1
|
Kumar S, Bhushan B, Kumar A, Panigrahi M, Bharati J, Kumari S, Kaiho K, Banik S, Karthikeyan A, Chaudhary R, Gaur GK, Dutt T. Elucidation of novel SNPs affecting immune response to classical swine fever vaccination in pigs using immunogenomics approach. Vet Res Commun 2024; 48:941-953. [PMID: 38017322 DOI: 10.1007/s11259-023-10262-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/19/2023] [Indexed: 11/30/2023]
Abstract
The host genetic makeup plays a significant role in causing the within-breed variation among individuals after vaccination. The present study was undertaken to elucidate the genetic basis of differential immune response between high and low responder Landlly (Landrace X Ghurrah) piglets vis-à-vis CSF vaccination. For the purpose, E2 antibody response against CSF vaccination was estimated in sampled animals on the day of vaccination and 21-day post-vaccination as a measure of humoral immune response. Double-digestion restriction associated DNA (ddRAD) sequencing was undertaken on 96 randomly chosen Landlly piglets using Illumina HiSeq platform. SNP markers were called using standard methodology. Genome-wide association study (GWAS) was undertaken in PLINK program to identify the informative SNP markers significantly associated with differential immune response. The results revealed significant SNPs associated with E2 antibody response against CSF vaccination. The genome-wide informative SNPs for the humoral immune response against CSF vaccination were located on SSC10, SSC17, SSC9, SSC2, SSC3 and SSC6. The overlapping and flanking genes (500Kb upstream and downstream) of significant SNPs were CYB5R1, PCMTD2, WT1, IL9R, CD101, TMEM64, TLR6, PIGG, ADIPOR1, PRSS37, EIF3M, and DNAJC24. Functional enrichment and annotation analysis were undertaken for these genes in order to gain maximum insights into the association of these genes with immune system functionality in pigs. The genetic makeup was associated with differential immune response against CSF vaccination in Landlly piglets while the identified informative SNPs may be used as suitable markers for determining variation in host immune response against CSF vaccination in pigs.
Collapse
Affiliation(s)
- Satish Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India.
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India.
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India.
| | - Amit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India.
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India
| | - Jaya Bharati
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Soni Kumari
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India
| | - Kaisa Kaiho
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India
| | - Santanu Banik
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - A Karthikeyan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India
| | - Rajni Chaudhary
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India
| | - G K Gaur
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India
| |
Collapse
|
2
|
Sun Y, Wang Y, Wang L, Zou M, Peng X. STAT5-mediated transcription of miR-33-5p in Mycoplasma gallisepticum-infected DF-1 cells. Avian Pathol 2024; 53:68-79. [PMID: 37855868 DOI: 10.1080/03079457.2023.2272617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/15/2023] [Indexed: 10/20/2023]
Abstract
RESEARCH HIGHLIGHTS MG-HS regulates the expression of transcription factor STAT5.Transcription factor STAT5 can target miR-33-5p promoter element.MG-influenced STAT5 regulates miR-33-5p and its target gene expression.
Collapse
Affiliation(s)
- Yingfei Sun
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yingjie Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Lulu Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Mengyun Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiuli Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| |
Collapse
|
3
|
Lopez-Hernandez A, Sberna S, Campaner S. Emerging Principles in the Transcriptional Control by YAP and TAZ. Cancers (Basel) 2021; 13:cancers13164242. [PMID: 34439395 PMCID: PMC8391352 DOI: 10.3390/cancers13164242] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary YAP and TAZ are transcriptional cofactors that integrate several upstream signals to generate context-dependent transcriptional responses. This requires extensive integration with epigenetic regulators and other transcription factors. The molecular and genomic characterization of YAP and TAZ nuclear function has broad implications both in physiological and pathological settings. Abstract Yes-associated protein (YAP) and TAZ are transcriptional cofactors that sit at the crossroad of several signaling pathways involved in cell growth and differentiation. As such, they play essential functions during embryonic development, regeneration, and, once deregulated, in cancer progression. In this review, we will revise the current literature and provide an overview of how YAP/TAZ control transcription. We will focus on data concerning the modulation of the basal transcriptional machinery, their ability to epigenetically remodel the enhancer–promoter landscape, and the mechanisms used to integrate transcriptional cues from multiple pathways. This reveals how YAP/TAZ activation in cancer cells leads to extensive transcriptional control that spans several hallmarks of cancer. The definition of the molecular mechanism of transcriptional control and the identification of the pathways regulated by YAP/TAZ may provide therapeutic opportunities for the effective treatment of YAP/TAZ-driven tumors.
Collapse
|
4
|
Gu J, Zhang J, Huang W, Tao T, Huang Y, Yang L, Yang J, Fan Y, Wang H. Activating miRNA-mRNA network in gemcitabine-resistant pancreatic cancer cell associates with alteration of memory CD4 + T cells. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:279. [PMID: 32355723 PMCID: PMC7186712 DOI: 10.21037/atm.2020.03.53] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background To identify key microRNAs (miRNAs) and their target mRNAs related to gemcitabine-resistant pancreatic cancer (PC) and investigate the association between gemcitabine-resistant-related miRNAs and mRNAs and immune infiltration. Methods Expression profiles of miRNAs and mRNAs were obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed miRNAs and mRNAs (referred to as "DEmiRNAs" and "DEmRNAs", respectively) were distinguished between gemcitabine-resistant PC cells and its parental cells. The DEmRNAs targeted by the DEmiRNAs were retrieved using miRDB, microT, and Targetscan. Furthermore, GO and KEGG pathway enrichment analysis and GSEA were performed. The Kaplan-Meier plotter was used to analyze the prognosis of key DEmiRNAs and DEmRNAs on PC patients. The relationship between the key DEmRNAs and tumor-infiltrating immune cells in PC was investigated using CIBERSORT method using the LM22 signature as reference. Key infiltrating immune cells were further analyzed for the associations with prognosis of TCGA PAAD patients. Results Four DEmiRNAs, including hsa-miR-3178, hsa-miR-485-3p, hsa-miR-574-5p, and hsa-miR-584-5p, were identified to target seven DEmRNAs, including MSI2, TEAD1, GNPDA1, RND3, PRKACB, TRIM68, and YKT6, individually, in gemcitabine-resistant PC cells versus parental cells. Gemcitabine-resistant PC cells were enriched in proteasome-related, immune-related, and memory CD4+ T cell-related pathways, indicating a gemcitabine therapeutic effect on PC cells. All four DEmiRNAs and almost all DEmRNAs had an impact on the prognosis of PC patients. All seven DEmRNAs had remarkable effects on CD4+ memory T cells, which were affected by the gemcitabine therapeutic effect. Effector memory CD4+ T cells rather than central memory CD4+ T cells predicted a good prognosis according to the TCGA PAAD dataset. Conclusions Gemcitabine resistance can alter the fraction of memory CD4+ T cells via hsa-miR-3178, hsa-miR-485-3p, hsa-miR-574-5p and hsa-miR-584-5p targeted MSI2, TEAD1, GNPDA1, RND3, PRKACB, TRIM68, and YKT6 network in PC.
Collapse
Affiliation(s)
- Jianyou Gu
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Junfeng Zhang
- Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Wenjie Huang
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.,Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510000, China
| | - Tian Tao
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Yaohuan Huang
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Ludi Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Jiali Yang
- Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Yingfang Fan
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Huaizhi Wang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing 400038, China
| |
Collapse
|
5
|
Mao R, Wu Y, Ming Y, Xu Y, Wang S, Chen X, Wang X, Fan Y. Enhancer RNAs: a missing regulatory layer in gene transcription. SCIENCE CHINA-LIFE SCIENCES 2018; 62:905-912. [PMID: 30593613 DOI: 10.1007/s11427-017-9370-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/01/2018] [Indexed: 01/12/2023]
Abstract
Enhancers and super-enhancers exert indispensable roles in maintaining cell identity through spatiotemporally regulating gene transcription. Meanwhile, active enhancers and super-enhancers also produce transcripts termed enhancer RNAs (eRNAs) from their DNA elements. Although enhancers have been identified for more than 30 years, widespread transcription from enhancers are just discovered by genome-wide sequencing and considered as the key to understand longstanding questions in gene transcription. RNA-transcribed enhancers are marked by histone modifications such as H3K4m1/2 and H3K27Ac, and enriched with transcription regulatory factors such as LDTFs, P300, CBP, BRD4 and MED1. Those regulatory factors might constitute a Mega-Trans-like complex to potently activate enhancers. Compared to mRNAs, eRNAs are quite unstable and play roles at local. Functionally, it has been shown that eRNAs promote formation of enhancer-promoter loops. Several studies also demonstrated that eRNAs help the binding of RNA polymerase II (RNAPII) or transition of paused RNAPII by de-association of the negative elongation factor (NELF) complex. Nevertheless, these proposed mechanisms are not universally accepted and still under controversy. Here, we comprehensively summarize the reported findings and make perspectives for future exploration. We also believe that super-enhancer derived RNAs (seRNAs) might be informative to understand the nature of super-enhancers.
Collapse
Affiliation(s)
- Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yuanyuan Wu
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yue Ming
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yuanpei Xu
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Shouyan Wang
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China
| | - Xia Chen
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China
| | - Xiaoying Wang
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yihui Fan
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China.
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China.
| |
Collapse
|
6
|
Abstract
SIGNIFICANCE RNA is a heterogeneous class of molecules with the minority being protein coding. Noncoding RNAs (ncRNAs) are involved in translation and epigenetic control mechanisms of gene expression. Recent Advances: In recent years, the number of identified ncRNAs has dramatically increased and it is now clear that ncRNAs provide a complex layer of differential gene expression control. CRITICAL ISSUES NcRNAs exhibit interplay with redox regulation. Redox regulation alters the expression of ncRNAs; conversely, ncRNAs alter the expression of generator and effector systems of redox regulation in a complex manner, which will be the focus of this review article. FUTURE DIRECTIONS Understanding the role of ncRNA in redox control will lead to the development of new strategies to alter redox programs. Given that many ncRNAs (particularly microRNAs [miRNAs]) change large gene sets, these molecules are attractive drug candidates; already, now miRNAs can be targeted in patients. Therefore, the development of ncRNA therapies focusing on these molecules is an attractive future strategy. Antioxid. Redox Signal. 29, 793-812.
Collapse
Affiliation(s)
- Matthias S Leisegang
- 1 Institute for Cardiovascular Physiology, Goethe-University , Frankfurt, Germany .,2 German Center of Cardiovascular Research (DZHK) , Partner Site RheinMain, Frankfurt, Germany
| | - Katrin Schröder
- 1 Institute for Cardiovascular Physiology, Goethe-University , Frankfurt, Germany .,2 German Center of Cardiovascular Research (DZHK) , Partner Site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- 1 Institute for Cardiovascular Physiology, Goethe-University , Frankfurt, Germany .,2 German Center of Cardiovascular Research (DZHK) , Partner Site RheinMain, Frankfurt, Germany
| |
Collapse
|
7
|
Ding M, Liu Y, Liao X, Zhan H, Liu Y, Huang W. Enhancer RNAs (eRNAs): New Insights into Gene Transcription and Disease Treatment. J Cancer 2018; 9:2334-2340. [PMID: 30026829 PMCID: PMC6036709 DOI: 10.7150/jca.25829] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/30/2018] [Indexed: 12/23/2022] Open
Abstract
Enhancers are cis-acting elements that have the ability to increase the expression of target genes. Recent studies have shown that enhancers can act as transcriptional units for the production of enhancer RNAs (eRNAs), which are hallmarks of activity enhancers and are involved in the regulation of gene transcription. The in-depth study of eRNAs is of great significance for us to better understand enhancer function and transcriptional regulation in various diseases. Therefore, eRNAs may be a potential therapeutic target for diseases. Here, we review the current knowledge of the characteristics of eRNAs, the molecular mechanisms of eRNAs action, as well as diseases related to dysregulation of eRNAs.
Collapse
Affiliation(s)
- Mengting Ding
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Clinical Medicine College of Anhui Medical University, Shenzhen 518000, Guangdong, China.,Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Yuhan Liu
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Clinical Medicine College of Anhui Medical University, Shenzhen 518000, Guangdong, China.,Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Xinhui Liao
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Hengji Zhan
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Clinical Medicine College of Anhui Medical University, Shenzhen 518000, Guangdong, China.,Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Yuchen Liu
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Weiren Huang
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| |
Collapse
|
8
|
Gao Y, Yang Y, Yuan F, Huang J, Xu W, Mao B, Yuan Z, Bi W. TNFα-YAP/p65-HK2 axis mediates breast cancer cell migration. Oncogenesis 2017; 6:e383. [PMID: 28945218 PMCID: PMC5623908 DOI: 10.1038/oncsis.2017.83] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/30/2017] [Accepted: 08/19/2017] [Indexed: 12/16/2022] Open
Abstract
Clinical and experimental evidence indicates that macrophages could promote solid-tumor progression and metastasis. However, the mechanisms underlying this process remain unclear. Here we show that yes-associated protein 1 (YAP1), a transcriptional regulator that controls tissue growth and regeneration, has an important role in tumor necrosis factor α (TNF α)-induced breast cancer migration. Mechanistically, macrophage conditioned medium (CM) or TNFα triggers IκB kinases (IKKs)-mediated YAP phosphorylation and activation in breast cancer cells. We further found that TNFα or macrophage CM treatment increases the interaction between p65 and YAP. Chromatin immunoprecipitation (ChIP) assay shows that YAP/TEAD (TEA domain family member) and p65 proteins synergistically regulate the transcription of hexokinase 2 (HK2), a speed-limiting enzyme in glycolysis, and promotes TNFα-induced or macrophage CM-induced cell migration. Together, our findings indicate an important role of TNFα-IKK-YAP/p65-HK2 signaling axis in the process of inflammation-driven migration in breast cancer cells, which reveals a new molecular link between inflammation and breast cancer metastasis.
Collapse
Affiliation(s)
- Y Gao
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Y Yang
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - F Yuan
- Department of Oncology, Chinese PLA General Hospital, Beijing, China
| | - J Huang
- Department of Orthopedics, Clinical Division of Surgery, Chinese PLA General Hospital, Beijing, China
| | - W Xu
- General Surgery Center, Chinese PLA General Hospital, Beijing, China
| | - B Mao
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Z Yuan
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China.,Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - W Bi
- Department of Orthopedics, Clinical Division of Surgery, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|