | - Qiuling Lin
- Department of Clinical ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Binbin Jiang
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Shicheng Zhan
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Xueyan Wei
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Junjie Wei
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Yingchun Liu
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Qiuping Wen
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Peiqin Chen
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Yanji Jiang
- Department of Scientific ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Zihan Zhou
- Department of Cancer Prevention and ControlGuangxi Medical University Cancer HospitalNanningChina
| | - Xiumei Liang
- Department of Disease Process ManagementGuangxi Medical University Cancer HospitalNanningChina
| | - Ji Cao
- Department of Cancer Prevention and ControlGuangxi Medical University Cancer HospitalNanningChina
| | - Yizhen Gong
- Department of Clinical ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Yuying Wei
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Xiaoxia Wei
- Department of Clinical ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Hongping Yu
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor(Guangxi Medical University), Ministry of EducationNanningChina
- Key Cultivated Laboratory of Cancer Molecular Medicine of Guangxi Health CommissionGuangxi Medical University Cancer HospitalNanningChina
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16
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Gao R, Yang G, Wang M, Xiao J, Yi S, Huang Y, Guo Z, Kang Y, Fu Q, Wang M, Xu B, Shen S, Zhu Q, Liu M, Wang L, Cui X, Yi S, Kou X, Zhao Y, Gu L, Wang H, Gao S, Jiang C, Chen J. Defining a TFAP2C-centered transcription factor network during murine peri-implantation. Dev Cell 2024:S1534-5807(24)00185-0. [PMID: 38574734 DOI: 10.1016/j.devcel.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/07/2023] [Accepted: 03/06/2024] [Indexed: 04/06/2024]
Abstract
Transcription factors (TFs) play important roles in early embryonic development, but factors regulating TF action, relationships in signaling cascade, genome-wide localizations, and impacts on cell fate transitions during this process have not been clearly elucidated. In this study, we used uliCUT&RUN-seq to delineate a TFAP2C-centered regulatory network, showing that it involves promoter-enhancer interactions and regulates TEAD4 and KLF5 function to mediate cell polarization. Notably, we found that maternal retinoic acid metabolism regulates TFAP2C expression and function by inducing the active demethylation of SINEs, indicating that the RARG-TFAP2C-TEAD4/KLF5 axis connects the maternal-to-zygotic transition to polarization. Moreover, we found that both genomic imprinting and SNP-transferred genetic information can influence TF positioning to regulate parental gene expressions in a sophisticated manner. In summary, we propose a ternary model of TF regulation in murine embryonic development with TFAP2C as the core element and metabolic, epigenetic, and genetic information as nodes connecting the pathways.
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Affiliation(s)
- Rui Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Guang Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Mengting Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Jing Xiao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanru Yi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanxin Huang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Zhenxiang Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yunzhe Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Qianzheng Fu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Mingzhu Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Ben Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shijun Shen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Qianshu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Meng Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Liping Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xinyu Cui
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanshan Yi
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanhong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Liang Gu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai 200120, China.
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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Fang T, Liu MN, Liu MQ, Tian XY, Zhang XJ, Liu F, Hao W, Wu N, Li H, Li J. A preliminary study on the association of single nucleotide polymorphisms and methylation of dopamine system-related genes with psychotic symptoms in patients with methamphetamine use disorder. Eur J Neurosci 2024; 59:1428-1440. [PMID: 38151046 DOI: 10.1111/ejn.16238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023]
Abstract
Methamphetamine use disorder (MAUD) can substantially jeopardize public security due to its high-risk social psychology and behaviour. Given that the dopamine reward system is intimately correlated with MAUD, we investigated the association of single nucleotide polymorphisms (SNPs), as well as methylation status of dopamine receptor type 4 (DRD4), catechol-O-methyltransferase (COMT) genes, and paranoid and motor-impulsive symptoms in MAUD patients. A total of 189 MAUD patients participated in our study. Peripheral blood samples were used to detect 3 SNPs and 35 CpG units of methylation in the DRD4 gene promoter region and 5 SNPs and 39 CpG units in the COMT gene. MAUD patients with the DRD4 rs1800955 C allele have a lower percentage of paranoid symptoms than those with the rs1800955 TT allele. Individuals with paranoid symptoms exhibited a reduced methylation degree at a particular DRD4 CpG2.3 unit. The interaction of the DRD4 rs1800955 C allele and the reduced DRD4CpG2.3 methylation degree were associated with a lower occurrence of paranoid symptoms. Meanwhile, those with the COMT rs4818 CC allele had lower motor-impulsivity scores in MAUD patients but greater COMT methylation levels in the promoter region and methylation degree at the COMT CpG 51.52 unit. Therefore, based only on the COMT rs4818 CC polymorphism, there was a negative correlation between COMT methylation and motor-impulsive scores. Our preliminary results provide a clue that the combination of SNP genotype and methylation status of the DRD4 and COMT genes serve as biological indicators for the prevalence of relatively high-risk psychotic symptoms in MAUD patients.
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Affiliation(s)
- Ting Fang
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Meng-Nan Liu
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Meng-Qi Liu
- National Clinical Research Center for Mental Disorders, and Department of Psychiatry, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiao-Yu Tian
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Xiao-Jie Zhang
- National Clinical Research Center for Mental Disorders, and Department of Psychiatry, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Feng Liu
- Compulsory Detoxification Center of Changsha Public Security Bureau, Changsha, China
| | - Wei Hao
- National Clinical Research Center for Mental Disorders, and Department of Psychiatry, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ning Wu
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Hong Li
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Jin Li
- Beijing Key Laboratory of Neuropsychopharmacology, State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
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18
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Oliveira SR, de Arruda JAA, Schneider AH, Bemquerer LM, de Souza RMS, Barbim P, de Mattos-Pereira GH, Calderaro DC, Machado CC, Alves SF, Moreira PR, de Oliveira RDR, Louzada-Júnior P, Abreu LG, Cunha FQ, Silva TA. Neutrophil extracellular traps in rheumatoid arthritis and periodontitis: Contribution of PADI4 gene polymorphisms. J Clin Periodontol 2024; 51:452-463. [PMID: 38115803 DOI: 10.1111/jcpe.13921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/26/2023] [Accepted: 12/03/2023] [Indexed: 12/21/2023]
Abstract
AIM We sought to investigate the release of neutrophil extracellular traps (NETs) in neutrophils from individuals with rheumatoid arthritis (RA) and controls and compare the presence of NETs in gingival tissues according to periodontal status. Also, the association between single nucleotide polymorphisms (SNPs) of the peptidyl arginine deaminase type 4 (PADI4) gene and the GTG haplotype with RA, periodontitis and NETs was evaluated in vitro. MATERIALS AND METHODS Peripheral neutrophils were isolated by density gradient, and NET concentration was determined by the PicoGreen method. Immunofluorescence was studied to identify NETs by co-localization of myeloperoxidase (MPO)-citrullinated histone H3 (H3Cit). Genotyping for SNPs (PADI4_89; PADI4_90; PADI4_92; and PADI4_104) was performed in 87 individuals with RA and 111 controls. RESULTS The release of NETs in vitro was significantly higher in individuals with RA and periodontitis and when stimulated with Porphyromonas gingivalis. Gingival tissues from subjects with RA and periodontitis revealed increased numbers of MPO-H3Cit-positive cells. Individuals with the GTG haplotype showed a higher release of NETs in vitro and worse periodontal parameters. CONCLUSIONS The release of NETs by circulating neutrophils is associated with RA and periodontitis and is influenced by the presence of the GTG haplotype.
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Affiliation(s)
- Sicília Rezende Oliveira
- Department of Oral Surgery, Pathology and Clinical Dentistry, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - José Alcides Almeida de Arruda
- Department of Oral Surgery, Pathology and Clinical Dentistry, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ayda Henriques Schneider
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Larissa Marques Bemquerer
- Department of Oral Surgery, Pathology and Clinical Dentistry, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rayssa Maria Soalheiro de Souza
- Department of Oral Surgery, Pathology and Clinical Dentistry, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Paula Barbim
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Gustavo Henrique de Mattos-Pereira
- Department of Oral Surgery, Pathology and Clinical Dentistry, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Débora Cerqueira Calderaro
- Department of Locomotor Apparatus, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Caio Cavalcante Machado
- Division of Clinical Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Sandra Fukada Alves
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Paula Rocha Moreira
- Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Paulo Louzada-Júnior
- Division of Clinical Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Lucas Guimarães Abreu
- Department of Child and Adolescent Oral Health, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernando Queiroz Cunha
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Tarcília Aparecida Silva
- Department of Oral Surgery, Pathology and Clinical Dentistry, School of Dentistry, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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19
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Zhang M, Liang J, Han J, Zhang W, Wan P, Yang L, Zang X, Ren W, Zhang L, Dai H, Wu Y, Jin T. SOWAHB polymorphisms affect thyroid cancer risk in the Chinese Han population. Expert Rev Mol Diagn 2024; 24:333-339. [PMID: 38263767 DOI: 10.1080/14737159.2024.2305183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024]
Abstract
OBJECTIVES This study aimed to detect the correlation between SOWAHB polymorphisms and Thyroid cancer (TC) risk in the Chinese Han population. METHODS We genotyped SOWAHB variants in 510 TC patients and 509 controls using Agena MassARRAY. We assessed the association between SOWAHB polymorphisms and TC susceptibility, with the significant results evaluated through FPRP analysis. We predicted TC risk by the SNP-SNP interaction, analyzed by MDR. RESULTS Carriers with rs2703129 CC had a lower probability of TC (codominant, recessive: p = 0.002), while subjects with rs1874564 AG had an increased risk of developing TC (codominant, recessive: p = 0.000, log-additive: p = 0.028). In subjects aged > 45 years, rs2703129 may reduce TC predisposition (codominant: p = 0.011, recessive: p = 0.007), but there was an increased association between rs1874564 and TC risk (codominant: p = 0.030, dominant: p = 0.047). Also, rs2703129 was associated with a lower risk of TC among males (codominant: p = 0.018, recessive: p = 0.013). Conversely, rs1874564 was associated with an increased risk of TC in females (codominant: p = 0.001, dominant: p = 0.003). CONCLUSION SOWAHB SNPs were related to the occurrence of TC, and rs2703129 may be a protective site for TC.
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Affiliation(s)
- Man Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University institution, Xi'an, Shaanxi, China
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Biotechnology, Northwest University, Xi'an, Shaanxi, China
| | - Jing Liang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University institution, Xi'an, Shaanxi, China
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Biotechnology, Northwest University, Xi'an, Shaanxi, China
| | - Junhui Han
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University institution, Xi'an, Shaanxi, China
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Biotechnology, Northwest University, Xi'an, Shaanxi, China
| | - Wenjing Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University institution, Xi'an, Shaanxi, China
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Biotechnology, Northwest University, Xi'an, Shaanxi, China
| | - Panpan Wan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University institution, Xi'an, Shaanxi, China
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Biotechnology, Northwest University, Xi'an, Shaanxi, China
| | - Leteng Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University institution, Xi'an, Shaanxi, China
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Biotechnology, Northwest University, Xi'an, Shaanxi, China
| | - Xufeng Zang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University institution, Xi'an, Shaanxi, China
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Biotechnology, Northwest University, Xi'an, Shaanxi, China
| | - Wanli Ren
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ling Zhang
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hao Dai
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yue Wu
- Operation Department, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University institution, Xi'an, Shaanxi, China
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Biotechnology, Northwest University, Xi'an, Shaanxi, China
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Larios-Serrato V, Valdez-Salazar HA, Ruiz-Tachiquín ME. The landscape of 8q24 cytoband in gastric cancer (Review). Oncol Lett 2024; 27:179. [PMID: 38464340 PMCID: PMC10921260 DOI: 10.3892/ol.2024.14311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024] Open
Abstract
Worldwide, gastric cancer (GC) is estimated to be the fifth most common type of cancer type in both sexes, ranking sixth for new cases, with >640,850 cases per year, and fourth in terms of mortality rate. Cancer presents numerical and structural alterations in chromosomes, often through gains and losses of regions. In GC, there are multiple genetic alterations, in which those located in cytoband 8q24 have been frequently described; essential genes are present in this cytoband, regulating the homeostasis of crucial biological processes, such as the MYC gene, which induces expression of selective genes to promote cell growth and proliferation. Conversely, DNA sequence variations can also occur when a single nucleotide in the genome sequence is altered, and this is termed a single nucleotide polymorphism (SNP). These alterations, which can serve as a biological marker, are present in at least 1% of the population and assist in identifying genes associated with GC. In the present review, 12 genes present in cytoband 8q24 related to GC (NSMCE2, PCAT1, CASC19, CASC8, CCAT2, PRNCR1, POU5F1B, PSCA, JRK, MYC, PVT1 and PTK2) are discussed. The PSCA gene was cited more frequently than others; it has four known SNPs associated with GC (rs2978980, rs2294008, rs2976392 and rs9297976). Thus, these SNPs should be further studied in different populations to determine their risk value in patients with GC.
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Affiliation(s)
- Violeta Larios-Serrato
- Genomics Biotechnology and Bioinformatics Laboratory, National School of Biological Sciences (ENCB), National Polytechnic Institute (IPN), Lázaro Cárdenas Professional Unit, Mexico City 11340, Mexico
| | - Hilda-Alicia Valdez-Salazar
- Medical Research Unit in Infectious and Parasitic Diseases (UIMEIP), Pediatrics Hospital ‘Dr. Silvestre Frenk Freund’, Mexico City 06720, Mexico
| | - Martha-Eugenia Ruiz-Tachiquín
- Medical Research Unit in Oncological Diseases (UIMEO), Oncology Hospital, Century XXI National Medical Center, Mexican Social Security Institute (IMSS), Mexico City 06720, Mexico
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21
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Wu H, Zhang X, Lin G, Zhang Q, He Z, Wang Z, Xu W, Yin X, Su L, Zhuang Y, Gong A. Correlation of single nucleotide polymorphisms in the AGT gene with susceptibility to systemic lupus erythematosus in Northeast China. Int J Immunogenet 2024; 51:81-88. [PMID: 38265173 DOI: 10.1111/iji.12655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/31/2023] [Accepted: 01/06/2024] [Indexed: 01/25/2024]
Abstract
To investigate the correlation between susceptibility to systemic lupus erythematosus (SLE) and single nucleotide polymorphisms (SNPs) rs699, rs4762 and rs1926723 in the AGT gene in the population of Northeast China, while also introducing a new method for early detection of SLE. A total of 856 cases of SLE patients and healthy volunteers who attended the First Affiliated Hospital of Harbin Medical University from January 2020 to December 2022 were recruited. Clinical information and biood samples were collected from particpants in this study. SNaPshot sequencing technology was used to sequence the bases of the rs699, rs4762 and rs1926723 in the AGT gene. The genetic stability of SNPs was analysed by means of Hardy-Weinberg (HWE) genetic equilibrium. The study examined the correlation between genetically stable SNPs and susceptibility to SLE using logistic regression analysis. Rs699 did not adhere to the principles of the HWE genetic equilibrium (p < .01). Conversely, both rs4762 and rs1926723 conformed to the HWE genetic equilibrium (p > .05). However, no significant differences in genotypes and alleles frequencies of the rs4762 were observed between the two groups (p > .05). Furthermore, there was a significant difference in the distribution of AG, GG genotypes frequency and G allele frequency at the rs1926723 between the two groups (p < .001). Individuals with AG and GG genotypes and the G allele had a significantly lower frequency of SLE, indicating a potential genetic protective factor against susceptibility to the SLE. The SNPs rs1926723 may be linked to the susceptibility to SLE, and the AG, GG genotypes and the G allele may be important protective factors for the development of SLE in Northeast China.
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Affiliation(s)
- Huitao Wu
- Heilongjiang Academy of Sciences of TCM, Harbin, Heilongjiang, China
| | - Xuan Zhang
- College of Traditional Chinese Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Guiling Lin
- College of Traditional Chinese Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Qi Zhang
- Heilongjiang Academy of Sciences of TCM, Harbin, Heilongjiang, China
| | - Ziman He
- Heilongjiang Academy of Sciences of TCM, Harbin, Heilongjiang, China
| | - Zhe Wang
- College of Traditional Chinese Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Wenlu Xu
- College of Traditional Chinese Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Xiyu Yin
- Heilongjiang Academy of Sciences of TCM, Harbin, Heilongjiang, China
| | - Linglan Su
- Heilongjiang Academy of Sciences of TCM, Harbin, Heilongjiang, China
| | - Yanping Zhuang
- International Research Center for Aging and Cancer, Hainan Medical University, Haikou, Hainan, China
| | - Aimin Gong
- College of Traditional Chinese Medicine, Hainan Medical University, Haikou, Hainan, China
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22
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Niu R, Zhang X, Yu Y, Bao Z, Yang J, Yuan J, Li F. Identification of Growth-Related Gene BAMBI and Analysis of Gene Structure and Function in the Pacific White Shrimp Litopenaeus vannamei. Animals (Basel) 2024; 14:1074. [PMID: 38612313 PMCID: PMC11011141 DOI: 10.3390/ani14071074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/30/2024] [Accepted: 03/30/2024] [Indexed: 04/14/2024] Open
Abstract
As one of the most important aquaculture species in the world, the improvement of growth traits of the Pacific white shrimp (Litopenaeus vannamei), has always been a primary focus. In this study, we conducted SNP-specific locus analysis and identified a growth-related gene, BAMBI, in L. vannamei. We analyzed the structure and function of LvBAMBI using genomic, transcriptomic, metabolomic, and RNA interference (RNAi) assays. The LvBAMBI possessed highly conserved structural domains and widely expressed in various tissues. Knockdown of LvBAMBI significantly inhibited the gain of body length and weight of the shrimp, underscoring its role as a growth-promoting factor. Specifically, knockdown of LvBAMBI resulted in a significant downregulation of genes involved in lipid metabolism, protein synthesis, catabolism and transport, and immunity. Conversely, genes related to glucose metabolism exhibited significant upregulations. Analysis of differential metabolites (DMs) in metabolomics further revealed that LvBAMBI knockdown may primarily affect shrimp growth by regulating biological processes related to lipid and glucose metabolism. These results suggested that LvBAMBI plays a crucial role in regulating lipid metabolism, glucose metabolism, and protein transport in shrimp. This study provides valuable insights for future research and utilization of BAMBI genes in shrimp and crustaceans.
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Affiliation(s)
- Ruigang Niu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhenning Bao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junqing Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (R.N.); (Y.Y.); (Z.B.); (J.Y.); (J.Y.); (F.L.)
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
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Su B, Du G, Hou S, Chen Z, Wu X, He G, Yuan J, Xie C. Antimicrobial Resistance Analysis and Whole-Genome Sequencing of Salmonella Isolates from Environmental Sewage - Guangzhou City, Guangdong Province, China, 2022-2023. China CDC Wkly 2024; 6:254-260. [PMID: 38633200 PMCID: PMC11018552 DOI: 10.46234/ccdcw2024.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 02/29/2024] [Indexed: 04/19/2024] Open
Abstract
What is already known about this topic? S.1,4,[5],12:i:- and S. Rissen are emerging serotypes of Salmonella that require close monitoring for antimicrobial resistance and containment of their spread. What is added by this report? The study aimed to identify antimicrobial resistance genes (ARGs) in S.1,4,[5],12:i:- and S. Rissen strains isolated from environmental sewage in Guangzhou City, Guangdong Province, China. A phylogenetic tree was constructed using single nucleotide polymorphism data to assess genetic relatedness among strains, offering insights for Salmonella infection outbreak investigations in the future. What are the implications for public health practice? It is crucial to implement strategies, such as integrating different networks, to control the spread of drug-resistant Salmonella. Novel technologies must be utilized to disinfect sewage and eliminate ARGs. Ensuring food safety and proper sewage disinfection are essential to curb the dissemination of Salmonella.
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Affiliation(s)
- Bihui Su
- Tuberculosis Management and Treatment Department, Guangzhou Chest Hospital, Guangzhou City, Guangdong Province, China
| | - Guanghong Du
- School of Public Health, Guangzhou Medical University, Guangzhou City, Guangdong Province, China
| | - Shuiping Hou
- Guangzhou Center for Disease Control and Prevention, Guangzhou City, Guangdong Province, China
| | - Zongqiu Chen
- Guangzhou Center for Disease Control and Prevention, Guangzhou City, Guangdong Province, China
| | - Xiaoying Wu
- Tuberculosis Management and Treatment Department, Guangzhou Chest Hospital, Guangzhou City, Guangdong Province, China
| | - Gang He
- Tuberculosis Management and Treatment Department, Guangzhou Chest Hospital, Guangzhou City, Guangdong Province, China
| | - Jun Yuan
- Guangzhou Center for Disease Control and Prevention, Guangzhou City, Guangdong Province, China
| | - Chaojun Xie
- Office of the Director, Huadu District Center for Disease Control and Prevention, Guangzhou City, Guangdong Province, China
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24
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Ćeran M, Đorđević V, Miladinović J, Vasiljević M, Đukić V, Ranđelović P, Jaćimović S. Selective Genotyping and Phenotyping for Optimization of Genomic Prediction Models for Populations with Different Diversity. Plants (Basel) 2024; 13:975. [PMID: 38611503 PMCID: PMC11013471 DOI: 10.3390/plants13070975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
To overcome the different challenges to food security caused by a growing population and climate change, soybean (Glycine max (L.) Merr.) breeders are creating novel cultivars that have the potential to improve productivity while maintaining environmental sustainability. Genomic selection (GS) is an advanced approach that may accelerate the rate of genetic gain in breeding using genome-wide molecular markers. The accuracy of genomic selection can be affected by trait architecture and heritability, marker density, linkage disequilibrium, statistical models, and training set. The selection of a minimal and optimal marker set with high prediction accuracy can lower genotyping costs, computational time, and multicollinearity. Selective phenotyping could reduce the number of genotypes tested in the field while preserving the genetic diversity of the initial population. This study aimed to evaluate different methods of selective genotyping and phenotyping on the accuracy of genomic prediction for soybean yield. The evaluation was performed on three populations: recombinant inbred lines, multifamily diverse lines, and germplasm collection. Strategies adopted for marker selection were as follows: SNP (single nucleotide polymorphism) pruning, estimation of marker effects, randomly selected markers, and genome-wide association study. Reduction of the number of genotypes was performed by selecting a core set from the initial population based on marker data, yet maintaining the original population's genetic diversity. Prediction ability using all markers and genotypes was different among examined populations. The subsets obtained by the model-based strategy can be considered the most suitable for marker selection for all populations. The selective phenotyping based on makers in all cases had higher values of prediction ability compared to minimal values of prediction ability of multiple cycles of random selection, with the highest values of prediction obtained using AN approach and 75% population size. The obtained results indicate that selective genotyping and phenotyping hold great potential and can be integrated as tools for improving or retaining selection accuracy by reducing genotyping or phenotyping costs for genomic selection.
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Affiliation(s)
- Marina Ćeran
- Laboratory for Biotechnology, Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maksima Gorkog 30, 21000 Novi Sad, Serbia
| | - Vuk Đorđević
- Legumes Department, Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (V.Đ.); (J.M.); (M.V.); (V.Đ.); (P.R.); (S.J.)
| | - Jegor Miladinović
- Legumes Department, Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (V.Đ.); (J.M.); (M.V.); (V.Đ.); (P.R.); (S.J.)
| | - Marjana Vasiljević
- Legumes Department, Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (V.Đ.); (J.M.); (M.V.); (V.Đ.); (P.R.); (S.J.)
| | - Vojin Đukić
- Legumes Department, Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (V.Đ.); (J.M.); (M.V.); (V.Đ.); (P.R.); (S.J.)
| | - Predrag Ranđelović
- Legumes Department, Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (V.Đ.); (J.M.); (M.V.); (V.Đ.); (P.R.); (S.J.)
| | - Simona Jaćimović
- Legumes Department, Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (V.Đ.); (J.M.); (M.V.); (V.Đ.); (P.R.); (S.J.)
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25
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Moctezuma B, Santiago Á, Burguete-García A, Martínez-Barnetche J, Morales-Gómez C, Hernandez-Chavez C, Gil G, Peterson KE, Tellez-Rojo MM, Lamadrid-Figueroa H. Single nucleotide polymorphisms of ANKK1, DDR4, and GRIN2B genes predict behavior in a prospective cohort of Mexican children and adolescents. Int J Dev Neurosci 2024. [PMID: 38530142 DOI: 10.1002/jdn.10326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/10/2024] [Accepted: 02/13/2024] [Indexed: 03/27/2024] Open
Abstract
Numerous studies have established associations between single nucleotide polymorphisms (SNPs) and various behavioral and neurodevelopmental conditions. This study explores the links between SNPs in candidate genes involved in central nervous system (CNS) physiology and their implications for the behavioral and emotional aspects in children and teenagers. A total of 590 participants, aged 7-15 years, from the Early Life Exposures In Mexico To Environmental Toxicants (ELEMENT) cohort study in Mexico City, underwent genotyping for at least one of 15 CNS gene-related SNPs at different timepoints. We employed multiple linear regression models to assess the potential impact of genetic variations on behavioral and cognitive traits, as measured by the Behavioral Assessment System for Children (BASC) and Conners parent rating scales. Significant associations were observed, including the rs1800497 TC genotype (ANKK1) with the Cognitive Problems/Inattention variable (p value = 0.003), the rs1800955 CT genotype (DDR4) with the Emotional Lability Global index variable (p value = 0.01), and the rs10492138 GA and rs7970177 TC genotypes (GRIN2B) with the Depression variable (p values 0.007 and 0.012, respectively). These finds suggest potential genetic profiles associated with "risk" and "protective" behaviors for these SNPs. Our results provide valuable insights into the role of genetic variations in neurobehavior and highlight the need for further research in the early identification and intervention in individuals at risk for these conditions.
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Affiliation(s)
- Barbara Moctezuma
- School of Public Health of Mexico, National Institute of Public Health, Cuernavaca, Mexico
| | - Ángel Santiago
- Department of Perinatal Health, National Institute of Public Health, Cuernavaca, Mexico
| | - Ana Burguete-García
- Center for Population Health Research, National Institute of Public Health, Cuernavaca, Mexico
| | | | - Claudia Morales-Gómez
- Epidemiologic Surveillance, Mexican Institute of Social Security-Bienestar, Mexico City, Mexico
| | - Carmen Hernandez-Chavez
- Department of Developmental Neurobiology, National Institute of Perinatology, Mexico City, Mexico
| | - Gabriela Gil
- Department of Developmental Neurobiology, National Institute of Perinatology, Mexico City, Mexico
| | - Karen E Peterson
- Nutritional Sciences Department, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Martha M Tellez-Rojo
- Center for Research in Nutrition and Health, National Institute of Public Health, Cuernavaca, Mexico
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26
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Burridge AJ, Winfield M, Przewieslik-Allen A, Edwards KJ, Siddique I, Barral-Arca R, Griffiths S, Cheng S, Huang Z, Feng C, Dreisigacker S, Bentley AR, Brown-Guedira G, Barker GL. Development of a next generation SNP genotyping array for wheat. Plant Biotechnol J 2024. [PMID: 38520342 DOI: 10.1111/pbi.14341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/25/2024]
Abstract
High-throughput genotyping arrays have provided a cost-effective, reliable and interoperable system for genotyping hexaploid wheat and its relatives. Existing, highly cited arrays including our 35K Wheat Breeder's array and the Illumina 90K array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in wheat sequencing has given us access to a vast pool of SNP diversity, whilst technological improvements have allowed us to fit significantly more probes onto a 384-well format Axiom array than previously possible. Here we describe a novel Axiom genotyping array, the 'Triticum aestivum Next Generation' array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins 'Core Collection'. We used a novel haplotype optimization approach to select SNPs with the highest combined varietal discrimination and a design iteration step to test and replace SNPs which failed to convert to reliable markers. The final design with 43 372 SNPs contains a combination of haplotype-optimized novel SNPs and legacy cross-platform markers. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome-wide association studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available.
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Affiliation(s)
| | - Mark Winfield
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Keith J Edwards
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Imteaz Siddique
- Thermo Fisher Scientific, 3450 Central Expressway, Santa Clara, CA, USA
| | - Ruth Barral-Arca
- Thermo Fisher Scientific, 3450 Central Expressway, Santa Clara, CA, USA
| | | | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zejian Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Cong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | | | - Gina Brown-Guedira
- Plant Science Research Unit, USDA Agricultural Research Service, Raleigh, NC, USA
| | - Gary L Barker
- School of Biological Sciences, University of Bristol, Bristol, UK
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27
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Solodilova M, Drozdova E, Azarova I, Klyosova E, Bykanova M, Bushueva O, Polonikova A, Churnosov M, Polonikov A. The discovery of GGT1 as a novel gene for ischemic stroke conferring protection against disease risk in non-smokers and non-abusers of alcohol. J Stroke Cerebrovasc Dis 2024:107685. [PMID: 38522756 DOI: 10.1016/j.jstrokecerebrovasdis.2024.107685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/09/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024] Open
Abstract
OBJECTIVES Increased plasma gamma-glutamyl transferase (GGT1) has been identified as a robust and independent risk factor for ischemic stroke (IS), but the molecular mechanisms of the enzyme-disease association are unclear. The present study investigated whether polymorphisms in the GGT1 gene contribute to IS susceptibility. MATERIALS AND METHODS DNA samples obtained from 1288 unrelated individuals (600 IS patients and 688 controls) were genotyped for common single nucleotide polymorphisms of GGT1 using the MassArray-4 platform. RESULTS The rs5751909 polymorphism was significantly associated with decreased risk of ischemic stroke regardless sex and age (Pperm≤0.01, dominant genetic model). The haplotype rs4820599A-rs5760489A-rs5751909A showed strong protection against ischemic stroke (OR 0.53, 95%CI 0.36 - 0.77, Pperm≤0.0001). The protective effect of SNP rs5751909 in the stroke phenotype was successfully replicated in the UK Biobank, SiGN, and ISGC cohorts (P≤0.01). GGT1 polymorphisms showed joint (epistatic) effects on the risk of ischemic stroke, with some known IS-associated GWAS loci (e.g., rs4322086 and rs12646447) investigated in our population. In addition, SNP rs5751909 was found to be strongly associated with a decreased risk of ischemic stroke in non-smokers (OR 0.54 95%CI 0.39-0.75, Pperm=0.0002) and non-alcohol abusers (OR 0.43 95%CI 0.30-0.61, Pperm=2.0 × 10-6), whereas no protective effects of this SNP against disease risk were observed in smokers and alcohol abusers (Pperm<0.05). CONCLUSIONS We propose mechanisms underlying the observed associations between GGT1 polymorphisms and ischemic stroke risk. This pilot study is the first to demonstrate that GGT1 is a novel susceptibility gene for ischemic stroke and provides additional evidence of the genetic contribution to impaired redox homeostasis underlying disease pathogenesis.
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Affiliation(s)
- Maria Solodilova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk 305041, Russian Federation.
| | - Elena Drozdova
- Department of General Hygiene, 3 Karl Marx Street, Kursk 305041, Russian Federation.
| | - Iuliia Azarova
- Department of Biological Chemistry, Kursk State Medical University, 3 Karl Marx Street, Kursk 305041, Russian Federation; Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk 305041, Russian Federation.
| | - Elena Klyosova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk 305041, Russian Federation; Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk 305041, Russian Federation.
| | - Marina Bykanova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk 305041, Russian Federation; Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk 305041, Russian Federation.
| | - Olga Bushueva
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk 305041, Russian Federation; Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk 305041, Russian Federation.
| | - Anna Polonikova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk 305041, Russian Federation.
| | - Mikhail Churnosov
- Department of Medical Biological Disciplines, Belgorod State University, 85 Pobedy Street, Belgorod 308015, Russian Federation.
| | - Alexey Polonikov
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, Kursk 305041, Russian Federation; Laboratory of Statistical Genetics and Bioinformatics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., Kursk 305041, Russian Federation.
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Zhong LS, Chen XY, Xiao J. Associations between interleukin-13, interleukin-4 and their receptor gene polymorphisms and susceptibility to atopic dermatitis in a Chinese Han population. Indian J Dermatol Venereol Leprol 2024; 0:1-8. [PMID: 38594991 DOI: 10.25259/ijdvl_470_2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 12/15/2023] [Indexed: 04/11/2024]
Abstract
Background Atopic dermatitis (AD) is a common skin condition that occurs due to a combined effect of immune dysregulation, skin barrier dysfunction, changes in the cutaneous microbiome, and genetic factors. Recent data from both clinical trials and real-world studies indicate that dupilumab, a biological agent that inhibits interleukin 4 receptor-α is an effective drug in the treatment of AD, which further suggests the important role of IL-13 and IL-4 in the pathogenesis of AD. Objectives To assess the association between gene polymorphisms of IL-13, IL-13 receptor, IL-4, and IL-4 receptor and susceptibility to AD. Methods The single nucleotide polymorphisms (SNPs) of the above-mentioned genes were detected by single base extension (SNaPshot) assay. The association between these SNPs and AD risk was analysed using SPSS software. Results Two hundred and seventy-one subjects including 130 patients with AD and 141 healthy controls were enrolled. There were statistical differences between AD patients and controls in genotype distribution at rs2265753, rs6646259, and rs2254672 of the IL-13 receptor gene (P all < 0.001). Subjects with CG at rs2265753, AG at rs6646259 and TG at rs2254672 had increased risks for AD (P all < 0.001), and subjects with GG at rs2265753, rs6646259, and rs2254672 had reduced risks for AD (P all < 0.001). Limitation This was a single-centre and single-race study, with a relatively small sample size. Conclusions Findings from this study show that rs2265753, rs6646259 and rs2254672 of the IL-13 receptor gene are associated with susceptibility to AD.
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Affiliation(s)
- Lian-Sheng Zhong
- Department of Dermatology, Xiamen Children's Hospital (Children's Hospital of Fudan University Xiamen Branch), Xiamen, Fujian, China
| | - Xiao-Yi Chen
- Department of Dermatology, Xiamen Children's Hospital (Children's Hospital of Fudan University Xiamen Branch), Xiamen, Fujian, China
| | - Jing Xiao
- Department of Dermatology, Xiamen Children's Hospital (Children's Hospital of Fudan University Xiamen Branch), Xiamen, Fujian, China
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Lin SH, Lu JW, Hsieh WT, Chou YE, Su TC, Tsai TJ, Tsai YJ, Yang PJ, Yang SF. Evaluation of the clinical significance of long non-coding RNA MALAT1 genetic variants in human lung adenocarcinoma. Aging (Albany NY) 2024; 16:5740-5750. [PMID: 38517388 PMCID: PMC11006483 DOI: 10.18632/aging.205675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Lung adenocarcinoma (LUAD) is the most frequent histological subtype of lung cancer, which is the most common malignant tumor and the main cause of cancer-related mortality globally. Recent reports revealed that long non-coding RNA (lncRNA) of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) plays a crucial role in tumorigenesis and metastasis development in lung cancer. However, the contribution of MALAT1 genetic variants to the development of LUAD is unclear, especially in epidermal growth factor receptor (EGFR) mutation status. In this study, 272 LADC patients with different EGFR status were recruited to dissect the allelic discrimination of the MALAT1 polymorphisms at rs3200401, rs619586, and rs1194338. The findings of the study showed that MALAT1 polymorphisms rs3200401, rs619586, and rs1194338 were not associated to LUAD susceptibility; however, rs3200401 polymorphisms was significantly correlated to EGFR wild-type status and tumor stages in LUAD patients in dominant model (p=0.016). Further analyses using the datasets from The Cancer Genome Atlas (TCGA) revealed that lower MALAT1 mRNA levels were associated with the advanced stage, and lymph node metastasis in LADC patients. In conclusion, our results showed that MALAT1 rs3200401 polymorphisms dramatically raised the probability of LUAD development.
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Affiliation(s)
- Shu-Hui Lin
- Department of Pathology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Jeng-Wei Lu
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet/National University Hospital, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wang-Ting Hsieh
- The Affiliated High School of Tunghai University, Taichung, Taiwan
- Department of Occupational Therapy, Asia University, Taichung, Taiwan
| | - Ying-Erh Chou
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Tzu-Cheng Su
- Department of Pathology, Changhua Christian Hospital, Changhua, Taiwan
| | - Tun-Jen Tsai
- The Affiliated High School of Tunghai University, Taichung, Taiwan
| | - Yun-Jung Tsai
- Translational Pathology Core Laboratory, Changhua Christian Hospital, Changhua, Taiwan
| | - Po-Jen Yang
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Family and Community Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
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Upadhyay S, Dubey PK. Gene variants polymorphisms and uterine leiomyoma: an updated review. Front Genet 2024; 15:1330807. [PMID: 38572418 PMCID: PMC10987786 DOI: 10.3389/fgene.2024.1330807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/22/2024] [Indexed: 04/05/2024] Open
Abstract
Uterine leiomyoma, commonly referred to as fibroids, is a benign tumor that develops in the muscular wall of the uterus. These growths are non-cancerous and can vary in size, ranging from tiny nodules to larger masses. Uterine leiomyomas often occur during a woman's reproductive years and can lead to symptoms such as heavy menstrual bleeding, pelvic pain, and pressure on nearby organs. While the exact cause is not fully understood, hormonal factors, particularly estrogen and progesterone, are believed to play a role in their development. The exploration of connections between genetic variants and uterine leiomyoma has captivated scientific attention for numerous years. The results from investigations remain a subject of intrigue within the scientific community. To date, the findings regarding the relationships between single nucleotide polymorphisms (SNPs) and uterine leiomyoma have exhibited some inconsistencies. However, amidst these inconsistencies, several promising outcomes have emerged that hold the potential to shape future research endeavors. These promising leads could pave the way for the development of innovative targeted therapies and novel prognostic biomarkers. This review specifically centers on accentuating the existing literature data concerning genetic variants that have been explored for their potential connections to uterine leiomyoma. Additionally, it underscores the prospects of employing genetic variations as diagnostic and prognostic biomarkers for individuals diagnosed with uterine leiomyoma.
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Affiliation(s)
| | - Pawan K. Dubey
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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Ye Z, Deng X, Zhang J, Shao R, Song C, Zhao J, Tang H. Causal relationship between immune cells and prostate cancer: a Mendelian randomization study. Front Cell Dev Biol 2024; 12:1381920. [PMID: 38566827 PMCID: PMC10985200 DOI: 10.3389/fcell.2024.1381920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Despite the abundance of research indicating the participation of immune cells in prostate cancer development, establishing a definitive cause-and-effect relationship has proven to be a difficult undertaking. Methods This study employs Mendelian randomization (MR), leveraging genetic variables related to immune cells from publicly available genome-wide association studies (GWAS), to investigate this association. The primary analytical method used in this study is inverse variance weighting (IVW) analysis. Comprehensive sensitivity analyses were conducted to assess the heterogeneity and horizontal pleiotropy of the results. Results The study identifies four immune cell traits as causally contributing to prostate cancer risk, including CD127- CD8+ T cell %CD8+ T cell (OR = 1.0042, 95%CI:1.0011-1.0073, p = 0.0077), CD45RA on CD39+ resting CD4 regulatory T cell (OR = 1.0029, 95%CI:1.0008-1.0050, p = 0.0065), CD62L- Dendritic Cell Absolute Count (OR = 1.0016; 95%CI:1.0005-1.0026; p = 0.0039), CX3CR1 on CD14+ CD16- monocyte (OR = 1.0024, 95%CI:1.0007-1.0040, p = 0.0060). Additionally, two immune cell traits are identified as causally protective factors: CD4 on monocyte (OR = 0.9975, 95%CI:0.9958-0.9992, p = 0.0047), FSC-A on plasmacytoid Dendritic Cell (OR = 0.9983, 95%CI:0.9970-0.9995, p = 0.0070). Sensitivity analyses indicated no horizontal pleiotropy. Discussion Our MR study provide evidence for a causal relationship between immune cells and prostate cancer, holding implications for clinical diagnosis and treatment.
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Affiliation(s)
- Zhipeng Ye
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Jinhui Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Ruonan Shao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Cailu Song
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Jianfu Zhao
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
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Dadousis C, Ablondi M, Cipolat-Gotet C, van Kaam JT, Finocchiaro R, Marusi M, Cassandro M, Sabbioni A, Summer A. Genomic inbreeding coefficients using imputation genotypes: assessing the effect of ancestral genotyping in Holstein-Friesian dairy cows. J Dairy Sci 2024:S0022-0302(24)00545-9. [PMID: 38490541 DOI: 10.3168/jds.2024-24042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024]
Abstract
The objective of this study was to assess the effect of using or not the genotypes of the parents of a cow for imputing single nucleotide polymorphisms (SNP), on the estimation of genomic inbreeding coefficients of cows. Imputation (i.e., genotyped plus imputed) genotypes from 68,127 Italian Holstein dairy cows registered in the Italian National Association of Holstein, Brown and Jersey Breeders (ANAFIBJ) were analyzed. Cows were genotyped with the HD Illumina Infinium BovineHD BeadChip and GeneSeek Genomic Profiler HD-150K, and the MD GeneSeek Genomic Profiler 3, GeneSeek Genomic Profiler 4, GeneSeek MD and the Labogena MD. To assess differences among estimators genomic inbreeding coefficients were estimated with 4 PLINK v1.9 estimators (F, Fhat1, 2, 3), 2 genomic relationship matrix (grm) based estimators (Fgrm and Fgrm2; with the latter including also pedigree information) and one estimator of runs of homozygosity (ROH; FROH). Assuming that the correct genomic inbreeding coefficients should be those estimated from genotyped SNP, a comparison of the genomic inbreeding coefficients estimated either with the genotyped SNP or the SNP after imputation was made. Information on the presence or absence of genotypic information from sire, dam and maternal grandsire during the imputation was investigated. Genomic inbreeding coefficients estimated with genotyped SNP or SNP after imputation were consistent for F, Fhat3, Fgrm2 and FROH, when at least one of the parents was genotyped. Biased (mainly higher) genomic inbreeding coefficients of imputation SNP were observed in cows that were genotyped with MD SNP panels whose SNP were poorly represented in the selected imputation SNP data set and also did not have their parents genotyped compared with what expected based on actual genotype data. For cows genotyped with MD the estimators Fhat1, Fhat2 and Fgrm provided higher genomic inbreeding coefficients of imputation SNP even with both parents and the maternal grandsire genotyped. Overall, FROH was the most robust estimator, followed by F and Fhat3. Our findings suggest that SNP selection, parental genotyping and estimator should be considered for designing imputation strategies in dairy cattle for estimating genomic inbreeding with imputation SNP. For computing genomic inbreeding coefficients, it is recommendable to have at least one parent genotyped and use an ROH based estimator.
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Affiliation(s)
- Christos Dadousis
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
| | - Michela Ablondi
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
| | | | - Jan-Thijs van Kaam
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana, (ANAFIBJ), 26100 Cremona, Italy
| | - Raffaella Finocchiaro
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana, (ANAFIBJ), 26100 Cremona, Italy
| | - Maurizio Marusi
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana, (ANAFIBJ), 26100 Cremona, Italy
| | - Martino Cassandro
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana, (ANAFIBJ), 26100 Cremona, Italy
| | - Alberto Sabbioni
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
| | - Andrea Summer
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro (PD), Italy
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Erratum: Pertinence of glioma and single nucleotide polymorphism of TERT, CCDC26, CDKN2A/B, and RTEL1 genes in glioma: a meta-analysis. Front Oncol 2024; 14:1393063. [PMID: 38529370 PMCID: PMC10961609 DOI: 10.3389/fonc.2024.1393063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/27/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fonc.2023.1180099.].
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Xu B, Ren J, Zhu S, Ding Y, Zhou W, Guo Q, Fang Y, Zheng J. Causal relationship between telomere length and risk of intracranial aneurysm: a bidirectional Mendelian randomization study. Front Neurol 2024; 15:1355895. [PMID: 38533417 PMCID: PMC10964484 DOI: 10.3389/fneur.2024.1355895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
Background Telomere length is closely linked to the aging phenotype, where cellular aging results in the production of a cascade of cell factors and the senescence-associated secretory phenotype (SASP), leading to an inflammatory response. The presence of inflammation plays a crucial role in the formation of intracranial aneurysms. Nevertheless, the relationship between telomere length and intracranial aneurysms remains unclear. This study aims to explore the causal connection between telomere length and intracranial aneurysms through the utilization of Mendelian randomization (MR) analysis. Methods Data on telomere length were obtained from the genome-wide association studies conducted on the UK Biobank, comprising a total of 472,174 participants. Data on intracranial aneurysms were obtained from the summary dataset of the Global Genome-wide Association Study (GWAS) conducted by the International Stroke Genetics Consortium. The dataset consisted of 7,495 cases and 71,934 controls, all of European descent. Initially, the linkage disequilibrium score was used to investigate the connection between telomere length and intracranial aneurysms. Subsequently, a bidirectional MR was conducted using two-sample analysis to assess whether there is a causal connection between telomere length and intracranial aneurysm risk. The results were analyzed utilizing five MR methods, with the inverse variance weighted method serving as the main methodology. In addition, we did various analyses to evaluate the presence of heterogeneity, pleiotropy, and sensitivity in the study results. A reverse MR analysis was conducted to investigate potential reverse causal links. Results In the forward MR analysis, it was observed that both the inverse variance-weighted and weighted median analyses implied a potential causal relationship between longer telomere length and a decreased incidence of intracranial aneurysms (IVW: OR = 0.66, 95% CI: 0.47-0.92, p = 1.49 × 10-2). There was no heterogeneity or horizontal pleiotropy. The findings were verified to be robust through the utilization of leave-one-out analysis. The use of reverse MR analysis did not establish a potential causal link between the occurrence of intracranial aneurysms and telomere length. Conclusion There may exist a potential correlation between longer telomere length and a decreased likelihood of intracranial aneurysms within the European population. The present study offers novel insights into the correlation between telomere length and intracranial aneurysms. Additional research is required to clarify the underlying mechanisms and validate our discoveries in diverse populations.
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Affiliation(s)
- Bangjie Xu
- Department of Neurosurgery, The Affiliated Suqian Hospital of Xuzhou Medical University, Suqian, China
| | - Jiangbin Ren
- Department of Neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
| | - Siqi Zhu
- Department of Oncology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, China
| | - Yu Ding
- Department of Neurosurgery, The Affiliated Suqian Hospital of Xuzhou Medical University, Suqian, China
| | - Wei Zhou
- Department of Neurosurgery, The Affiliated Suqian Hospital of Xuzhou Medical University, Suqian, China
| | - Qing Guo
- Department of Neurosurgery, The Affiliated Suqian Hospital of Xuzhou Medical University, Suqian, China
| | - Yan Fang
- Department of Neurosurgery, The Affiliated Suqian Hospital of Xuzhou Medical University, Suqian, China
| | - Jing Zheng
- Department of Neurosurgery, The Affiliated Suqian Hospital of Xuzhou Medical University, Suqian, China
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Jiang H, Giarratana AO, Theis T, Nagaraj V, Zhou X, Thakker-Varia S, Schachner M, Alder J. Single Nucleotide Polymorphism in Cell Adhesion Molecule L1 Affects Learning and Memory in a Mouse Model of Traumatic Brain Injury. Int J Mol Sci 2024; 25:3043. [PMID: 38474289 DOI: 10.3390/ijms25053043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/02/2024] [Indexed: 03/14/2024] Open
Abstract
The L1 cell adhesion molecule (L1) has demonstrated a range of beneficial effects in animal models of spinal cord injury, neurodegenerative disease, and ischemia; however, the role of L1 in TBI has not been fully examined. Mutations in the L1 gene affecting the extracellular domain of this type 1 transmembrane glycoprotein have been identified in patients with L1 syndrome. These patients suffer from hydrocephalus, MASA (mental retardation, adducted thumbs, shuffling gait, aphasia) symptoms, and corpus callosum agenesis. Clinicians have observed that recovery post-traumatic brain injury (TBI) varies among the population. This variability may be explained by the genetic differences present in the general population. In this study, we utilized a novel mouse model of L1 syndrome with a mutation at aspartic acid position 201 in the extracellular domain of L1 (L1-201). We assessed the impact of this specific single nucleotide polymorphism (SNP) localized to the X-chromosome L1 gene on recovery outcomes following TBI by comparing the L1-201 mouse mutants with their wild-type littermates. We demonstrate that male L1-201 mice exhibit significantly worse learning and memory outcomes in the Morris water maze after lateral fluid percussion (LFP) injury compared to male wild-type mice and a trend to worse motor function on the rotarod. However, no significant changes were observed in markers for inflammatory responses or apoptosis after TBI.
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Affiliation(s)
- Haoyu Jiang
- Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Anna O Giarratana
- Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Thomas Theis
- Cell Biology and Neuroscience, Rutgers School of Arts and Sciences, Piscataway, NJ 08854, USA
| | - Vini Nagaraj
- Cell Biology and Neuroscience, Rutgers School of Arts and Sciences, Piscataway, NJ 08854, USA
| | - Xiaofeng Zhou
- Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Smita Thakker-Varia
- Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Melitta Schachner
- Cell Biology and Neuroscience, Rutgers School of Arts and Sciences, Piscataway, NJ 08854, USA
| | - Janet Alder
- Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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Ma X, Yang G, Zhang J, Ma R, Shen J, Feng F, Yu D, Huang C, Ma X, La Y, Wu X, Guo X, Chu M, Yan P, Liang C. Association between Single Nucleotide Polymorphisms of PRKD1 and KCNQ3 Gene and Milk Quality Traits in Gannan Yak ( Bos grunniens). Foods 2024; 13:781. [PMID: 38472894 DOI: 10.3390/foods13050781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Protein kinase D1 (PRKD1) functions primarily in normal mammary cells, and the potassium voltage-gated channel subfamily Q member 3 (KCNQ3) gene plays an important role in controlling membrane potential and neuronal excitability, it has been found that this particular gene is linked to the percentage of milk fat in dairy cows. The purpose of this study was to investigate the relationship between nucleotide polymorphisms (SNPs) of PRKD1 and KCNQ3 genes and the milk quality of Gannan yak and to find molecular marker sites that may be used for milk quality breeding of Gannan yak. Three new SNPs were detected in the PRKD1 (g.283,619T>C, g.283,659C>A) and KCNQ3 gene (g.133,741T>C) of 172 Gannan lactating female yaks by Illumina yak cGPS 7K liquid-phase microarray technology. Milk composition was analyzed using a MilkoScanTM milk composition analyzer. We found that the mutations of these three loci significantly improved the lactose, milk fat, casein, protein, non-fat milk solid (SNF) content and acidity of Gannan yaks. The lactose content of the TC heterozygous genotype population at g.283,619T>C locus was significantly higher than that of the TT wild-type population (p < 0.05); the milk fat content of the CA heterozygous genotype population at g.283,659C>A locus was significantly higher than that of the CC wild-type and AA mutant populations (p < 0.05); the casein, protein and acidity of the CC mutant and TC heterozygous groups at the g.133,741T>C locus were significantly higher than those of the wild type (p < 0.05), and the SNF of the TC heterozygous group was significantly higher than that of the mutant group (p < 0.05). The results showed that PRKD1 and KCNQ3 genes could be used as candidate genes affecting the milk traits of Gannan yak.
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Affiliation(s)
- Xiaoyong Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Guowu Yang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Juanxiang Zhang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Rong Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jinwei Shen
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Fen Feng
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Daoning Yu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chun Huang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiaoming Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Yongfu La
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiaoyun Wu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Institute of Western Agriculture, The Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Chunnian Liang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
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Shirai T, Okazaki S, Tanifuji T, Otsuka I, Miyachi M, Okada S, Shindo R, Horai T, Mouri K, Takahashi M, Kondo T, Ueno Y, Hishimoto A. Association study of a single nucleotide polymorphism in the hypoxia response element of the macrophage migration inhibitory factor gene promoter with suicide completers in the Japanese population. Neuropsychopharmacol Rep 2024; 44:262-266. [PMID: 38267013 PMCID: PMC10932791 DOI: 10.1002/npr2.12410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/10/2023] [Accepted: 12/14/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND More than 800 000 people die by suicide annually. The heritability of suicide is 30%-50%. We focused on the hypoxia response element (HRE), which promotes the expression of macrophage migration inhibitory factor (MIF) via the hypoxia-inducible factor (HIF) pathway, important in neurogenesis and neuroprotection. We examined a genetic polymorphism of rs17004038, a single-nucleotide polymorphism (SNP), in suicide completers and controls. METHODS The study population included 1336 suicide completers and 814 unrelated healthy controls. All participants were Japanese. We obtained peripheral blood, extracted DNA, and genotyped the patients for SNP rs17004038 (C > A). RESULTS No significant differences were observed between the two groups in either the allele or genotype analyses. Subgroup analyses by sex, age (<40 or ≥40), and suicide method (violent or nonviolent suicide) were performed with similar results. CONCLUSION No association was observed between SNP rs17004038 and suicide completion. Although it is challenging to collect a large number of samples from suicide completers, further MIF-related genetic studies, including those of rs17004038, are necessary with larger sample sizes.
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Affiliation(s)
- Toshiyuki Shirai
- Department of PsychiatryKobe University Graduate School of MedicineKobeJapan
| | - Satoshi Okazaki
- Department of PsychiatryKobe University Graduate School of MedicineKobeJapan
| | - Takaki Tanifuji
- Department of PsychiatryKobe University Graduate School of MedicineKobeJapan
| | - Ikuo Otsuka
- Department of PsychiatryKobe University Graduate School of MedicineKobeJapan
| | - Masao Miyachi
- Department of PsychiatryKobe University Graduate School of MedicineKobeJapan
| | - Shohei Okada
- Department of PsychiatryKobe University Graduate School of MedicineKobeJapan
| | - Ryota Shindo
- Department of PsychiatryKobe University Graduate School of MedicineKobeJapan
| | - Tadasu Horai
- Department of PsychiatryKobe University Graduate School of MedicineKobeJapan
| | - Kentaro Mouri
- Department of PsychiatryKobe University Graduate School of MedicineKobeJapan
| | - Motonori Takahashi
- Division of Legal Medicine, Department of Community Medicine and Social Health ScienceKobe University Graduate School of MedicineKobeJapan
| | - Takeshi Kondo
- Division of Legal Medicine, Department of Community Medicine and Social Health ScienceKobe University Graduate School of MedicineKobeJapan
| | - Yasuhiro Ueno
- Division of Legal Medicine, Department of Community Medicine and Social Health ScienceKobe University Graduate School of MedicineKobeJapan
| | - Akitoyo Hishimoto
- Department of PsychiatryKobe University Graduate School of MedicineKobeJapan
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P P A, Kumari S, Dasmajumdar S, Mangaraj M. Matrix Metalloproteinase-7 Promoter Site Single Nucleotide Polymorphism (-181A>G) in Epithelial Ovarian Cancer in the Eastern Indian Population. Cureus 2024; 16:e56417. [PMID: 38638796 PMCID: PMC11024387 DOI: 10.7759/cureus.56417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Matrix metalloproteinase-7 (MMP7) plays multiple roles in different stages of tumor development. Elevated MMP7 activity has been reported in ovarian cancer. Single nucleotide polymorphism (SNP) of promoter sites of the MMP7 gene has been shown to cause alteration in gene expression, hence resulting in changes in susceptibility to various diseases and tumor development. METHODS The current study evaluated the association of epithelial ovarian cancer risk with MMP7 promoter site -181A>G polymorphism in the population of eastern India. The present case-control study included 64 histopathologically confirmed cases of epithelial ovarian cancer and 100 control subjects. The MMP7 -181A/G polymorphism was identified using polymerase chain reaction-restriction fragment length polymorphism. The association between genotypes and epithelial ovarian cancer risk was analyzed by odds ratio (OR) with a 95% confidence interval. RESULTS The frequencies of AA, AG, and GG genotypes in ovarian cancer cases were 37.5%, 46.9%, and 15.6%, respectively, while that of control subjects were 56%, 36%, and 8%, respectively, in the study population. By taking the wild-type AA genotype as a reference, it was found that genotype GG was associated with a significant risk for epithelial ovarian cancer (OR: 2.92). Frequency distribution of genotypes did not show any significant association with tumor characteristics like the International Federation of Gynecology and Obstetrics (FIGO) stage, histology, lymph node status, and distant metastasis. CONCLUSION The present study demonstrated the association of MMP7 promoter site -181 GG genotype and the G allele with increased risk for epithelial ovarian cancer in the eastern Indian population.
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Affiliation(s)
- Anudeep P P
- Biochemistry, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Suchitra Kumari
- Biochemistry, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Saroj Dasmajumdar
- Radiation Oncology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Manaswini Mangaraj
- Biochemistry, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
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Gao Y, Liu Y, Jiang Y, Qin M, Guan Z, Gao Y, Yang Y. Association between polymorphism and haplotype of ATP2B1 gene and skeletal fluorosis in Han population. Int J Environ Health Res 2024; 34:1410-1420. [PMID: 37211801 DOI: 10.1080/09603123.2023.2213159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023]
Abstract
To evaluate the association between ATP2B1 gene polymorphisms and skeletal fluorosis, a cross-sectional study was conducted. In China, 962 individuals were recruited, including 342 cases of skeletal fluorosis. Four TP2BA1 polymorphisms (rs2070759, rs12817819, rs17249754, and rs7136259) were analysed. The results suggested that rs17249754 and rs7136259 were associated with skeletal fluorosis. After controlling confounders, the protective effect of GG genotype in rs17249754 was apparent in individuals over 45 years old, female, with urine fluoride concentration below 1.6 mg/L, serum calcium above 2.25 mmol/L or serum phosphorus between 1.1 and 1.3. Heterozygote TC in rs7136259 increased the risk of skeletal fluorosis in subjects who are elderly, female, with urinary fluoride more than 1.6 mg/L, serum calcium more than 2.25 mmol/L and blood phosphorus between 1.1 and 1.3 mmol/L. Four loci were found to be tightly related by linkage disequilibrium analysis, and the frequency of distribution of haplotype GCGT was lower in the skeletal fluorosis group.
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Affiliation(s)
- Yue Gao
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province, Ministry of Health of P. R. China, Harbin Medical University, Harbin, China
| | - Yang Liu
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province, Ministry of Health of P. R. China, Harbin Medical University, Harbin, China
| | - Yuting Jiang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province, Ministry of Health of P. R. China, Harbin Medical University, Harbin, China
| | - Ming Qin
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province, Ministry of Health of P. R. China, Harbin Medical University, Harbin, China
| | - Zhizhong Guan
- Department of Pathology, Hospital of Guizhou Medical University, Guiyang, China
- Key Laboratory of Endemic and Ethnic Diseases of the Ministry of Education of P. R. China, Guizhou Medical University, Guiyang, China
| | - Yanhui Gao
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province, Ministry of Health of P. R. China, Harbin Medical University, Harbin, China
| | - Yanmei Yang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province, Ministry of Health of P. R. China, Harbin Medical University, Harbin, China
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Yuan R, Cai B, Ma M, Zhao C, Xian Y, Nie Q, Zhang X, Zhang D. LncEDCH1 g.1703613 T>C regulates chicken carcass traits by targeting miR-196-2-3p. Poult Sci 2024; 103:103412. [PMID: 38198912 PMCID: PMC10825527 DOI: 10.1016/j.psj.2023.103412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/21/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Single nucleotide polymorphisms (SNPs) are valuable genetic markers that can provide insights into the genetic diversity and variation within chicken populations. In poultry breeding, SNP analysis is widely utilized to accelerate the selection of desirable traits, improving the efficiency and effectiveness of chicken breeding programs. In our previous research, we identified an association between LncEDCH1 and muscle development. To further investigate its specific mechanism, we conducted SNP detection and performed genotyping, linkage disequilibrium, and haplotype analysis. Our research findings indicate that 16 SNPs in the LncEDCH1. Among these SNPs, g.1703497 C>T and g.1704262 C>T were significantly associated with breast muscle weight percentage, g.1703497 C>T and g.1703613 T>C were significantly associated with leg weight percentage, and g.1703497 C>T, g.1703589 T>C, g.1703613 T>C, g.1703636 C>A, g.1703768 T>C, g.1704079 C>T, g.1704250 T>C, g.1704253 G>A were significantly associated with skin yellowness. Two haplotype blocks composed of 6 SNPs that were significantly associated with wing skin yellowness, breast skin yellowness, full-bore weight, and carcass weight percentage. Furthermore, through dual-luciferase reporter assays, biotin-coupled miRNA pull-down assays, 5-ethynyl-2'-deoxyuridine (EDU) assays, immunofluorescence, and quantitative real-time polymerase chain reaction (qPCR), it has been confirmed that miR-196-2-3p inhibits the expression of LncEDCH1 directly by binding to LncEDCH1 g.1703613T>C, thereby achieving indirect regulation of muscle development. These findings provide valuable molecular markers for chicken molecular breeding and broaden our understanding of the regulatory mechanisms.
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Affiliation(s)
- Rongshuai Yuan
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Bolin Cai
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Manting Ma
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Changbin Zhao
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Yuanrong Xian
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Qinghua Nie
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Xiquan Zhang
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Dexiang Zhang
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.
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Macleod KL, Jenkins TL, Witt MJ, Stevens JR. Rare, long-distance dispersal underpins genetic connectivity in the pink sea fan, Eunicella verrucosa. Evol Appl 2024; 17:e13649. [PMID: 38463749 PMCID: PMC10918604 DOI: 10.1111/eva.13649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 03/12/2024] Open
Abstract
Characterizing patterns of genetic connectivity in marine species is of critical importance given the anthropogenic pressures placed on the marine environment. For sessile species, population connectivity can be shaped by many processes, such as pelagic larval duration, oceanographic boundaries and currents. This study combines restriction-site associated DNA sequencing (RADseq) and passive particle dispersal modelling to delineate patterns of population connectivity in the pink sea fan, Eunicella verrucosa, a temperate octocoral. Individuals were sampled from 20 sites covering most of the species' northeast Atlantic range, and a site in the northwest Mediterranean Sea to inform on connectivity across the Atlantic-Mediterranean transition. Using 7510 neutral SNPs, a geographic cline of genetic clusters was detected, partitioning into Ireland, Britain, France, Spain (Atlantic), and Portugal and Spain (Mediterranean). Evidence of significant inbreeding was detected at all sites, a finding not detected in a previous study of this species based on microsatellite loci. Genetic connectivity was characterized by an isolation by distance pattern (IBD) (r 2 = 0.78, p < 0.001), which persisted across the Mediterranean-Atlantic boundary. In contrast, exploration of ancestral population assignment using the program ADMIXTURE indicated genetic partitioning across the Bay of Biscay, which we suggest represents a natural break in the species' range, possibly linked to a lack of suitable habitat. As the pelagic larval duration (PLD) is unknown, passive particle dispersal simulations were run for 14 and 21 days. For both modelled PLDs, inter-annual variations in particle trajectories suggested that in a long-lived, sessile species, range-wide IBD is driven by rare, longer dispersal events that act to maintain gene flow. These results suggest that oceanographic patterns may facilitate range-wide stepping-stone genetic connectivity in E. verrucosa and highlight that both oceanography and natural breaks in a species' range should be considered in the designation of ecologically coherent MPA networks.
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Affiliation(s)
- Kirsty L. Macleod
- Department of Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - Tom L. Jenkins
- Department of Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - Matthew J. Witt
- Department of Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - Jamie R. Stevens
- Department of Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
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Park N, Kim H, Oh J, Kim J, Heo C, Kim J. PAPipe: A Pipeline for Comprehensive Population Genetic Analysis. Mol Biol Evol 2024; 41:msae040. [PMID: 38427787 PMCID: PMC10919927 DOI: 10.1093/molbev/msae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
Advancements in next-generation sequencing (NGS) technologies have led to a substantial increase in the availability of population genetic variant data, thus prompting the development of various population analysis tools to enhance our understanding of population structure and evolution. The tools that are currently used to analyze population genetic variant data generally require different environments, parameters, and formats of the input data, which can act as a barrier preventing the wide-spread usage of such tools by general researchers who may not be familiar with bioinformatics. To address this problem, we have developed an automated and comprehensive pipeline called PAPipe to perform nine widely used population genetic analyses using population NGS data. PAPipe seamlessly interconnects and serializes multiple steps, such as read trimming and mapping, genetic variant calling, data filtering, and format converting, along with nine population genetic analyses such as principal component analysis, phylogenetic analysis, population tree analysis, population structure analysis, linkage disequilibrium decay analysis, selective sweep analysis, population admixture analysis, sequentially Markovian coalescent analysis, and fixation index analysis. PAPipe also provides an easy-to-use web interface that allows for the parameters to be set and the analysis results to be browsed in intuitive manner. PAPipe can be used to generate extensive results that provide insights that can help enhance user convenience and data usability. PAPipe is freely available at https://github.com/jkimlab/PAPipe.
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Affiliation(s)
- Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyeonji Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jeongmin Oh
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jinseok Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Charyeong Heo
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
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Almaani N, Farhan F, Bani Hamad S, Abuhawileh EA, Koubaitary L, Ahram M, Aladily TN. Genetic predisposition to early mycosis fungoides: investigating genetic polymorphisms in tissue-resident memory T-cell genes. J Int Med Res 2024; 52:3000605241239034. [PMID: 38546260 PMCID: PMC10981233 DOI: 10.1177/03000605241239034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/26/2024] [Indexed: 04/01/2024] Open
Abstract
OBJECTIVES Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma; it arises from tissue-resident memory T-cells (TRM). In the present study, we investigated potential functional genetic variations that may predispose MF development. METHODS A case-control study was conducted using whole-exome sequencing, with a focus on genes that are essential to TRM function. RESULTS We included 21 patients and 19 healthy subjects in the study. Single nucleotide polymorphisms in the following genes were significantly more common in patients than in healthy subjects: GZMB, HLA-DRB1, CD103, and NOTCH1. Moreover, the number of patients carrying single nucleotide polymorphisms in LAG3, NR4A2, and CD26L was significantly greater in the patient group than in the control group. CONCLUSIONS The presence of genetic variations in one or more TRM functional gene may predispose patients to develop MF. Further studies involving a larger patient population and a comparative analysis of protein expression will be necessary to validate these findings.
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Affiliation(s)
- Nour Almaani
- Department of Dermatology, The University of Jordan, Amman, Jordan
| | - Fatima Farhan
- Department of Health Data Analysis, Electronic Health Solution, Amman, Jordan
| | | | | | - Lana Koubaitary
- Department of Pathology, The University of Jordan, Amman, Jordan
| | - Mamoun Ahram
- Department of Physiology and Biochemistry, The University of Jordan, Amman, Jordan
| | - Tariq N Aladily
- Department of Pathology, The University of Jordan, Amman, Jordan
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Annanya A, Priyadharshini B, Suresh V, Dilipan E. Computational Analysis of Single Nucleotide Polymorphisms in Human HIC1 Gene. Cureus 2024; 16:e56664. [PMID: 38646326 PMCID: PMC11032261 DOI: 10.7759/cureus.56664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 03/21/2024] [Indexed: 04/23/2024] Open
Abstract
Background A putative tumor suppressor gene called HIC1 (hypermethylated in cancer) is situated at 17p13.3, a locus where the allelic loss occurs often in human malignancies, including breast cancer. Hypermethylated in cancer 1 protein is a protein that in humans is encoded by the HIC1 gene and it's a Homo sapiens (Human). This gene functions as a growth regulatory and tumor repressor gene. The molecular function of HIC1 gene includes DNA-binding transcription factor activity, sequence-specific DNA binding, DNA binding, histone deacetylase binding, protein binding, metal ion binding, nucleic acid binding, DNA-binding transcription repressor activity, RNA polymerase II-specific, DNA-binding transcription factor activity, RNA polymerase II-specific. The biological process of HIC1 gene includes multicellular organism development, negative regulation of Wnt signaling pathway, positive regulation of DNA damage response, signal transduction by p53 class mediator regulation of transcription, DNA-templated, negative regulation of transcription by RNA polymerase II, Wnt signaling pathway, transcription, DNA-templated, intrinsic apoptotic signaling pathway in response to DNA damage, cellular response to DNA damage stimulus. The study aimed to predict the stability and structure of the protein that will arise from single nucleotide polymorphisms (SNPs) in the human HIC1 gene. Methodology To investigate the possible negative effects associated with these SNPs, bioinformatic analysis is typically essential. The following tools were employed for forecasting harmful SNPs: scale-invariant feature transform (SIFT), Protein Analysis Through Evolutionary Relationships (PANTHER), nonsynonymous SNP by Protein Variation Effect Analyzer (PROVEAN), and nonsynonymous SNP by Single Nucleotide Polymorphism Annotation Platform (SNAP). Results The present study identified a total of 36 SNPs using the SIFT approach, which were shown to have functional significance. Twenty-six were determined to be tolerable, whereas 10 were shown to be detrimental. Out of 20 SNPs, seven (P370A, P646S, R654P, A476T, S400S, D666N, D7V) SNPs were predicted as "Possibly damaging" and seven (L9F, G468R, G490R, L482R, S12W, G489D, S12P) were identified as "probably benign", and six (R725G, G620S, A56V, E463D, D394N, L338V) were identified as "probably damaging" according to the predictions made by PANTHER tools. The majority of the pixels on the strip were red, indicating that the gene changes may have dangerous consequences. These results highlight the need for more research to fully comprehend how these mutations affect the hic1 protein's function, which is essential for the emergence of different types of cancer. Conclusion The current research has provided us with essential information about how SNPs might be used as a diagnostic marker for cancer, given that SNPs may be candidates for cellular changes caused by mutations linked to cancer.
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Affiliation(s)
- Arora Annanya
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, IND
| | - Boopathi Priyadharshini
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Vasugi Suresh
- Medical Physiology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Elangovan Dilipan
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
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Hiraoka Y, Ferrante SP, Wu GA, Federici CT, Roose ML. Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives. Plants (Basel) 2024; 13:691. [PMID: 38475537 DOI: 10.3390/plants13050691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, "PolyHighResolution" (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.
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Affiliation(s)
- Yoko Hiraoka
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Sergio Pietro Ferrante
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Guohong Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Claire T Federici
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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Ahmadi S, Surmava S, Kvaratskhelia D, Gogolashvili A, Kvaratskhelia E, Abzianidze E, Kankava K. Association Between Multiple Single Nucleotide Polymorphisms in Folate Metabolism Pathway and Breast Cancer Risk in Georgian Women: A Case-Control Study. Clin Med Insights Oncol 2024; 18:11795549241233693. [PMID: 38433849 PMCID: PMC10908228 DOI: 10.1177/11795549241233693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
Background The folate metabolism pathway plays an integral part in DNA synthesis, methylation, and repair. Methylenetetrahydrofolate reductase (MTHFR) and methylenetetrahydrofolate dehydrogenase (MTHFD1) are both enzymes that are involved in this pathway, and the single nucleotide polymorphisms (SNPs) in genes coding for them have modulatory effects on DNA expression. This study aimed to investigate the relationship between MTHFR C677T (rs1801133) and MTHFD1 G1958A (rs2236225) polymorphisms and the risk of developing breast cancer in Georgian women. Methods A case-control study was performed examining the MTHFR C677T and MTHFD1 G1958A SNP in breast cancer-confirmed cases and healthy matched controls. Real time-polymerase chain reaction (PCR) was used to genotype SNPs. The case individuals' pathology reports were obtained following surgeries for cancer characteristic data. Statistical analysis was performed to investigate the significance of the acquired data. Results Statistical analysis of MTHFR C677T SNP revealed that the CT genotype increased the risk of breast cancer by 2.17 folds in the over-dominant model. Statistical analysis of MTHFD1 G1958A SNP showed that the GA genotype increased the risk of breast cancer by 4.12 folds in the codominant model and 2.41 folds in the over-dominant model. No statistically significant link was found between genotypes and lymph node status, however, patients with the CT genotype had higher percentages of proliferative activity. Conclusions Breast cancer seems to have a statistically significant association with the CT genotype in MTHFR C677T and the GA genotype in MTHFD1 G1958A in Georgian women.
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Affiliation(s)
- Saba Ahmadi
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Sandro Surmava
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Davit Kvaratskhelia
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Ana Gogolashvili
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Eka Kvaratskhelia
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
- V. Bakhutashvili Institute of Medical Biotechnology, Tbilisi State Medical University, Tbilisi, Georgia
| | - Elene Abzianidze
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
- Ivane Beritashvili Center Of Experimental Biomedicine, Tbilisi, Georgia
| | - Ketevani Kankava
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
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Xu L, Zhang J, Yang H, Cao C, Fang R, Liu P, Luo S, Wang B, Zhang K, Wang L. Epistasis in neurotransmitter receptors linked to posttraumatic stress disorder and major depressive disorder comorbidity in traumatized Chinese. Front Psychiatry 2024; 15:1257911. [PMID: 38487579 PMCID: PMC10937445 DOI: 10.3389/fpsyt.2024.1257911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024] Open
Abstract
Background Posttraumatic stress disorder (PTSD) and major depressive disorder (MDD) comorbidity occurs through exposure to trauma with genetic susceptibility. Neuropeptide-Y (NPY) and dopamine are neurotransmitters associated with anxiety and stress-related psychiatry through receptors. We attempted to explore the genetic association between two neurotransmitter receptor systems and the PTSD-MDD comorbidity. Methods Four groups were identified using latent profile analysis (LPA) to examine the patterns of PTSD and MDD comorbidity among survivors exposed to earthquake-related trauma: low symptoms, predominantly depression, predominantly PTSD, and PTSD-MDD comorbidity. NPY2R (rs4425326), NPY5R (rs11724320), DRD2 (rs1079597), and DRD3 (rs6280) were genotyped from 1,140 Chinese participants exposed to earthquake-related trauma. Main, gene-environment interaction (G × E), and gene-gene interaction (G × G) effects for low symptoms, predominantly depression, and predominantly PTSD were tested using a multinomial logistic model with PTSD-MDD comorbidity as a reference. Results The results demonstrated that compared to PTSD-MDD comorbidity, epistasis (G × G) NPY2R-DRD2 (rs4425326 × rs1079597) affects low symptoms (β = -0.66, OR = 0.52 [95% CI: 0.32-0.84], p = 0.008, pperm = 0.008) and predominantly PTSD (β = -0.56, OR = 0.57 [95% CI: 0.34-0.97], p = 0.037, pperm = 0.039), while NPY2R-DRD3 (rs4425326 × rs6280) impacts low symptoms (β = 0.82, OR = 2.27 [95% CI: 1.26-4.10], p = 0.006, pperm = 0.005) and predominantly depression (β = 1.08, R = 2.95 [95% CI: 1.55-5.62], p = 0.001, pperm = 0.001). The two G × G effects are independent. Conclusion NPY and dopamine receptor genes are related to the genetic etiology of PTSD-MDD comorbidity, whose specific mechanisms can be studied at multiple levels.
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Affiliation(s)
- Ling Xu
- Laboratory for Traumatic Stress Studies and Center for Genetics and BioMedical Informatics Research, CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Jingyi Zhang
- Laboratory for Traumatic Stress Studies and Center for Genetics and BioMedical Informatics Research, CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Haibo Yang
- Academy of Psychology and Behavior, Tianjin Normal University, Tianjin, China
| | - Chengqi Cao
- Laboratory for Traumatic Stress Studies and Center for Genetics and BioMedical Informatics Research, CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Ruojiao Fang
- Laboratory for Traumatic Stress Studies and Center for Genetics and BioMedical Informatics Research, CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Ping Liu
- People’s Hospital of Deyang City, Deyang, Sichuan, China
| | - Shu Luo
- People’s Hospital of Deyang City, Deyang, Sichuan, China
| | - Binbin Wang
- Laboratory for Traumatic Stress Studies and Center for Genetics and BioMedical Informatics Research, CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Kunlin Zhang
- Laboratory for Traumatic Stress Studies and Center for Genetics and BioMedical Informatics Research, CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Li Wang
- Laboratory for Traumatic Stress Studies and Center for Genetics and BioMedical Informatics Research, CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
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Kogure M, Kanahara N, Miyazawa A, Shiko Y, Otsuka I, Matsuyama K, Takase M, Kimura M, Kimura H, Ota K, Idemoto K, Tamura M, Oda Y, Yoshida T, Okazaki S, Yamasaki F, Nakata Y, Watanabe Y, Niitsu T, Hishimoto A, Iyo M. Association of SLC6A3 variants with treatment-resistant schizophrenia: a genetic association study of dopamine-related genes in schizophrenia. Front Psychiatry 2024; 14:1334335. [PMID: 38476817 PMCID: PMC10929739 DOI: 10.3389/fpsyt.2023.1334335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/21/2023] [Indexed: 03/14/2024] Open
Abstract
Background Most genetic analyses that have attempted to identify a locus or loci that can distinguish patients with treatment-resistant schizophrenia (TRS) from those who respond to treatment (non-TRS) have failed. However, evidence from multiple studies suggests that patients with schizophrenia who respond well to antipsychotic medication have a higher dopamine (DA) state in brain synaptic clefts whereas patients with TRS do not show enhanced DA synthesis/release pathways. Patients and methods To examine the contribution (if any) of genetics to TRS, we conducted a genetic association analysis of DA-related genes in schizophrenia patients (TRS, n = 435; non-TRS, n = 539) and healthy controls (HC: n = 489). Results The distributions of the genotypes of rs3756450 and the 40-bp variable number tandem repeat on SLC6A3 differed between the TRS and non-TRS groups. Regarding rs3756450, the TRS group showed a significantly higher ratio of the A allele, whereas the non-TRS group predominantly had the G allele. The analysis of the combination of COMT and SLC6A3 yielded a significantly higher ratio of the putative low-DA type (i.e., high COMT activity + high SLC6A3 activity) in the TRS group compared to the two other groups. Patients with the low-DA type accounted for the minority of the non-TRS group and exhibited milder psychopathology. Conclusion The overall results suggest that (i) SLC6A3 could be involved in responsiveness to antipsychotic medication and (ii) genetic variants modulating brain DA levels may be related to the classification of TRS and non-TRS.
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Affiliation(s)
- Masanobu Kogure
- Department of Psychiatry, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Nobuhisa Kanahara
- Division of Medical Treatment and Rehabilitation, Center for Forensic Mental Health, Chiba University, Chiba, Japan
| | - Atsuhiro Miyazawa
- Department of Psychiatry, Chiba University Graduate School of Medicine, Chiba, Japan
- Doujin-kai Kisarazu Hospital, Kisarazu, Japan
| | - Yuki Shiko
- Biostatistics Section, Clinical Research Center, Chiba University Hospital, Chiba, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Koichi Matsuyama
- Department of Psychiatry, Chiba University Graduate School of Medicine, Chiba, Japan
- Douwa-kai Chiba Hospital, Funabashi, Japan
| | | | - Makoto Kimura
- Chiba Psychiatric Medical Center, Chiba, Japan
- Department of Psychiatry, Kameda Medical Center, Kamogawa, Japan
| | - Hiroshi Kimura
- Department of Psychiatry, Chiba University Graduate School of Medicine, Chiba, Japan
- Gakuji-kai Kimura Hospital, Chiba, Japan
- Department of Psychiatry, School of Medicine, International University of Health and Welfare, Narita, Japan
| | - Kiyomitsu Ota
- Doujin-kai Kisarazu Hospital, Kisarazu, Japan
- Choshi-kokoro Clinic, Choshi, Japan
| | - Keita Idemoto
- Department of Psychiatry, Chiba University Graduate School of Medicine, Chiba, Japan
- Doujin-kai Kisarazu Hospital, Kisarazu, Japan
| | - Masaki Tamura
- Doujin-kai Kisarazu Hospital, Kisarazu, Japan
- Department of Cognitive Behavioral Psychology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yasunori Oda
- Department of Psychiatry, Chiba University Graduate School of Medicine, Chiba, Japan
| | | | - Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Fumiaki Yamasaki
- Department of Psychiatry, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yusuke Nakata
- Department of Psychiatry, Chiba University Graduate School of Medicine, Chiba, Japan
| | | | - Tomihisa Niitsu
- Department of Psychiatry, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masaomi Iyo
- Department of Psychiatry, Chiba University Graduate School of Medicine, Chiba, Japan
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Reshetnikov E, Churnosova M, Reshetnikova Y, Stepanov V, Bocharova A, Serebrova V, Trifonova E, Ponomarenko I, Sorokina I, Efremova O, Orlova V, Batlutskaya I, Ponomarenko M, Churnosov V, Aristova I, Polonikov A, Churnosov M. Maternal Age at Menarche Genes Determines Fetal Growth Restriction Risk. Int J Mol Sci 2024; 25:2647. [PMID: 38473894 DOI: 10.3390/ijms25052647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
We aimed to explore the potential link of maternal age at menarche (mAAM) gene polymorphisms with risk of the fetal growth restriction (FGR). This case (FGR)-control (FGR free) study included 904 women (273 FGR and 631 control) in the third trimester of gestation examined/treated in the Departments of Obstetrics. For single nucleotide polymorphism (SNP) multiplex genotyping, 50 candidate loci of mAAM were chosen. The relationship of mAAM SNPs and FGR was appreciated by regression procedures (logistic/model-based multifactor dimensionality reduction [MB-MDR]) with subsequent in silico assessment of the assumed functionality pithy of FGR-related loci. Three mAAM-appertain loci were FGR-linked to genes such as KISS1 (rs7538038) (effect allele G-odds ratio (OR)allelic = 0.63/pperm = 0.0003; ORadditive = 0.61/pperm = 0.001; ORdominant = 0.56/pperm = 0.001), NKX2-1 (rs999460) (effect allele A-ORallelic = 1.37/pperm = 0.003; ORadditive = 1.45/pperm = 0.002; ORrecessive = 2.41/pperm = 0.0002), GPRC5B (rs12444979) (effect allele T-ORallelic = 1.67/pperm = 0.0003; ORdominant = 1.59/pperm = 0.011; ORadditive = 1.56/pperm = 0.009). The haplotype ACA FSHB gene (rs555621*rs11031010*rs1782507) was FRG-correlated (OR = 0.71/pperm = 0.05). Ten FGR-implicated interworking models were founded for 13 SNPs (pperm ≤ 0.001). The rs999460 NKX2-1 and rs12444979 GPRC5B interplays significantly influenced the FGR risk (these SNPs were present in 50% of models). FGR-related mAAM-appertain 15 polymorphic variants and 350 linked SNPs were functionally momentous in relation to 39 genes participating in the regulation of hormone levels, the ovulation cycle process, male gonad development and vitamin D metabolism. Thus, this study showed, for the first time, that the mAAM-appertain genes determine FGR risk.
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Affiliation(s)
- Evgeny Reshetnikov
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Maria Churnosova
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Yuliya Reshetnikova
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Vadim Stepanov
- Research Institute for Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634050 Tomsk, Russia
| | - Anna Bocharova
- Research Institute for Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634050 Tomsk, Russia
| | - Victoria Serebrova
- Research Institute for Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634050 Tomsk, Russia
| | - Ekaterina Trifonova
- Research Institute for Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634050 Tomsk, Russia
| | - Irina Ponomarenko
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Inna Sorokina
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Olga Efremova
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Valentina Orlova
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Irina Batlutskaya
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Marina Ponomarenko
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Vladimir Churnosov
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Inna Aristova
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Alexey Polonikov
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
- Department of Biology, Medical Genetics and Ecology and Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 305041 Kursk, Russia
| | - Mikhail Churnosov
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia
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He R, Zeng Y, Wang C, Chen L, Cai G, Chen Y, Wang Y, Ye Q, Chen X. Associative role of HLA-DRB1 as a protective factor for susceptibility and progression of Parkinson's disease: a Chinese cross-sectional and longitudinal study. Front Aging Neurosci 2024; 16:1361492. [PMID: 38586829 PMCID: PMC10995924 DOI: 10.3389/fnagi.2024.1361492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/13/2024] [Indexed: 04/09/2024] Open
Abstract
Background Previous genome-wide association studies investigating the relationship between the HLA-DRB1 and the risk of Parkinson's disease (PD) have shown limited racial diversity and have not explored clinical heterogeneity extensively. Methods The study consisted of three parts: a case-control study, a cross-sectional study, and a longitudinal cohort study. The case-control study included 477 PD patients and 477 healthy controls to explore the relationship between rs660895 and PD susceptibility. The cross-sectional study utilized baseline data from 429 PD patients to examine the correlation between rs660895 and PD features. The longitudinal study included 388 PD patients who completed a 3-year follow-up to investigate the effects of rs660895 on PD progression. Results In the case-control study, HLA-DRB1 rs660895-G allele was associated with a decreased risk of PD in allele model (adjusted OR=0.72, p = 0.003) and dominant model (AG + GG vs. AA: adjusted OR = 0.67, p = 0.003). In the cross-sectional analysis, there was no association between rs660895 and the onset age, motor phenotype, or initial motor symptoms. In the longitudinal analysis, PD patients with the G allele exhibited a slower progression of motor symptoms (MDS-UPDRS-III total score: β = -5.42, p < 0.001, interaction ptime × genotype < 0.001) and non-motor symptoms (NMSS score: β = -4.78, p = 0.030, interaction ptime × genotype < 0.001). Conclusion Our findings support HLA-DRB1 rs660895-G allele is a protective genetic factor for PD risk in Chinese population. Furthermore, we also provide new evidence for the protective effect of rs660895-G allele in PD progression.
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Affiliation(s)
- Raoli He
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Yuqi Zeng
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Chaodong Wang
- Department of Neurology, National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Lina Chen
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Guoen Cai
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Ying Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Yingqing Wang
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Qinyong Ye
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Xiaochun Chen
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
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