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Hong K, Yang Q, Yin H, Zhang J, Yu B. SDR16C5 promotes proliferation and migration and inhibits apoptosis in pancreatic cancer. Open Life Sci 2023; 18:20220630. [PMID: 37360782 PMCID: PMC10290281 DOI: 10.1515/biol-2022-0630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 06/28/2023] Open
Abstract
Pancreatic cancer (PAAD) is usually found when it is already in its advanced stage, which has limited options available for treatment and poor overall survival. The SDR16C5 gene is necessary for embryonic and adult tissue differentiation, development, and apoptosis, and it also participates in immune response and regulates energy metabolism. However, the role of SDR16C5 in PAAD remains unclear. In this study, we find that SDR16C5 was highly expressed in multiple tumors including PAAD. Furthermore, higher expression of SDR16C5 was significantly associated with poorer survival. We also find that the knockdown of SDR16C5 can inhibit PAAD cell proliferation and promote cell apoptosis by repressing Bcl-2, cleaved caspase 3, and cleaved caspase 9 protein expression. Moreover, silencing SDR16C5 inhibits the migration of PANC-1 and SW1990 cells by interrupting epithelial-mesenchymal transition. KEGG pathway analysis and immunofluorescence staining indicate that SDR16C5 is associated with immunity and may also participate in the development of PAAD through the IL-17 signaling pathway. Collectively, our findings provide evidence that SDR16C5 is overexpressed in PAAD patients and promotes its proliferation, migration, invasion, and apoptosis-inhibition of PAAD cells. Thus, SDR16C5 may be a potential prognostic and therapeutic target.
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Affiliation(s)
- Kunqiao Hong
- Department of Gastroenterology, Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qian Yang
- Department of Gastroenterology, Guizhou Provincial People's Hospital, Guiyang City, Guizhou Province, China
- NHC Key Laboratory of Pulmonary Immune-related Disease, Guizhou Provincial People’s Hospital, Guiyang City, Guizhou Province, China
| | - Haisen Yin
- Department of Gastroenterology, Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jianwei Zhang
- Department of Gastroenterology, Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
| | - Baoping Yu
- Department of Gastroenterology, Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
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Modorov MV, Kleshcheva AA, Osintseva KR, Tkachenko IV, Sevost’yanov MY, Zezin NN. The Use of KASP Technology to Study Associations of Single Nucleotide Polymorphisms in the GPAD4, CCL3, DGKG, PPARGC1A, STAT1, and TLR4 Genes with Milk Production in Cattle. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Ahmad SM, Bhat B, Bhat SA, Yaseen M, Mir S, Raza M, Iquebal MA, Shah RA, Ganai NA. SNPs in Mammary Gland Epithelial Cells Unraveling Potential Difference in Milk Production Between Jersey and Kashmiri Cattle Using RNA Sequencing. Front Genet 2021; 12:666015. [PMID: 34413874 PMCID: PMC8369411 DOI: 10.3389/fgene.2021.666015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Deep RNA sequencing experiment was employed to detect putative single nucleotide polymorphisms (SNP) in mammary epithelial cells between two diverse cattle breeds (Jersey and Kashmiri) to understand the variations in the coding regions that reflect differences in milk production traits. The low milk-producing Kashmiri cattle are being replaced by crossbreeding practices with Jersey cattle with the aim of improving milk production. However, crossbred animals are prone to infections and various other diseases resulting in unsustainable milk production. In this study, we tend to identify high-impact SNPs from Jersey and Kashmiri cows (utilizing RNA-Seq data) to delineate key pathways mediating milk production traits in both breeds. A total of 607 (442 SNPs and 169 INDELs) and 684 (464 SNPs and 220 INDELs) high-impact variants were found specific to Jersey and Kashmir cattle, respectively. Based on our results, we conclude that in Jersey cattle, genes with high-impact SNPs were enriched in nucleotide excision repair pathway, ABC transporter, and metabolic pathways like glycerolipid metabolism, pyrimidine metabolism, and amino acid synthesis (glycine, serine, and threonine). Whereas, in Kashmiri cattle, the most enriched pathways include endocytosis pathway, innate immunity pathway, antigen processing pathway, insulin resistance pathway, and signaling pathways like TGF beta and AMPK which could be a possible defense mechanism against mammary gland infections. A varied set of SNPs in both breeds, suggests a clear differentiation at the genomic level; further analysis of high-impact SNPs are required to delineate their effect on these pathways.
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Affiliation(s)
- Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
| | - Shakil Ahmad Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
| | - Mifftha Yaseen
- Division of Food Science, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
| | - Shabir Mir
- Division of Animal Genetics and Breeding, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
| | - Mustafa Raza
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Riaz Ahmad Shah
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
| | - Nazir Ahmad Ganai
- Directorate Planning and Monitoring, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
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Bioinformatics analysis and genetic polymorphisms in genomic region of the bovine SH2B2 gene and their associations with molecular breeding for body size traits in qinchuan beef cattle. Biosci Rep 2021; 40:222267. [PMID: 32110807 PMCID: PMC7069895 DOI: 10.1042/bsr20192113] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 02/21/2020] [Accepted: 02/28/2020] [Indexed: 11/17/2022] Open
Abstract
The Src homology 2 B 2 (SH2B2) gene regulate energy balance and body weight at least partially by enhancing Janus kinase-2 (JAK2)-mediated cytokine signaling, including leptin and/or GH signaling. Leptin is an adipose hormone that controls body weight. The objective of the present study is to evaluate the association between body measurement traits and SH2B2 gene polymorphisms as responsible mutations. For this purpose, we selected four single-nucleotide polymorphisms (SNPs) in SH2B2 gene, including two in intron 5 (g.20545A>G, and g.20570G>A, one synonymous SNP g.20693T>C, in exon 6 and one in intron 8 (g.24070C>A, and genotyped them in Qinchuan cattle. SNPs in sample populations were in medium polymorphism level (0.250<PIC<0.500). Association study indicated that the g.20570G>A, g.20693T>C, and g.24070C>A, significantly (P < 0.05) associated with body length (BL) and chest circumference (CC) in Qinchuan cattle. In addition, H4H3 and H5H5 diplotype had highly significantly (P < 0.01) greater body length (BL), rump length (RL), and chest circumference (CC) than H4H2. Our investigation will not only extend the spectrum of genetic variation of bovine SH2B2 gene, but also provide useful information for the marker assisted selection in beef cattle breeding program.
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Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection. PLoS One 2021; 16:e0248405. [PMID: 33720948 PMCID: PMC7959398 DOI: 10.1371/journal.pone.0248405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal nematodes (GIN) are an important constraint in small ruminant production. Genetic selection for resistant animals is a potential sustainable control strategy. Advances in molecular genetics have led to the identification of several molecular genetic markers associated with genes affecting economic relevant traits. In this study, the variants in the genome of Creole goats resistant or susceptible to GIN were discovered from RNA-sequencing. We identified SNPs, insertions and deletions that distinguish the two genotypes, resistant and susceptible and we characterized these variants through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible genotype with 78% of the genes involved in this pathway showing genomic variants. These genomic variants are expected to provide useful resources especially for molecular breeding for GIN resistance in goats.
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Pareek CS, Sachajko M, Jaskowski JM, Herudzinska M, Skowronski M, Domagalski K, Szczepanek J, Czarnik U, Sobiech P, Wysocka D, Pierzchala M, Polawska E, Stepanow K, Ogłuszka M, Juszczuk-Kubiak E, Feng Y, Kumar D. Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq. Vet Sci 2019; 6:vetsci6020036. [PMID: 30934933 PMCID: PMC6631511 DOI: 10.3390/vetsci6020036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/16/2019] [Accepted: 03/26/2019] [Indexed: 12/26/2022] Open
Abstract
Global gene expression in liver transcriptome varies among cattle breeds. The present investigation was aimed to identify the differentially expressed genes (DEGs), metabolic gene networks and metabolic pathways in bovine liver transcriptome of young bulls. In this study, we comparatively analyzed the bovine liver transcriptome of dairy (Polish Holstein Friesian (HF); n = 6), beef (Hereford; n = 6), and dual purpose (Polish-Red; n = 6) cattle breeds. This study identified 895, 338, and 571 significant (p < 0.01) differentially expressed (DE) gene-transcripts represented as 745, 265, and 498 hepatic DE genes through the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-HF versus Polish-Red breeds comparisons, respectively. By combining all breeds comparisons, 75 hepatic DE genes (p < 0.01) were identified as commonly shared among all the three breed comparisons; 70, 160, and 38 hepatic DE genes were commonly shared between the following comparisons: (i) Polish-Red versus Hereford and Polish-HF versus Hereford; (ii) Polish-Red versus Hereford and Polish-HF versus Polish-Red; and (iii) Polish-HF versus Hereford and Polish-HF versus Polish-Red, respectively. A total of 440, 82, and 225 hepatic DE genes were uniquely observed for the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-Red versus Polish-HF comparisons, respectively. Gene ontology (GO) analysis identified top-ranked enriched GO terms (p < 0.01) including 17, 16, and 31 functional groups and 151, 61, and 140 gene functions that were DE in all three breed liver transcriptome comparisons. Gene network analysis identified several potential metabolic pathways involved in glutamine family amino-acid, triglyceride synthesis, gluconeogenesis, p38MAPK cascade regulation, cholesterol biosynthesis (Polish-Red versus Hereford); IGF-receptor signaling, catecholamine transport, lipoprotein lipase, tyrosine kinase binding receptor (Polish-HF versus Hereford), and PGF-receptor binding, (Polish-HF versus Polish-Red). Validation results showed that the relative expression values were consistent to those obtained by RNA-seq, and significantly correlated between the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson’s r > 0.90). Our results provide new insights on bovine liver gene expressions among dairy versus dual versus beef breeds by identifying the large numbers of DEGs markers submitted to NCBI gene expression omnibus (GEO) accession number GSE114233, which can serve as useful genetic tools to develop the gene assays for trait-associated studies as well as, to effectively implement in genomics selection (GS) cattle breeding programs in Poland.
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Affiliation(s)
- Chandra Shekhar Pareek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Mateusz Sachajko
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Jedrzej M Jaskowski
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Magdalena Herudzinska
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Mariusz Skowronski
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Krzysztof Domagalski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Urszula Czarnik
- Faculty of Animal Bio-engineering, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland.
| | - Przymeslaw Sobiech
- Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, 10719 Olsztyn, Poland.
| | - Dominika Wysocka
- Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, 10719 Olsztyn, Poland.
| | - Mariusz Pierzchala
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Ewa Polawska
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Kamila Stepanow
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Magdalena Ogłuszka
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Edyta Juszczuk-Kubiak
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, 02-787 Warsaw, Poland.
| | - Yaping Feng
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08 854, USA.
| | - Dibyendu Kumar
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08 854, USA.
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Identification of genomic regions harboring diversity between Holstein and two local endangered breeds, Modenese and Maremmana. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gunawan A, Listyarini K, Furqon A, Sumantri C, Akter SH, Uddin MJ. Transcriptome signature of liver tissue with divergent mutton odour and flavour using RNA deep sequencing. Gene 2018; 676:86-94. [PMID: 29958950 DOI: 10.1016/j.gene.2018.06.086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 06/21/2018] [Accepted: 06/25/2018] [Indexed: 01/16/2023]
Abstract
Mutton consumption is less popular in many Asian countries including Indonesia, whose consumers often complain about the unpleasant flavour and odour of the meat. The main causes of mutton odour are the two compounds of branched chain fatty acid (BCFA): methylnonanoic (MNA), phenol, 3-methyl (MP), 4-methylnonanoic (MNA) and 4-ethyloctanoic (EOA) present in all the adipose tissue; and the 3-methylindole (MI) or skatole and indole, which are originated from pastoral diets. It is crucial to understand the genetic mechanism of mutton odour and flavour (MOF) to select sheep for lower BCFA and indole thus reduce the unpleasant flavour of meat. The aim of the present study was to investigate transcriptome profiling in liver tissue with divergent MOF using RNA deep sequencing. Liver tissues from higher (n = 3) and lower (n = 3) MOF sheep were analysed using Illumina HiSeq 2500. The total number of reads produced for each liver sample ranged from 21.37 to 25.37 million. Approximately 103 genes were differentially expressed (DEGs) with significance level of p-adjusted value <0.05. Among them, 60 genes were up-regulated, and 43 were down-regulated (p < 0.01, FC > 1.5) in higher MOF group. Differentially regulated genes in high MOF liver samples were enriched in biological processes such as cellular response to chemical stimulus and endogenous stimulus; cellular components such as such as basement membrane and extracellular matrix; and molecular functions such as haeme binding and oxidoreductase activity. Among the DEGs, metabolic phase I related genes belonging to the cytochrome P450 CYP2A6 were dominantly expressed. Additionally, phase II conjugation genes including UDP glucuronosyltransferases UGT2B18, sulfotransferase SULT1C1, and glutathione S-transferase GSTM1 were identified. The dominant candidate genes for SOF could be cytochrome P450, sodium-channel protein, transmembrane protein, glutathione transferase, UDP glucuronosyltransferases and sulfotransferase. Pathway analysis identified steroid hormone biosynthesis and chemical carcinogenesis by cytochrome P450 pathways which may play important roles in MOF-related molecules metabolism. This work highlighted potential genes and gene-networks that may affect meat off flavour and odour in sheep.
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Affiliation(s)
- Asep Gunawan
- Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, 16680 Bogor, Indonesia
| | - Kasita Listyarini
- Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, 16680 Bogor, Indonesia
| | - Ahmad Furqon
- Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, 16680 Bogor, Indonesia
| | - Cece Sumantri
- Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, 16680 Bogor, Indonesia
| | - Syeda Hasina Akter
- School of Veterinary Science, University of Queensland, Gatton Campus, QLD 4343, Australia; Faculty of Veterinary Science, Bangladesh Agricultural University, 2202, Bangladesh.
| | - Muhammad Jasim Uddin
- School of Veterinary Science, University of Queensland, Gatton Campus, QLD 4343, Australia; Faculty of Veterinary Science, Bangladesh Agricultural University, 2202, Bangladesh.
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