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Tan WLA, Hudson NJ, Porto Neto LR, Reverter A, Afonso J, Fortes MRS. An association weight matrix identified biological pathways associated with bull fertility traits in a multi-breed population. Anim Genet 2024; 55:495-510. [PMID: 38692842 DOI: 10.1111/age.13431] [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: 11/16/2023] [Revised: 02/26/2024] [Accepted: 04/01/2024] [Indexed: 05/03/2024]
Abstract
Using seven indicator traits, we investigated the genetic basis of bull fertility and predicted gene interactions from SNP associations. We used percent normal sperm as the key phenotype for the association weight matrix-partial correlation information theory (AWM-PCIT) approach. Beyond a simple list of candidate genes, AWM-PCIT predicts significant gene interactions and associations for the selected traits. These interactions formed a network of 537 genes: 38 genes were transcription cofactors, and 41 genes were transcription factors. The network displayed two distinct clusters, one with 294 genes and another with 243 genes. The network is enriched in fertility-associated pathways: steroid biosynthesis, p53 signalling, and the pentose phosphate pathway. Enrichment analysis also highlighted gene ontology terms associated with 'regulation of neurotransmitter secretion' and 'chromatin formation'. Our network recapitulates some genes previously implicated in another network built with lower-density genotypes. Sequence-level data also highlights additional candidate genes relevant to bull fertility, such as FOXO4, FOXP3, GATA1, CYP27B1, and EBP. A trio of regulatory genes-KDM5C, LRRK2, and PME-was deemed core to the network because of their overarching connections. This trio probably influences bull fertility through their interaction with genes, both known and unknown as to their role in male fertility. Future studies may target the trio and their target genes to enrich our understanding of male fertility further.
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Affiliation(s)
- Wei Liang Andre Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Nicholas James Hudson
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, Queensland, Australia
| | | | | | - Juliana Afonso
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
- Empresa Brasileira de Pesquisa Agropecuária, Pecuária Sudeste, São Carlos, São Paulo, Brazil
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2
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Huang J, Mao L, Lei Q, Guo AY. Bioinformatics tools and resources for cancer and application. Chin Med J (Engl) 2024:00029330-990000000-01162. [PMID: 39075637 DOI: 10.1097/cm9.0000000000003254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Indexed: 07/31/2024] Open
Abstract
ABSTRACT Tumor bioinformatics plays an important role in cancer research and precision medicine. The primary focus of traditional cancer research has been molecular and clinical studies of a number of fundamental pathways and genes. In recent years, driven by breakthroughs in high-throughput technologies, large-scale cancer omics data have accumulated rapidly. How to effectively utilize and share these data is particularly important. To address this crucial task, many computational tools and databases have been developed over the past few years. To help researchers quickly learn and understand the functions of these tools, in this review, we summarize publicly available bioinformatics tools and resources for pan-cancer multi-omics analysis, regulatory analysis of tumorigenesis, tumor treatment and prognosis, immune infiltration analysis, immune repertoire analysis, cancer driver gene and driver mutation analysis, and cancer single-cell analysis, which may further help researchers find more suitable tools for their research.
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Affiliation(s)
- Jin Huang
- Department of Thoracic Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lingzi Mao
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qian Lei
- Department of Thoracic Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - An-Yuan Guo
- Department of Thoracic Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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3
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Yan G, Wei T, Lan Y, Xu T, Qian P. Different parts of the mussel Gigantidas haimaensis holobiont responded differently to deep-sea sampling stress. Integr Zool 2024. [PMID: 39072987 DOI: 10.1111/1749-4877.12881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Acute environmental changes cause stress during conventional deep-sea biological sampling without in situ fixation and affect gene expressions of samples collected. However, the degree of influence and underlying mechanisms are hardly investigated. Here, we conducted comparative transcriptomic analyses between in situ and onboard fixed gills and between in situ and onboard fixed mantles of deep-sea mussel Gigantidas haimaensis to assess the effects of incidental sampling stress. Results showed that transcription, translation, and energy metabolism were upregulated in onboard fixed gills and mantles, thereby mobilizing rapid gene expression to tackle the stress. Autophagy and phagocytosis that related to symbiotic interactions between the host and endosymbiont were downregulated in the onboard fixed gills. These findings demonstrated that symbiotic gill and nonsymbiotic mantle responded differently to sampling stress, and symbiosis in the gill was perturbed. Further comparative metatranscriptomic analysis between in situ and onboard fixed gills revealed that stress response genes, peptidoglycan biosynthesis, and methane fixation were upregulated in the onboard fixed endosymbiotic Gammaproteobacteria inside the gills, implying that energy metabolism of the endosymbiont was increased to cope with sampling stress. Furthermore, comparative analysis between the mussel G. haimaensis and the limpet Bathyacmaea lactea transcriptomes resultedidentified six transcription factor orthologs upregulated in both onboard fixed mussel mantles and limpets, including sharply increased early growth response protein 1 and Kruppel-like factor 5. They potentially play key roles in initiating the response of sampled deep-sea macrobenthos to sampling stress. Our results clearly show that in situ fixed biological samples are vital for studying deep-sea environmental adaptation.
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Affiliation(s)
- Guoyong Yan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Tong Wei
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ting Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Peiyuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
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4
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Dai Y, Zhong Y, Pan R, Yuan L, Fu Y, Chen Y, Du J, Li M, Wang X, Liu H, Shi C, Liu G, Zhu P, Shimeld S, Zhou X, Li G. Evolutionary origin of the chordate nervous system revealed by amphioxus developmental trajectories. Nat Ecol Evol 2024:10.1038/s41559-024-02469-7. [PMID: 39025981 DOI: 10.1038/s41559-024-02469-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/17/2024] [Indexed: 07/20/2024]
Abstract
The common ancestor of all vertebrates had a highly sophisticated nervous system, but questions remain about the evolution of vertebrate neural cell types. The amphioxus, a chordate that diverged before the origin of vertebrates, can inform vertebrate evolution. Here we develop and analyse a single-cell RNA-sequencing dataset from seven amphioxus embryo stages to understand chordate cell type evolution and to study vertebrate neural cell type origins. We identified many new amphioxus cell types, including homologues to the vertebrate hypothalamus and neurohypophysis, rooting the evolutionary origin of these structures. On the basis of ancestor-descendant reconstruction of cell trajectories of the amphioxus and other species, we inferred expression dynamics of transcription factor genes throughout embryogenesis and identified three ancient developmental routes forming chordate neurons. We characterized cell specification at the mechanistic level and generated mutant lines to examine the function of five key transcription factors involved in neural specification. Our results show three developmental origins for the vertebrate nervous system: an anterior FoxQ2-dependent mechanism that is deeply conserved in invertebrates, a less-conserved route leading to more posterior neurons in the vertebrate spinal cord and a mechanism for specifying neuromesoderm progenitors that is restricted to chordates. The evolution of neuromesoderm progenitors may have led to a dramatic shift in posterior neural and mesodermal cell fate decisions and the body elongation process in a stem chordate.
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Affiliation(s)
- Yichen Dai
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Yanhong Zhong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rongrong Pan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Liang Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Yongheng Fu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuwei Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Huimin Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | | | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China.
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.
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5
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Garg P, Vanamamalai VK, Sharma S. In-silico analysis of cattle blood transcriptome to identify lncRNAs and their role during bovine tuberculosis. Sci Rep 2024; 14:16537. [PMID: 39019929 PMCID: PMC11255290 DOI: 10.1038/s41598-024-67001-0] [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: 03/01/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules with a length greater than 200 nucleotides that do not code for functional proteins. Although, genes play a vital role in immune response against a disease, it is less known that lncRNAs also contribute through gene regulation. Bovine tuberculosis is a significant zoonotic disease caused by Mycobacterium bovis (M. bovis) in cattle. Here, we report the in-silico analysis of the publicly available transcriptomic data of calves infected with M. bovis. A total of 51,812 lncRNAs were extracted across all the samples. A total of 216 genes and 260 lncRNAs were found to be differentially expressed across all the 4 conditions-infected vs uninfected at 8- and 20-week post-infection (WPI), 8 vs 20-WPI of both infected and uninfected. Gene Ontology and Functional annotation showed that 8 DEGs were annotated with immune system GOs and 2 DEGs with REACTOME immune system pathways. Co-expression analysis of DElncRNAs with DEGs revealed the involvement of lncRNAs with the genes annotated with Immune related GOs and pathways. Overall, our study sheds light on the dynamic transcriptomic changes in response to M. bovis infection, particularly highlighting the involvement of lncRNAs with immune-related genes. The identified immune pathways and gene-lncRNA interactions offer valuable insights for further research in understanding host-pathogen interactions and potential avenues for genetic improvement strategies in cattle.
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Affiliation(s)
- Priyanka Garg
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Venkata Krishna Vanamamalai
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
- Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, Faridabad Rd, Faridabad, Haryana, 121001, India
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India.
- Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, Faridabad Rd, Faridabad, Haryana, 121001, India.
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6
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Wang W, Chen M, Li H, Wu X, He C, Zhang C, Zhang H, Zheng H. Genome-wide analysis of the cytochrome P450 gene family in Pacific oyster Crassostrea gigas and their expression profiles during gonad development. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101291. [PMID: 39018793 DOI: 10.1016/j.cbd.2024.101291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/19/2024]
Abstract
The cytochrome P450 (CYP) gene superfamily plays a significant role in various physiological processes, producing different compounds such as hormones, fatty acids, and biomolecules. However, little information is known their roles during gonad development in Pacific oyster (Crassostrea gigas). In this study, total of 116 CgCYP (Crassostrea gigas cytochrome P450) genes were identified and their expression pattern was analyzed for the first time. The relative molecular weights of these CgCYP genes ranged from 63.52 to 113.41 kDa, and the length of encoded amino acids ranged from 103 to 993. And total 26 cis-acting elements of these CgCYP genes were identified. GO and KEGG enrichment analysis showed some CgCYP genes are essential for the metabolism of male and female sex hormones. Additionally, expression anslysis showed 69 CgCYP genes were over-expressed in early gonad development and triploid infertile individuals. More importantly, expression levels of CgCYP1, CgCYP15, CgCYP34, CgCYP46, CgCYP69, CgCYP87, CgCYP88, and CgCYP103, were found to be significantly higher in female gonad, suggesting their important roles in female gonad development. The results of this study will provide a better understanding of the CgCYP genes in the gonad development of Pacific oyster.
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Affiliation(s)
- Weili Wang
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Meizhen Chen
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Huiqi Li
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Xuanbing Wu
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Cheng He
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Chuanxu Zhang
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Hongkuan Zhang
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China.
| | - Huaiping Zheng
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China.
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7
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Wang X, Guo L, Yisha Z, Gu A, Liu T. Polo-like kinase 1 inhibition modulates urinary tract smooth muscle contraction and bladder cell transcriptional programs. Cytoskeleton (Hoboken) 2024. [PMID: 38994819 DOI: 10.1002/cm.21888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 05/11/2024] [Accepted: 06/08/2024] [Indexed: 07/13/2024]
Abstract
The serine/threonine kinase polo-like kinase 1 (PLK1) is a master regulator of cell proliferation and contraction, but its physiological role in the lower urinary tract is unknown. We utilized transcriptomic programs of human bladder smooth muscle cells (hBSMCs), 3D bladder spheroid viability assays, and human ureterovesical junction contractility measurements to elucidate the impacts of PLK1 inhibition. This work reveals PLK1 reduction with the selective inhibitor TAK-960 (500 nM) suppresses high K+-evoked contractions of human urinary smooth muscle ex vivo while decreasing urothelial cell viability. Transcriptomic analysis of hBSMCs treated with TAK-960 shows modulation of cell cycle and contraction pathways, specifically through altered expression of Cys2/His2-type zinc finger transcription factors. In bladder spheroids, PLK1 inhibition also suppresses smooth muscle contraction protein filamin. Taken together, these findings establish PLK1 is a critical governor of urinary smooth muscle contraction and urothelial proliferation with implications for lower urinary tract disorders. Targeting PLK1 pharmacologically may therefore offer therapeutic potential to ameliorate hypercontractility and aberrant growth. Further elucidation of PLK1 signaling networks promises new insights into pathogenesis and much needed treatment advances for debilitating urinary symptoms.
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Affiliation(s)
- Xiaolong Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Linfa Guo
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zuhaer Yisha
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Aodun Gu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Tongzu Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Urological Diseases, Wuhan, China
- Hubei Clinical Research Center for Laparoscopic/Endoscopic Urologic Surgery, Wuhan, China
- Institute of Urology, Wuhan University, Wuhan, China
- Hubei Medical Quality Control Center for Laparoscopic/Endoscopic Urologic Surgery, Wuhan, China
- Wuhan Clinical Research Center for Urogenital Tumors, Wuhan, China
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8
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Farhangi S, Gòdia M, Derks MFL, Harlizius B, Dibbits B, González-Prendes R, Crooijmans RPMA, Madsen O, Groenen MAM. Expression genome-wide association study identifies key regulatory variants enriched with metabolic and immune functions in four porcine tissues. BMC Genomics 2024; 25:684. [PMID: 38992576 PMCID: PMC11238464 DOI: 10.1186/s12864-024-10583-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Integration of high throughput DNA genotyping and RNA-sequencing data enables the discovery of genomic regions that regulate gene expression, known as expression quantitative trait loci (eQTL). In pigs, efforts to date have been mainly focused on purebred lines for traits with commercial relevance as such growth and meat quality. However, little is known on genetic variants and mechanisms associated with the robustness of an animal, thus its overall health status. Here, the liver, lung, spleen, and muscle transcriptomes of 100 three-way crossbred female finishers were studied, with the aim of identifying novel eQTL regulatory regions and transcription factors (TFs) associated with regulation of porcine metabolism and health-related traits. RESULTS An expression genome-wide association study with 535,896 genotypes and the expression of 12,680 genes in liver, 13,310 genes in lung, 12,650 genes in spleen, and 12,595 genes in muscle resulted in 4,293, 10,630, 4,533, and 6,871 eQTL regions for each of these tissues, respectively. Although only a small fraction of the eQTLs were annotated as cis-eQTLs, these presented a higher number of polymorphisms per region and significantly stronger associations with their target gene compared to trans-eQTLs. Between 20 and 115 eQTL hotspots were identified across the four tissues. Interestingly, these were all enriched for immune-related biological processes. In spleen, two TFs were identified: ERF and ZNF45, with key roles in regulation of gene expression. CONCLUSIONS This study provides a comprehensive analysis with more than 26,000 eQTL regions identified that are now publicly available. The genomic regions and their variants were mostly associated with tissue-specific regulatory roles. However, some shared regions provide new insights into the complex regulation of genes and their interactions that are involved with important traits related to metabolism and immunity.
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Affiliation(s)
- Samin Farhangi
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Marta Gòdia
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Topigs Norsvin Research Center, 's-Hertogenbosch, The Netherlands
| | | | - Bert Dibbits
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Rayner González-Prendes
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Ausnutria BV, Zwolle, The Netherlands
| | | | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
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9
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Pan X, Li X, Dong L, Liu T, Zhang M, Zhang L, Zhang X, Huang L, Shi W, Sun H, Fang Z, Sun J, Huang Y, Shao H, Wang Y, Yin M. Tumour vasculature at single-cell resolution. Nature 2024:10.1038/s41586-024-07698-1. [PMID: 38987599 DOI: 10.1038/s41586-024-07698-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
Tumours can obtain nutrients and oxygen required to progress and metastasize through the blood supply1. Inducing angiogenesis involves the sprouting of established vessel beds and their maturation into an organized network2,3. Here we generate a comprehensive atlas of tumour vasculature at single-cell resolution, encompassing approximately 200,000 cells from 372 donors representing 31 cancer types. Trajectory inference suggested that tumour angiogenesis was initiated from venous endothelial cells and extended towards arterial endothelial cells. As neovascularization elongates (through angiogenic stages SI, SII and SIII), APLN+ tip cells at the SI stage (APLN+ TipSI) advanced to TipSIII cells with increased Notch signalling. Meanwhile, stalk cells, following tip cells, transitioned from high chemokine expression to elevated TEK (also known as Tie2) expression. Moreover, APLN+ TipSI cells not only were associated with disease progression and poor prognosis but also hold promise for predicting response to anti-VEGF therapy. Lymphatic endothelial cells demonstrated two distinct differentiation lineages: one responsible for lymphangiogenesis and the other involved in antigen presentation. In pericytes, endoplasmic reticulum stress was associated with the proangiogenic BASP1+ matrix-producing pericytes. Furthermore, intercellular communication analysis showed that neovascular endothelial cells could shape an immunosuppressive microenvironment conducive to angiogenesis. This study depicts the complexity of tumour vasculature and has potential clinical significance for anti-angiogenic therapy.
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Affiliation(s)
- Xu Pan
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xin Li
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Liang Dong
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China
| | - Teng Liu
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Min Zhang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China
| | - Lining Zhang
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Xiyuan Zhang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China
| | - Lingjuan Huang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China
| | - Wensheng Shi
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyin Sun
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Zhaoyu Fang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering at Central South University, Changsha, China
| | - Jie Sun
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Yaoxuan Huang
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Hua Shao
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Yeqi Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, China
| | - Mingzhu Yin
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China.
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China.
- School of Medicine, Chongqing University, Chongqing, China.
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.
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10
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Stelloo S, Alejo-Vinogradova MT, van Gelder CAGH, Zijlmans DW, van Oostrom MJ, Valverde JM, Lamers LA, Rus T, Sobrevals Alcaraz P, Schäfers T, Furlan C, Jansen PWTC, Baltissen MPA, Sonnen KF, Burgering B, Altelaar MAFM, Vos HR, Vermeulen M. Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics. Cell Stem Cell 2024; 31:1072-1090.e8. [PMID: 38754429 DOI: 10.1016/j.stem.2024.04.017] [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: 04/24/2023] [Revised: 01/10/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Gastrulation is a critical stage in embryonic development during which the germ layers are established. Advances in sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and their derivatives. However, proteome-based studies of early mammalian development are scarce. To overcome this, we utilized gastruloids and a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho) protein expression during gastruloid differentiation. Our findings revealed many proteins with temporal expression and unique expression profiles for each germ layer, which we also validated using single-cell proteomics technology. Additionally, we profiled enhancer interaction landscapes using P300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron-based perturbations combined with single-cell RNA sequencing (scRNA-seq) identified a critical role for ZEB2 in mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis.
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Affiliation(s)
- Suzan Stelloo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
| | - Maria Teresa Alejo-Vinogradova
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Charlotte A G H van Gelder
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Dick W Zijlmans
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marek J van Oostrom
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Juan Manuel Valverde
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Lieke A Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Teja Rus
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Paula Sobrevals Alcaraz
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Tilman Schäfers
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Cristina Furlan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marijke P A Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Katharina F Sonnen
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Boudewijn Burgering
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Maarten A F M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands; Division of Molecular Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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11
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Yang Y, Dong L, Li Y, Huang Y, Zeng X. Summary data-based Mendelian randomization and single-cell RNA sequencing analyses identify immune associations with low-level LGALS9 in sepsis. J Cell Mol Med 2024; 28:e18559. [PMID: 39044269 PMCID: PMC11265992 DOI: 10.1111/jcmm.18559] [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: 05/02/2024] [Revised: 06/15/2024] [Accepted: 07/08/2024] [Indexed: 07/25/2024] Open
Abstract
Sepsis is one of the major challenges in intensive care units, characterized by the complexity of the host immune status. To gain a deeper understanding of the pathogenesis of sepsis, it is crucial to study the phenotypic changes in immune cells and their underlying molecular mechanisms. We conducted Summary data-based Mendelian randomization analysis by integrating genome-wide association studies data for sepsis with expression quantitative trait locus data, revealing a significant decrease in the expression levels of 17 biomarkers in sepsis patients. Furthermore, based on single-cell RNA sequencing data, we elucidated potential molecular mechanisms at single-cell resolution and identified that LGALS9 inhibition in sepsis patients leads to the activation and differentiation of monocyte and T-cell subtypes. These findings are expected to assist researchers in gaining a more in-depth understanding of the immune dysregulation in sepsis.
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Affiliation(s)
- Yongsan Yang
- Intensive Care Unit and West China Biomedical Big Data CenterWest China Hospital, Sichuan UniversityChengduChina
- Med‐X Center for InformaticsSichuan UniversityChengduChina
| | - Lei Dong
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Yanguo Li
- Institute of Drug Discovery Technology, Ningbo UniversityNingboChina
| | - Ye Huang
- Department of Emergency MedicineXiyuan Hospital of China Academy of Chinese Medical SciencesBeijingChina
| | - Xiaoxi Zeng
- Med‐X Center for InformaticsSichuan UniversityChengduChina
- West China Biomedical Big Data CenterWest China Hospital, Sichuan UniversityChengduChina
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12
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Moeckel C, Mouratidis I, Chantzi N, Uzun Y, Georgakopoulos-Soares I. Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights. Bioessays 2024; 46:e2300210. [PMID: 38715516 DOI: 10.1002/bies.202300210] [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: 10/31/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Understanding the influence of cis-regulatory elements on gene regulation poses numerous challenges given complexities stemming from variations in transcription factor (TF) binding, chromatin accessibility, structural constraints, and cell-type differences. This review discusses the role of gene regulatory networks in enhancing understanding of transcriptional regulation and covers construction methods ranging from expression-based approaches to supervised machine learning. Additionally, key experimental methods, including MPRAs and CRISPR-Cas9-based screening, which have significantly contributed to understanding TF binding preferences and cis-regulatory element functions, are explored. Lastly, the potential of machine learning and artificial intelligence to unravel cis-regulatory logic is analyzed. These computational advances have far-reaching implications for precision medicine, therapeutic target discovery, and the study of genetic variations in health and disease.
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Affiliation(s)
- Camille Moeckel
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ioannis Mouratidis
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Nikol Chantzi
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Yasin Uzun
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ilias Georgakopoulos-Soares
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
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13
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Ni D, Qi Z, Wang Y, Man Y, Pang J, Tang W, Chen J, Li J, Li G. KLF15-activated MARCH2 boosts cell proliferation and epithelial-mesenchymal transition and presents diagnostic significance for hepatocellular carcinoma. Exp Cell Res 2024; 440:114117. [PMID: 38848952 DOI: 10.1016/j.yexcr.2024.114117] [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: 01/22/2024] [Revised: 05/07/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
PURPOSE Membrane associated ubiquitin ligase MARCH2 majorly involves in inflammation response and protein trafficking. However, its comprehensive role in hepatocellular carcinoma (HCC) is largely unknown. METHODS Firstly, multiple bioinformatic analyses were applied to determine MARCH2 mRNA level, its expression comparison in diverse molecular and immune subtypes, and diagnostic value in HCC. Subsequently, RNA-seq, real-time quantitative PCR, immunohistochemistry and cell proliferation assay are used to explore the epithelial-mesenchymal transition (EMT) and proliferation by gene-silencing or overexpressing in cultured HCC cells or in vivo xenograft. Moreover, dual luciferase reporter assay and immunoblotting are delved into verify the transcription factor that activating MARCH2 promoter. RESULTS Multiple bioinformatic analyses demonstrate that MARCH2 is upregulated in multiple cancer types and exhibits startling diagnostic value as well as distinct molecular and immune subtypes in HCC. RNA-seq analysis reveals MARCH2 may promote EMT, cell proliferation and migration in HepG2 cells. Furthermore, overexpression of MARCH2 triggers EMT and significantly enhances HCC cell migration, proliferation and colony formation in a ligase activity-dependent manner. Additionally, above observations are validated in the HepG2 mice xenografts. For up-stream mechanism, transcription factor KLF15 is highly expressed in HCC and activates MARCH2 expression. CONCLUSION KLF15 activated MARCH2 triggers EMT and serves as a fascinating biomarker for precise diagnosis of HCC. Consequently, MARCH2 emerges as a promising candidate for target therapy in cancer management.
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Affiliation(s)
- Dongsheng Ni
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, PR China; Graduate School of Peking Union Medical College, Beijing, 100730, PR China
| | - Zhaolai Qi
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, PR China; Graduate School of Peking Union Medical College, Beijing, 100730, PR China
| | - Yuefeng Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, PR China
| | - Yong Man
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, PR China
| | - Jing Pang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, PR China
| | - Weiqing Tang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, PR China
| | - Jingzhou Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China; National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Fuwai Central-China Hospital, Central-China Branch of National Center for Cardiovascular Diseases, Zhengzhou, PR China
| | - Jian Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, PR China
| | - Guoping Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, PR China; Graduate School of Peking Union Medical College, Beijing, 100730, PR China.
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14
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Fernandes AC, Reverter A, Keogh K, Alexandre PA, Afonso J, Palhares JCP, Cardoso TF, Malheiros JM, Bruscadin JJ, de Oliveira PSN, Mourão GB, de Almeida Regitano LC, Coutinho LL. Transcriptional response to an alternative diet on liver, muscle, and rumen of beef cattle. Sci Rep 2024; 14:13682. [PMID: 38871745 PMCID: PMC11176196 DOI: 10.1038/s41598-024-63619-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
Feed cost represents a major economic determinant within cattle production, amounting to an estimated 75% of the total variable costs. Consequently, comprehensive approaches such as optimizing feed utilization through alternative feed sources, alongside the selection of feed-efficient animals, are of great significance. Here, we investigate the effect of two diets, traditional corn-grain fed and alternative by-product based, on 14 phenotypes related to feed, methane emission and production efficiency and on multi-tissue transcriptomics data from liver, muscle, and rumen wall, derived from 52 Nellore bulls, 26 on each diet. To this end, diets were contrasted at the level of phenotype, gene expression, and gene-phenotype network connectivity. As regards the phenotypic level, at a P value < 0.05, significant differences were found in favour of the alternative diet for average daily weight gain at finishing, dry matter intake at finishing, methane emission, carcass yield and subcutaneous fat thickness at the rib-eye muscle area. In terms of the transcriptional level of the 14,776 genes expressed across the examined tissues, we found 487, 484, and 499 genes differentially expressed due to diet in liver, muscle, and rumen, respectively (P value < 0.01). To explore differentially connected phenotypes across both diet-based networks, we focused on the phenotypes with the largest change in average number of connections within diets and tissues, namely methane emission and carcass yield, highlighting, in particular, gene expression changes involving SREBF2, and revealing the largest differential connectivity in rumen and muscle, respectively. Similarly, from examination of differentially connected genes across diets, the top-ranked most differentially connected regulators within each tissue were MEOX1, PTTG1, and BASP1 in liver, muscle, and rumen, respectively. Changes in gene co-expression patterns suggest activation or suppression of specific biological processes and pathways in response to dietary interventions, consequently impacting the phenotype. The identification of genes that respond differently to diets and their associated phenotypic effects serves as a crucial stepping stone for further investigations, aiming to build upon our discoveries. Ultimately, such advancements hold the promise of improving animal welfare, productivity, and sustainability in livestock farming.
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Affiliation(s)
- Anna Carolina Fernandes
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brazil
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Antonio Reverter
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Kate Keogh
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Pâmela Almeida Alexandre
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Juliana Afonso
- Brazilian Agricultural Research Corporation, Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
| | | | - Tainã Figueiredo Cardoso
- Brazilian Agricultural Research Corporation, Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
| | - Jessica Moraes Malheiros
- Brazilian Agricultural Research Corporation, Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
- Beef Cattle Research Center, Animal Science Institute (IZ), Sertãozinho, São Paulo, Brazil
| | - Jennifer Jessica Bruscadin
- Center of Biological and Health Sciences, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | | | - Gerson Barreto Mourão
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brazil
| | | | - Luiz Lehmann Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brazil.
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15
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Vanamamalai VK, Priyanka E, Kannaki TR, Sharma S. Breed and timepoint-based analysis of chicken harderian gland transcriptome during Newcastle disease virus challenge. Front Mol Biosci 2024; 11:1365888. [PMID: 38915939 PMCID: PMC11194529 DOI: 10.3389/fmolb.2024.1365888] [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: 01/05/2024] [Accepted: 05/07/2024] [Indexed: 06/26/2024] Open
Abstract
Introduction: Newcastle disease is a highly infectious disease caused by the Newcastle Disease Virus (NDV) and has a devastating financial impact on the global chicken industry. It was previously established that Leghorn and Fayoumi breeds of chicken exhibit variable resistance against NDV infection. The harderian gland is the less studied tissue of the chicken, known to play an essential role in the immune response. Methods: Our previous study, we reported differential gene expression and long noncoding RNAs (lncRNAs) between challenged and non-challenged chickens in the Harderian gland transcriptomic data. Now, we report the analysis of the same data studying the differential expression patterns between Leghorn and Fayoumi and between different timepoints during disease. First, the pipeline FHSpipe was used for identification of lncRNAs, followed by differential expression analysis by edgeR (GLM), functional annotation by OmicsBox, co-expression analysis using WGCNA and finally validation of selected lncRNAs and co-expressing genes using qRT-PCR. Results: Here, we observed that Leghorn showed a higher number of upregulated immune-related genes than Fayoumi in timepoint-based analysis, especially during the initial stages. Surprisingly, Fayoumi, being comparatively resistant, showed little difference between challenged and non-challenged conditions and different time points of the challenge. The breed-based analysis, which compared Leghorn with Fayoumi in both challenged and non-challenged conditions separately, identified several immune-related genes and positive co-expressing cis lncRNAs to be upregulated in Fayoumi when compared to Leghorn in both challenged and non-challenged conditions. Discussion: The current study shows that Leghorn, being comparatively more susceptible to NDV than Fayoumi, showed several immune-related genes and positive co-expressing cis lncRNAs upregulated in challenged Leghorn when compared to non-challenged Leghorn and also in different timepoints during challenge. While, breed-based analysis showed that there were more upregulated immune genes and positive cis-lncRNAs in Fayoumi than Leghorn. This result clearly shows that the differences in the expression of genes annotated with immune-related GO terms and pathways, i.e., immune-related genes and the co-expressing cis-lncRNAs between Leghorn and Fayoumi, and their role in the presence of differences in the resistance of Leghorn and Fayoumi chicken against NDV. Conclusion: These immune-genes and cis-lncRNAs could play a role in Fayoumi being comparatively more resistant to NDV than Leghorn. Our study elucidated the importance of lncRNAs during the host defense against NDV infection, paving the way for future research on the mechanisms governing the genetic improvement of chicken breeds.
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Affiliation(s)
- Venkata Krishna Vanamamalai
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - E. Priyanka
- ICAR-Directorate of Poultry Research, Hyderabad, Telangana, India
| | - T. R. Kannaki
- ICAR-Directorate of Poultry Research, Hyderabad, Telangana, India
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
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16
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Tang M, Liu Y, Zhang H, Sun L, Lü P, Chen K. Comprehensive transcriptome sequencing of silkworm Midguts: Uncovering extensive isoform diversity and alternative splicing in BmNPV-Sensitive and BmNPV-resistant strains. J Invertebr Pathol 2024; 204:108104. [PMID: 38608751 DOI: 10.1016/j.jip.2024.108104] [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: 12/05/2023] [Revised: 03/06/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024]
Abstract
The silkworm, Bombyx mori, stands out as one of the few economically valuable insects within the realm of model organisms. However, Bombyx mori nucleopolyhedrovirus (BmNPV) poses a significant threat, decreasing the quality and quantity of silkworm cocoons. Over the past few decades, a multitude of researchers has delved into the mechanisms that underlie silkworm resistance to BmNPV, employing diverse methodologies and approaching the problem from various angles. Despite this extensive research, the role of alternative splicing (AS) in the silkworm's response to BmNPV infection has been largely unexplored. This study leveraged both third-generation (Oxford Nanopore Technologies) and second-generation (Illumina) high-throughput sequencing technologies to meticulously identify and analyze AS patterns in the context of BmNPV response, utilizing two distinct silkworm strains-the susceptible strain 306 and the resistant strain NB. Consequently, we identified five crucial genes (Dsclp, LOC692903, LOC101743583, LOC101742498, LOC101743809) that are linked to the response to BmNPV infection through AS and differential expression. Additionally, a thorough comparative analysis was conducted on their diverse transcriptomic expression profiles, including alternative polyadenylation, simple sequence repeats, and transcription factors.
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Affiliation(s)
- Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Lindan Sun
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Peng Lü
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China.
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17
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Oriol F, Alberto M, Joachim AP, Patrick G, M BP, Ruben MF, Jaume B, Altair CH, Ferran P, Oriol G, Narcis FF, Baldo O. Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity in cis-regulatory elements. NAR Genom Bioinform 2024; 6:lqae068. [PMID: 38867914 PMCID: PMC11167492 DOI: 10.1093/nargab/lqae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/18/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
Transcription factor (TF) binding is a key component of genomic regulation. There are numerous high-throughput experimental methods to characterize TF-DNA binding specificities. Their application, however, is both laborious and expensive, which makes profiling all TFs challenging. For instance, the binding preferences of ∼25% human TFs remain unknown; they neither have been determined experimentally nor inferred computationally. We introduce a structure-based learning approach to predict the binding preferences of TFs and the automated modelling of TF regulatory complexes. We show the advantage of using our approach over the classical nearest-neighbor prediction in the limits of remote homology. Starting from a TF sequence or structure, we predict binding preferences in the form of motifs that are then used to scan a DNA sequence for occurrences. The best matches are either profiled with a binding score or collected for their subsequent modeling into a higher-order regulatory complex with DNA. Co-operativity is modelled by: (i) the co-localization of TFs and (ii) the structural modeling of protein-protein interactions between TFs and with co-factors. We have applied our approach to automatically model the interferon-β enhanceosome and the pioneering complexes of OCT4, SOX2 (or SOX11) and KLF4 with a nucleosome, which are compared with the experimentally known structures.
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Affiliation(s)
- Fornes Oriol
- Centre for Molecular Medicine and Therapeutics. BC Children's Hospital Research Institute. Department of Medical Genetics. University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Meseguer Alberto
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | | | - Gohl Patrick
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Bota Patricia M
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Molina-Fernández Ruben
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Bonet Jaume
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
- Laboratory of Protein Design & Immunoengineering. School of Engineering. Ecole Polytechnique Federale de Lausanne. Lausanne 1015, Vaud, Switzerland
| | - Chinchilla-Hernandez Altair
- Live-Cell Structural Biology. Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Pegenaute Ferran
- Live-Cell Structural Biology. Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Gallego Oriol
- Live-Cell Structural Biology. Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Fernandez-Fuentes Narcis
- Institute of Biological, Environmental and Rural Science. Aberystwyth University, SY23 3DA Aberystwyth, UK
| | - Oliva Baldo
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
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Yang K, Zhu T, Yin J, Zhang Q, Li J, Fan H, Han G, Xu W, Liu N, Lv X. The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis. J Genet Genomics 2024; 51:594-607. [PMID: 38403115 DOI: 10.1016/j.jgg.2024.02.003] [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: 10/23/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The post-transcriptional regulation of mRNA is a crucial component of gene expression. The disruption of this process has detrimental effects on the normal development and gives rise to various diseases. Searching for novel post-transcriptional regulators and exploring their roles are essential for understanding development and disease. Through a multimodal analysis of red blood cell trait genome-wide association studies (GWAS) and transcriptomes of erythropoiesis, we identify FAM46C, a non-canonical RNA poly(A) polymerase, as a necessary factor for proper red blood cell development. FAM46C is highly expressed in the late stages of the erythroid lineage, and its developmental upregulation is controlled by an erythroid-specific enhancer. We demonstrate that FAM46C stabilizes mRNA and regulates erythroid differentiation in a polymerase activity-dependent manner. Furthermore, we identify transcripts of lysosome and mitochondria components as highly confident in vivo targets of FAM46C, which aligns with the need of maturing red blood cells for substantial clearance of organelles and maintenance of cellular redox homeostasis. In conclusion, our study unveils a unique role of FAM46C in positively regulating lysosome and mitochondria components, thereby promoting erythropoiesis.
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Affiliation(s)
- Ke Yang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China; The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
| | - Tianqi Zhu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Jiaying Yin
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Qiaoli Zhang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Jing Li
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Hong Fan
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Gaijing Han
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Weiyin Xu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Nan Liu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China.
| | - Xiang Lv
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Medical Epigenetics Research Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
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19
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Chen C, Lee S, Zyner KG, Fernando M, Nemeruck V, Wong E, Marshall LL, Wark JR, Aryamanesh N, Tam PPL, Graham ME, Gonzalez-Cordero A, Yang P. Trans-omic profiling uncovers molecular controls of early human cerebral organoid formation. Cell Rep 2024; 43:114219. [PMID: 38748874 DOI: 10.1016/j.celrep.2024.114219] [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: 01/03/2024] [Revised: 04/01/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
Defining the molecular networks orchestrating human brain formation is crucial for understanding neurodevelopment and neurological disorders. Challenges in acquiring early brain tissue have incentivized the use of three-dimensional human pluripotent stem cell (hPSC)-derived neural organoids to recapitulate neurodevelopment. To elucidate the molecular programs that drive this highly dynamic process, here, we generate a comprehensive trans-omic map of the phosphoproteome, proteome, and transcriptome of the exit of pluripotency and neural differentiation toward human cerebral organoids (hCOs). These data reveal key phospho-signaling events and their convergence on transcriptional factors to regulate hCO formation. Comparative analysis with developing human and mouse embryos demonstrates the fidelity of our hCOs in modeling embryonic brain development. Finally, we demonstrate that biochemical modulation of AKT signaling can control hCO differentiation. Together, our data provide a comprehensive resource to study molecular controls in human embryonic brain development and provide a guide for the future development of hCO differentiation protocols.
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Affiliation(s)
- Carissa Chen
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Scott Lee
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Katherine G Zyner
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Milan Fernando
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Victoria Nemeruck
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Emilie Wong
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Lee L Marshall
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Jesse R Wark
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Nader Aryamanesh
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Patrick P L Tam
- Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark E Graham
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Anai Gonzalez-Cordero
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Pengyi Yang
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.
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20
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Jiang YZ, Hu LY, Chen MS, Wang XJ, Tan CN, Xue PP, Yu T, He XY, Xiang LX, Xiao YN, Li XL, Ran Q, Li ZJ, Chen L. GATA binding protein 2 mediated ankyrin repeat domain containing 26 high expression in myeloid-derived cell lines. World J Stem Cells 2024; 16:538-550. [PMID: 38817334 PMCID: PMC11135246 DOI: 10.4252/wjsc.v16.i5.538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/12/2024] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Thrombocytopenia 2, an autosomal dominant inherited disease characterized by moderate thrombocytopenia, predisposition to myeloid malignancies and normal platelet size and function, can be caused by 5'-untranslated region (UTR) point mutations in ankyrin repeat domain containing 26 (ANKRD26). Runt related transcription factor 1 (RUNX1) and friend leukemia integration 1 (FLI1) have been identified as negative regulators of ANKRD26. However, the positive regulators of ANKRD26 are still unknown. AIM To prove the positive regulatory effect of GATA binding protein 2 (GATA2) on ANKRD26 transcription. METHODS Human induced pluripotent stem cells derived from bone marrow (hiPSC-BM) and urothelium (hiPSC-U) were used to examine the ANKRD26 expression pattern in the early stage of differentiation. Then, transcriptome sequencing of these iPSCs and three public transcription factor (TF) databases (Cistrome DB, animal TFDB and ENCODE) were used to identify potential TF candidates for ANKRD26. Furthermore, overexpression and dual-luciferase reporter experiments were used to verify the regulatory effect of the candidate TFs on ANKRD26. Moreover, using the GENT2 platform, we analyzed the relationship between ANKRD26 expression and overall survival in cancer patients. RESULTS In hiPSC-BMs and hiPSC-Us, we found that the transcription levels of ANKRD26 varied in the absence of RUNX1 and FLI1. We sequenced hiPSC-BM and hiPSC-U and identified 68 candidate TFs for ANKRD26. Together with three public TF databases, we found that GATA2 was the only candidate gene that could positively regulate ANKRD26. Using dual-luciferase reporter experiments, we showed that GATA2 directly binds to the 5'-UTR of ANKRD26 and promotes its transcription. There are two identified binding sites of GATA2 that are located 2 kb upstream of the TSS of ANKRD26. In addition, we discovered that high ANKRD26 expression is always related to a more favorable prognosis in breast and lung cancer patients. CONCLUSION We first discovered that the transcription factor GATA2 plays a positive role in ANKRD26 transcription and identified its precise binding sites at the promoter region, and we revealed the importance of ANKRD26 in many tissue-derived cancers.
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Affiliation(s)
- Yang-Zhou Jiang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Lan-Yue Hu
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Mao-Shan Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Xiao-Jie Wang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Cheng-Ning Tan
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Pei-Pei Xue
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Teng Yu
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Xiao-Yan He
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Li-Xin Xiang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Yan-Ni Xiao
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Xiao-Liang Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Qian Ran
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Zhong-Jun Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Li Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China.
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21
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Gao L, Lee H, Goodman JH, Ding L. Hematopoietic stem cell niche generation and maintenance are distinguishable by an epitranscriptomic program. Cell 2024; 187:2801-2816.e17. [PMID: 38657601 PMCID: PMC11148849 DOI: 10.1016/j.cell.2024.03.032] [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: 05/10/2023] [Revised: 12/06/2023] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
The niche is typically considered as a pre-established structure sustaining stem cells. Therefore, the regulation of its formation remains largely unexplored. Whether distinct molecular mechanisms control the establishment versus maintenance of a stem cell niche is unknown. To address this, we compared perinatal and adult bone marrow mesenchymal stromal cells (MSCs), a key component of the hematopoietic stem cell (HSC) niche. MSCs exhibited enrichment in genes mediating m6A mRNA methylation at the perinatal stage and downregulated the expression of Mettl3, the m6A methyltransferase, shortly after birth. Deletion of Mettl3 from developing MSCs but not osteoblasts led to excessive osteogenic differentiation and a severe HSC niche formation defect, which was significantly rescued by deletion of Klf2, an m6A target. In contrast, deletion of Mettl3 from MSCs postnatally did not affect HSC niche. Stem cell niche generation and maintenance thus depend on divergent molecular mechanisms, which may be exploited for regenerative medicine.
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Affiliation(s)
- Longfei Gao
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Heather Lee
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Joshua H Goodman
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lei Ding
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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22
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Zhao B, Cai J, Zhang X, Li J, Bao Z, Chen Y, Wu X. Single nucleotide polymorphisms in the KRT82 promoter region modulate irregular thickening and patchiness in the dorsal skin of New Zealand rabbits. BMC Genomics 2024; 25:458. [PMID: 38730432 PMCID: PMC11088042 DOI: 10.1186/s12864-024-10370-7] [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: 09/26/2023] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND While rabbits are used as models in skin irritation tests, the presence of irregular patches and thickening on the dorsal skin can affect precise evaluation. In this study, genes associated with patchiness or non-patchiness on the dorsal skin of New Zealand rabbits were investigated to identify potential regulators of the patchiness phenotype. RESULTS The results showed that parameters associated with hair follicles (HFs), such as HF density, skin thickness, and HF depth, were augmented in rabbits with the patchiness phenotype relative to the non-patchiness phenotype. A total of 592 differentially expressed genes (DEGs) were identified between the two groups using RNA-sequencing. These included KRT72, KRT82, KRT85, FUT8, SOX9, and WNT5B. The functions of the DEGs were investigated by GO and KEGG enrichment analyses. A candidate gene, KRT82, was selected for further molecular function verification. There was a significant positive correlation between KRT82 expression and HF-related parameters, and KRT82 overexpression and knockdown experiments with rabbit dermal papilla cells (DPCs) showed that it regulated genes related to skin and HF growth and development. Investigation of single nucleotide polymorphisms (SNPs) in the exons and promoter region of KRT82 identified four SNPs in the promoter region but none in the exons. The G.-631G > T, T.-696T > C, G.-770G > T and A.-873 A > C alleles conformed to the Hardy - Weinberg equilibrium, and three identified haplotypes showed linkage disequilibrium. Luciferase reporter assays showed that the core promoter region of KRT82 was located in the - 600 to - 1200 segment, in which the four SNPs were located. CONCLUSIONS The morphological characteristics of the patchiness phenotype were analyzed in New Zealand rabbits and DEGs associated with this phenotype were identified by RNA-sequencing. The biological functions of the gene KRT82 associated with this phenotype were analyzed, and four SNPs were identified in the promoter region of the gene. These findings suggest that KRT82 may be a potential biomarker for the breeding of experimental New Zealand rabbits.
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Affiliation(s)
- Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Jiawei Cai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xiyu Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Zhiyuan Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
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23
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Liukang C, Zhao J, Tian J, Huang M, Liang R, Zhao Y, Zhang G. Deciphering infected cell types, hub gene networks and cell-cell communication in infectious bronchitis virus via single-cell RNA sequencing. PLoS Pathog 2024; 20:e1012232. [PMID: 38743760 PMCID: PMC11125504 DOI: 10.1371/journal.ppat.1012232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/24/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Infectious bronchitis virus (IBV) is a coronavirus that infects chickens, which exhibits a broad tropism for epithelial cells, infecting the tracheal mucosal epithelium, intestinal mucosal epithelium, and renal tubular epithelial cells. Utilizing single-cell RNA sequencing (scRNA-seq), we systematically examined cells in renal, bursal, and tracheal tissues following IBV infection and identified tissue-specific molecular markers expressed in distinct cell types. We evaluated the expression of viral RNA in diverse cellular populations and subsequently ascertained that distal tubules and collecting ducts within the kidney, bursal mucosal epithelial cells, and follicle-associated epithelial cells exhibit susceptibility to IBV infection through immunofluorescence. Furthermore, our findings revealed an upregulation in the transcription of proinflammatory cytokines IL18 and IL1B in renal macrophages as well as increased expression of apoptosis-related gene STAT in distal tubules and collecting duct cells upon IBV infection leading to renal damage. Cell-to-cell communication unveiled potential interactions between diverse cell types, as well as upregulated signaling pathways and key sender-receiver cell populations after IBV infection. Integrating single-cell data from all tissues, we applied weighted gene co-expression network analysis (WGCNA) to identify gene modules that are specifically expressed in different cell populations. Based on the WGCNA results, we identified seven immune-related gene modules and determined the differential expression pattern of module genes, as well as the hub genes within these modules. Our comprehensive data provides valuable insights into the pathogenesis of IBV as well as avian antiviral immunology.
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Affiliation(s)
- Chengyin Liukang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jing Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiaxin Tian
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Min Huang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Rong Liang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Ye Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guozhong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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24
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Majeres LE, Dilger AC, Shike DW, McCann JC, Beever JE. Defining a Haplotype Encompassing the LCORL-NCAPG Locus Associated with Increased Lean Growth in Beef Cattle. Genes (Basel) 2024; 15:576. [PMID: 38790206 PMCID: PMC11121065 DOI: 10.3390/genes15050576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Numerous studies have shown genetic variation at the LCORL-NCAPG locus is strongly associated with growth traits in beef cattle. However, a causative molecular variant has yet to be identified. To define all possible candidate variants, 34 Charolais-sired calves were whole-genome sequenced, including 17 homozygous for a long-range haplotype associated with increased growth (QQ) and 17 homozygous for potential ancestral haplotypes for this region (qq). The Q haplotype was refined to an 814 kb region between chr6:37,199,897-38,014,080 and contained 218 variants not found in qq individuals. These variants include an insertion in an intron of NCAPG, a previously documented mutation in NCAPG (rs109570900), two coding sequence mutations in LCORL (rs109696064 and rs384548488), and 15 variants located within ATAC peaks that were predicted to affect transcription factor binding. Notably, rs384548488 is a frameshift variant likely resulting in loss of function for long isoforms of LCORL. To test the association of the coding sequence variants of LCORL with phenotype, 405 cattle from five populations were genotyped. The two variants were in complete linkage disequilibrium. Statistical analysis of the three populations that contained QQ animals revealed significant (p < 0.05) associations with genotype and birth weight, live weight, carcass weight, hip height, and average daily gain. These findings affirm the link between this locus and growth in beef cattle and describe DNA variants that define the haplotype. However, further studies will be required to define the true causative mutation.
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Affiliation(s)
- Leif E. Majeres
- UTIA Genomics Center for the Advancement of Agriculture, Institute of Agriculture, University of Tennessee, Knoxville, TN 37996, USA;
| | - Anna C. Dilger
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (A.C.D.); (D.W.S.); (J.C.M.)
| | - Daniel W. Shike
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (A.C.D.); (D.W.S.); (J.C.M.)
| | - Joshua C. McCann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (A.C.D.); (D.W.S.); (J.C.M.)
| | - Jonathan E. Beever
- UTIA Genomics Center for the Advancement of Agriculture, Institute of Agriculture, University of Tennessee, Knoxville, TN 37996, USA;
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25
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Xu Q, Zhang Y, Xu W, Liu D, Jin W, Chen X, Hong N. The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis. Nucleic Acids Res 2024; 52:3106-3120. [PMID: 38364856 PMCID: PMC11014328 DOI: 10.1093/nar/gkae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Chromatin accessibility plays a critical role in the regulation of cell fate decisions. Although gene expression changes have been extensively profiled at the single-cell level during early embryogenesis, the dynamics of chromatin accessibility at cis-regulatory elements remain poorly studied. Here, we used a plate-based single-cell ATAC-seq method to profile the chromatin accessibility dynamics of over 10 000 nuclei from zebrafish embryos. We investigated several important time points immediately after zygotic genome activation (ZGA), covering key developmental stages up to dome. The results revealed key chromatin signatures in the first cell fate specifications when cells start to differentiate into enveloping layer (EVL) and yolk syncytial layer (YSL) cells. Finally, we uncovered many potential cell-type specific enhancers and transcription factor motifs that are important for the cell fate specifications.
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Affiliation(s)
- Qiushi Xu
- Harbin Institute of Technology, Harbin, China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Yunlong Zhang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Wei Xu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangdong, China
| | - Dong Liu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
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26
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Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Campbell DM, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584681. [PMID: 38617209 PMCID: PMC11014633 DOI: 10.1101/2024.03.12.584681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Most human Transcription factors (TFs) genes encode multiple protein isoforms differing in DNA binding domains, effector domains, or other protein regions. The global extent to which this results in functional differences between isoforms remains unknown. Here, we systematically compared 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Relative to reference isoforms, two-thirds of alternative TF isoforms exhibit differences in one or more molecular activities, which often could not be predicted from sequence. We observed two primary categories of alternative TF isoforms: "rewirers" and "negative regulators", both of which were associated with differentiation and cancer. Our results support a model wherein the relative expression levels of, and interactions involving, TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.
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Affiliation(s)
- Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clarissa Santoso
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Gloria Sheynkman
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Babita Kaundal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Berenson
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
| | - Kerstin Spirohn-Fitzgerald
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anukana Bhattacharjee
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Zhipeng Yang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Deepa Bisht
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared A Sewell
- Department of Biology, Boston University, Boston, MA, USA
| | - Guangyuan Li
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anisa Prasad
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard College, Cambridge MA, USA
| | - Sabrina Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ryan Lane
- Department of Biology, Boston University, Boston, MA, USA
| | | | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marinella Gebbia
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Jean-Claude Twizere
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adam Frankish
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Josh A Riback
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
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Wiese J, Richards E, Kowalko JE, McGaugh SE. Loci associated with cave-derived traits concentrate in specific regions of the Mexican cavefish genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587360. [PMID: 38585759 PMCID: PMC10996652 DOI: 10.1101/2024.03.29.587360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A major goal of modern evolutionary biology is connecting phenotypic evolution with its underlying genetic basis. The Mexican cavefish (Astyanax mexicanus), a characin fish species comprised of a surface ecotype and a cave-derived ecotype, is well suited as a model to study the genetic mechanisms underlying adaptation to extreme environments. Here we map 206 previously published quantitative trait loci (QTL) for cave-derived traits in A. mexicanus to the newest version of the surface fish genome assembly, AstMex3. This analysis revealed that QTL cluster in the genome more than expected by chance, and this clustering is not explained by the distribution of genes in the genome. To investigate whether certain characteristics of the genome facilitate phenotypic evolution, we tested whether genomic characteristics, such as highly mutagenic CpG sites, are reliable predictors of the sites of trait evolution but did not find any significant trends. Finally, we combined the QTL map with previously collected expression and selection data to identify a list of 36 candidate genes that may underlie the repeated evolution of cave phenotypes, including rgrb which is predicted to be involved in phototransduction. We found this gene has disrupted exons in all non-hybrid cave populations but intact reading frames in surface fish. Overall, our results suggest specific "evolutionary hotspots" in the genome may play significant roles in driving adaptation to the cave environment in Astyanax mexicanus and demonstrate how this compiled dataset can facilitate our understanding of the genetic basis of repeated evolution in the Mexican cavefish.
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Affiliation(s)
- Jonathan Wiese
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | - Emilie Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | | | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
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28
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Xu J, Hörner M, Nagel M, Korneck M, Noß M, Hauser S, Schöls L, Admard J, Casadei N, Schüle R. Unraveling Axonal Transcriptional Landscapes: Insights from iPSC-Derived Cortical Neurons and Implications for Motor Neuron Degeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586780. [PMID: 38585749 PMCID: PMC10996649 DOI: 10.1101/2024.03.26.586780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Neuronal function and pathology are deeply influenced by the distinct molecular profiles of the axon and soma. Traditional studies have often overlooked these differences due to the technical challenges of compartment specific analysis. In this study, we employ a robust RNA-sequencing (RNA-seq) approach, using microfluidic devices, to generate high-quality axonal transcriptomes from iPSC-derived cortical neurons (CNs). We achieve high specificity of axonal fractions, ensuring sample purity without contamination. Comparative analysis revealed a unique and specific transcriptional landscape in axonal compartments, characterized by diverse transcript types, including protein-coding mRNAs, ribosomal proteins (RPs), mitochondrial-encoded RNAs, and long non-coding RNAs (lncRNAs). Previous works have reported the existence of transcription factors (TFs) in the axon. Here, we detect a subset of previously unreported TFs specific to the axon and indicative of their active participation in transcriptional regulation. To investigate transcripts and pathways essential for central motor neuron (MN) degeneration and maintenance we analyzed KIF1C-knockout (KO) CNs, modeling hereditary spastic paraplegia (HSP), a disorder associated with prominent length-dependent degeneration of central MN axons. We found that several key factors crucial for survival and health were absent in KIF1C-KO axons, highlighting a possible role of these also in other neurodegenerative diseases. Taken together, this study underscores the utility of microfluidic devices in studying compartment-specific transcriptomics in human neuronal models and reveals complex molecular dynamics of axonal biology. The impact of KIF1C on the axonal transcriptome not only deepens our understanding of MN diseases but also presents a promising avenue for exploration of compartment specific disease mechanisms.
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29
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Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD, Calof AL. Gastrulation-stage gene expression in Nipbl+/- mouse embryos foreshadows the development of syndromic birth defects. SCIENCE ADVANCES 2024; 10:eadl4239. [PMID: 38507484 PMCID: PMC10954218 DOI: 10.1126/sciadv.adl4239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
In animal models, Nipbl deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange syndrome, the most common cause of which is Nipbl haploinsufficiency. Previous studies in Nipbl+/- mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA sequencing on wild-type and Nipbl+/- mouse embryos at gastrulation and early cardiac crescent stages. Nipbl+/- embryos had fewer mesoderm cells than wild-type and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition, Nanog was found to be overexpressed in all germ layers, and many gene expression changes observed in Nipbl+/- embryos could be attributed to Nanog overexpression. These findings establish a link between Nipbl deficiency, Nanog overexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects in Nipbl+/- animals and Cornelia de Lange syndrome.
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Affiliation(s)
- Stephenson Chea
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Jesse Kreger
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Martha E. Lopez-Burks
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Anne L. Calof
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
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30
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Wang X, Tang X, Zhu P, Hua D, Xie Z, Guo M, Que M, Yan J, Li X, Xia Q, Luo X, Bi J, Zhao Y, Zhou Z, Li S, Luo A. CircAKT3 alleviates postoperative cognitive dysfunction by stabilizing the feedback cycle of miR-106a-5p/HDAC4/MEF2C axis in hippocampi of aged mice. Cell Mol Life Sci 2024; 81:138. [PMID: 38478029 PMCID: PMC10937803 DOI: 10.1007/s00018-024-05156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/10/2024] [Accepted: 02/05/2024] [Indexed: 03/17/2024]
Abstract
Circular RNAs (circRNAs) have garnered significant attention in the field of neurodegenerative diseases including Alzheimer's diseases due to their covalently closed loop structure. However, the involvement of circRNAs in postoperative cognitive dysfunction (POCD) is still largely unexplored. To identify the genes differentially expressed between non-POCD (NPOCD) and POCD mice, we conducted the whole transcriptome sequencing initially in this study. According to the expression profiles, we observed that circAKT3 was associated with hippocampal neuronal apoptosis in POCD mice. Moreover, we found that circAKT3 overexpression reduced apoptosis of hippocampal neurons and alleviated POCD. Subsequently, through bioinformatics analysis, our data showed that circAKT3 overexpression in vitro and in vivo elevated the abundance of miR-106a-5p significantly, resulting in a decrease of HDAC4 protein and an increase of MEF2C protein. Additionally, this effect of circAKT3 was blocked by miR-106a-5p inhibitor. Interestingly, MEF2C could activate the transcription of miR-106a-5p promoter and form a positive feedback loop. Therefore, our findings revealed more potential modulation ways between circRNA-miRNA and miRNA-mRNA, providing different directions and targets for preclinical studies of POCD.
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Affiliation(s)
- Xuan Wang
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Xiaole Tang
- State Key Laboratory of Oncology in Southern China, Department of Anesthesiology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, China
| | - Pengfei Zhu
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Dongyu Hua
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Zheng Xie
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Mingke Guo
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Mengxin Que
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Jing Yan
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Xing Li
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Qian Xia
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Xiaoxiao Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jiangjiang Bi
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Yilin Zhao
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Zhiqiang Zhou
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Shiyong Li
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China.
| | - Ailin Luo
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China.
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31
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Dong X, Zhan Y, Li S, Yang M, Gao Y. MKRN1 regulates the expression profiles and transcription factor activity in HeLa cells inhibition suppresses cervical cancer cell progression. Sci Rep 2024; 14:6129. [PMID: 38480859 PMCID: PMC10937657 DOI: 10.1038/s41598-024-56830-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/12/2024] [Indexed: 03/17/2024] Open
Abstract
Cervical cancer is one of the most common gynecologic malignancies worldwide, necessitating the identification of novel biomarkers and therapeutic targets. This study aimed to investigate the significance of MKRN1 in cervical cancer and explore its potential as a diagnostic marker and therapeutic target. The results indicated that MKRN1 expression was up-regulated in cervical cancer tissues and correlated with advanced tumor stage, higher grade, and poor patient survival. Functional studies demonstrated that targeting MKRN1 effectively inhibited cell proliferation, migration, and invasion, highlighting its critical role in tumor progression and metastasis. Moreover, the knockdown of MKRN1 resulted in altered expression patterns of six transcription factor-encoding genes, revealing its involvement in gene regulation. Co-expression network analysis unveiled complex regulatory mechanisms underlying the effects of MKRN1 knockdown on gene expression. Furthermore, the results suggested that MKRN1 might serve as a diagnostic marker for personalized treatment strategies and a therapeutic target to inhibit tumor growth, metastasis, and overcome drug resistance. The development of MKRN1-targeted interventions might hold promise for advancing personalized medicine approaches in cervical cancer treatment. Further research is warranted to validate these findings, elucidate underlying mechanisms, and translate these insights into improved management and outcomes for cervical cancer patients.
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Affiliation(s)
- Xiang Dong
- School of Life Science, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, Anhui, China
- Research Center of Clinical Laboratory Science, School of Laboratory Medicine, Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Yuling Zhan
- School of Life Science, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, Anhui, China
- Research Center of Clinical Laboratory Science, School of Laboratory Medicine, Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Suwan Li
- School of Life Science, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, Anhui, China
- Research Center of Clinical Laboratory Science, School of Laboratory Medicine, Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Minghui Yang
- Research Center of Clinical Laboratory Science, School of Laboratory Medicine, Bengbu Medical College, Bengbu, 233030, Anhui, China
- School of Basic Courses, Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Yu Gao
- School of Life Science, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, Anhui, China.
- Laboratory Animal Center, Bengbu Medical College, Bengbu, 233030, Anhui, China.
- Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, Bengbu, 233030, Anhui, China.
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32
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Liu H, Xing H, Xia Z, Wu T, Liu J, Li A, Bi F, Sun Y, Zhang J, He P. Mechanisms of harmful effects of Microcystis aeruginosa on a brackish water organism Moina mongolica based on physiological and transcriptomic responses. HARMFUL ALGAE 2024; 133:102588. [PMID: 38485443 DOI: 10.1016/j.hal.2024.102588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/09/2024] [Accepted: 01/31/2024] [Indexed: 03/19/2024]
Abstract
To investigate the detrimental impacts of cyanobacterial bloom, specifically Microcystis aeruginosa, on brackish water ecosystems, the study used Moina mongolica, a cladoceran species, as the test organism. In a chronic toxicology experiment, the survival and reproductive rates of M. mongolica were assessed under M. aeruginosa stress. It was observed that the survival rate of M. mongolica fed with M. aeruginosa significantly decreased with time and their reproduction rate dropped to zero, while the control group remained maintained stable and normal reproduction. To further explore the underlying molecular mechanisms of the effects of M. aeruginosa on M. mongolica, we conducted a transcriptomic analysis on newly hatched M. mongolica cultured under different food conditions for 24 h. The results revealed significant expression differences in 572 genes, with 233 genes significantly up-regulated and 339 genes significantly down-regulated. Functional analysis of these differentially expressed genes identified six categories of physiological functional changes, including nutrition and metabolism, oxidative phosphorylation, neuroimmunology, cuticle and molting, reproduction, and programmed cell death. Based on these findings, we outlined the basic mechanisms of microcystin toxicity. The discovery provides critical insights into the mechanisms of Microcystis toxicity on organisms and explores the response mechanisms of cladocerans under the stress of Microcystis.
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Affiliation(s)
- Hongtao Liu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, China; Water Environment and Ecology Engineering Research Center of the Shanghai Institution of Higher Education, Shanghai Ocean University, Shanghai, 201306, China.
| | - Hao Xing
- Water Environment and Ecology Engineering Research Center of the Shanghai Institution of Higher Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhangyi Xia
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, China; Water Environment and Ecology Engineering Research Center of the Shanghai Institution of Higher Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Tingting Wu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, China; Water Environment and Ecology Engineering Research Center of the Shanghai Institution of Higher Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jinlin Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Aiqin Li
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, China; Water Environment and Ecology Engineering Research Center of the Shanghai Institution of Higher Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Fangling Bi
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, China; Water Environment and Ecology Engineering Research Center of the Shanghai Institution of Higher Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yuqing Sun
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, China; Water Environment and Ecology Engineering Research Center of the Shanghai Institution of Higher Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jianheng Zhang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, China; Water Environment and Ecology Engineering Research Center of the Shanghai Institution of Higher Education, Shanghai Ocean University, Shanghai, 201306, China.
| | - Peimin He
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, China; Water Environment and Ecology Engineering Research Center of the Shanghai Institution of Higher Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of River and Lake Biochain Construction and Resource Utilization, Shanghai, 201702, China.
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Miglioli A, Tredez M, Boosten M, Sant C, Carvalho JE, Dru P, Canesi L, Schubert M, Dumollard R. The Mediterranean mussel Mytilus galloprovincialis: a novel model for developmental studies in mollusks. Development 2024; 151:dev202256. [PMID: 38270401 DOI: 10.1242/dev.202256] [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: 08/10/2023] [Accepted: 01/18/2024] [Indexed: 01/26/2024]
Abstract
A model organism in developmental biology is defined by its experimental amenability and by resources created for the model system by the scientific community. For the most powerful invertebrate models, the combination of both has already yielded a thorough understanding of developmental processes. However, the number of developmental model systems is still limited, and their phylogenetic distribution heavily biased. Members of one of the largest animal lineages, the Spiralia, for example, have long been neglected. In order to remedy this shortcoming, we have produced a detailed developmental transcriptome for the bivalve mollusk Mytilus galloprovincialis, and have expanded the list of experimental protocols available for this species. Our high-quality transcriptome allowed us to identify transcriptomic signatures of developmental progression and to perform a first comparison with another bivalve mollusk: the Pacific oyster Crassostrea gigas. To allow co-labelling studies, we optimized and combined protocols for immunohistochemistry and hybridization chain reaction to create high-resolution co-expression maps of developmental genes. The resources and protocols described here represent an enormous boost for the establishment of Mytilus galloprovincialis as an alternative model system in developmental biology.
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Affiliation(s)
- Angelica Miglioli
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer 06230, France
| | - Marion Tredez
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer 06230, France
| | - Manon Boosten
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer 06230, France
- Laboratoire d'Océanologie de Villefranche (LOV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer 06230, France
| | - Camille Sant
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer 06230, France
- Laboratoire d'Océanologie de Villefranche (LOV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer 06230, France
| | - João E Carvalho
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer 06230, France
| | - Philippe Dru
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer 06230, France
| | - Laura Canesi
- Università degli Studi di Genova, Dipartimento di Scienze della Terra dell Ambiente e della Vita (DISTAV), Genova 16132, Italy
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer 06230, France
| | - Rémi Dumollard
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer 06230, France
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Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD, Calof AL. Gastrulation-stage gene expression in Nipbl +/- mouse embryos foreshadows the development of syndromic birth defects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.558465. [PMID: 37905011 PMCID: PMC10614802 DOI: 10.1101/2023.10.16.558465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In animal models, Nipbl-deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange Syndrome (CdLS), the most common cause of which is Nipbl-haploinsufficiency. Previous studies in Nipbl+/- mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA-sequencing on wildtype (WT) and Nipbl+/- mouse embryos at gastrulation and early cardiac crescent stages. Nipbl+/- embryos had fewer mesoderm cells than WT and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition, Nanog was found to be overexpressed in all germ layers, and many gene expression changes observed in Nipbl+/- embryos could be attributed to Nanog overexpression. These findings establish a link between Nipbl-deficiency, Nanog overexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects in Nipbl+/- animals and CdLS. Teaser Gene expression changes during gastrulation of Nipbl-deficient mice shed light on early origins of structural birth defects.
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Xue M, Huang N, Luo Y, Yang X, Wang Y, Fang M. Combined Transcriptomics and Metabolomics Identify Regulatory Mechanisms of Porcine Vertebral Chondrocyte Development In Vitro. Int J Mol Sci 2024; 25:1189. [PMID: 38256262 PMCID: PMC10816887 DOI: 10.3390/ijms25021189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Porcine body length is closely related to meat production, growth, and reproductive performance, thus playing a key role in the profitability of the pork industry. Cartilage development is critical to longitudinal elongation of individual vertebrae. This study isolated primary porcine vertebral chondrocytes (PVCs) to clarify the complex mechanisms of elongation. We used transcriptome and target energy metabolome technologies to confirm crucial genes and metabolites in primary PVCs at different differentiation stages (0, 4, 8, and 12 days). Pairwise comparisons of the four stages identified 4566 differentially expressed genes (DEGs). Time-series gene cluster and functional analyses of these DEGs revealed four clusters related to metabolic processes, cartilage development, vascular development, and cell cycle regulation. We constructed a transcriptional regulatory network determining chondrocyte maturation. The network indicated that significantly enriched transcription factor (TF) families, including zf-C2H2, homeobox, TF_bZIP, and RHD, are important in cell cycle and differentiation processes. Further, dynamic network biomarker (DNB) analysis revealed that day 4 was the tipping point for chondrocyte development, consistent with morphological and metabolic changes. We found 24 DNB DEGs, including the TFs NFATC2 and SP7. Targeted energy metabolome analysis showed that most metabolites were elevated throughout chondrocyte development; notably, 16 differentially regulated metabolites (DRMs) were increased at three time points after cell differentiation. In conclusion, integrated metabolome and transcriptome analyses highlighted the importance of amino acid biosynthesis in chondrocyte development, with coordinated regulation of DEGs and DRMs promoting PVC differentiation via glucose oxidation. These findings reveal the regulatory mechanisms underlying PVC development and provide an important theoretical reference for improving pork production.
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Affiliation(s)
- Mingming Xue
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Y.L.); (X.Y.)
| | - Ning Huang
- Sanya Research Institute, China Agricultural University, Sanya 572025, China; (N.H.); (Y.W.)
| | - Yabiao Luo
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Y.L.); (X.Y.)
| | - Xiaoyang Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Y.L.); (X.Y.)
| | - Yubei Wang
- Sanya Research Institute, China Agricultural University, Sanya 572025, China; (N.H.); (Y.W.)
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Y.L.); (X.Y.)
- Sanya Research Institute, China Agricultural University, Sanya 572025, China; (N.H.); (Y.W.)
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Vishnevsky OV, Bocharnikov AV, Ignatieva EV. Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks. Int J Mol Sci 2024; 25:1011. [PMID: 38256085 PMCID: PMC10816497 DOI: 10.3390/ijms25021011] [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: 10/31/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) is a central genome-wide method for in vivo analyses of DNA-protein interactions in various cellular conditions. Numerous studies have demonstrated the complex contextual organization of ChIP-seq peak sequences and the presence of binding sites for transcription factors in them. We assessed the dependence of the ChIP-seq peak score on the presence of different contextual signals in the peak sequences by analyzing these sequences from several ChIP-seq experiments using our fully enumerative GPU-based de novo motif discovery method, Argo_CUDA. Analysis revealed sets of significant IUPAC motifs corresponding to the binding sites of the target and partner transcription factors. For these ChIP-seq experiments, multiple regression models were constructed, demonstrating a significant dependence of the peak scores on the presence in the peak sequences of not only highly significant target motifs but also less significant motifs corresponding to the binding sites of the partner transcription factors. A significant correlation was shown between the presence of the target motifs FOXA2 and the partner motifs HNF4G, which found experimental confirmation in the scientific literature, demonstrating the important contribution of the partner transcription factors to the binding of the target transcription factor to DNA and, consequently, their important contribution to the peak score.
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Affiliation(s)
- Oleg V. Vishnevsky
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Andrey V. Bocharnikov
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Elena V. Ignatieva
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
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37
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Feng C, Song C, Song S, Zhang G, Yin M, Zhang Y, Qian F, Wang Q, Guo M, Li C. KnockTF 2.0: a comprehensive gene expression profile database with knockdown/knockout of transcription (co-)factors in multiple species. Nucleic Acids Res 2024; 52:D183-D193. [PMID: 37956336 PMCID: PMC10767813 DOI: 10.1093/nar/gkad1016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/17/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
Transcription factors (TFs), transcription co-factors (TcoFs) and their target genes perform essential functions in diseases and biological processes. KnockTF 2.0 (http://www.licpathway.net/KnockTF/index.html) aims to provide comprehensive gene expression profile datasets before/after T(co)F knockdown/knockout across multiple tissue/cell types of different species. Compared with KnockTF 1.0, KnockTF 2.0 has the following improvements: (i) Newly added T(co)F knockdown/knockout datasets in mice, Arabidopsis thaliana and Zea mays and also an expanded scale of datasets in humans. Currently, KnockTF 2.0 stores 1468 manually curated RNA-seq and microarray datasets associated with 612 TFs and 172 TcoFs disrupted by different knockdown/knockout techniques, which are 2.5 times larger than those of KnockTF 1.0. (ii) Newly added (epi)genetic annotations for T(co)F target genes in humans and mice, such as super-enhancers, common SNPs, methylation sites and chromatin interactions. (iii) Newly embedded and updated search and analysis tools, including T(co)F Enrichment (GSEA), Pathway Downstream Analysis and Search by Target Gene (BLAST). KnockTF 2.0 is a comprehensive update of KnockTF 1.0, which provides more T(co)F knockdown/knockout datasets and (epi)genetic annotations across multiple species than KnockTF 1.0. KnockTF 2.0 facilitates not only the identification of functional T(co)Fs and target genes but also the investigation of their roles in the physiological and pathological processes.
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Affiliation(s)
- Chenchen Feng
- National Health Commission Key Laboratory of Birth Defect Research and Prevention & School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Chao Song
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Shuang Song
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Guorui Zhang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Mingxue Yin
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yuexin Zhang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Fengcui Qian
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Qiuyu Wang
- National Health Commission Key Laboratory of Birth Defect Research and Prevention & School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Maozu Guo
- School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
| | - Chunquan Li
- National Health Commission Key Laboratory of Birth Defect Research and Prevention & School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- MOE Key Lab of Rare Pediatric Diseases, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
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Huang X, Song C, Zhang G, Li Y, Zhao Y, Zhang Q, Zhang Y, Fan S, Zhao J, Xie L, Li C. scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse. Nucleic Acids Res 2024; 52:D293-D303. [PMID: 37889053 PMCID: PMC10767939 DOI: 10.1093/nar/gkad885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/19/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Gene regulatory networks (GRNs) are interpretable graph models encompassing the regulatory interactions between transcription factors (TFs) and their downstream target genes. Making sense of the topology and dynamics of GRNs is fundamental to interpreting the mechanisms of disease etiology and translating corresponding findings into novel therapies. Recent advances in single-cell multi-omics techniques have prompted the computational inference of GRNs from single-cell transcriptomic and epigenomic data at an unprecedented resolution. Here, we present scGRN (https://bio.liclab.net/scGRN/), a comprehensive single-cell multi-omics gene regulatory network platform of human and mouse. The current version of scGRN catalogs 237 051 cell type-specific GRNs (62 999 692 TF-target gene pairs), covering 160 tissues/cell lines and 1324 single-cell samples. scGRN is the first resource documenting large-scale cell type-specific GRN information of diverse human and mouse conditions inferred from single-cell multi-omics data. We have implemented multiple online tools for effective GRN analysis, including differential TF-target network analysis, TF enrichment analysis, and pathway downstream analysis. We also provided details about TF binding to promoters, super-enhancers and typical enhancers of target genes in GRNs. Taken together, scGRN is an integrative and useful platform for searching, browsing, analyzing, visualizing and downloading GRNs of interest, enabling insight into the differences in regulatory mechanisms across diverse conditions.
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Affiliation(s)
- Xuemei Huang
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Chao Song
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Guorui Zhang
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Ye Li
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yu Zhao
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Qinyi Zhang
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yuexin Zhang
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Shifan Fan
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Jun Zhao
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Liyuan Xie
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Chunquan Li
- The First Affiliated Hospital & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases & College of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Maternal and Child Health Care Hospital, National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
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Acencio ML, Vazquez M, Chawla K, Lægreid A, Kuiper M. TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat. Nucleic Acids Res 2024; 52:D334-D344. [PMID: 37992291 PMCID: PMC10767992 DOI: 10.1093/nar/gkad1030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/24/2023] Open
Abstract
Prior knowledge about DNA-binding transcription factors (dbTFs), transcription co-regulators (coTFs) and general transcriptional factors (GTFs) is crucial for the study and understanding of the regulation of transcription. This is reflected by the many publications and database resources describing knowledge about TFs. We previously launched the TFCheckpoint database, an integrated resource focused on human, mouse and rat dbTFs, providing users access to a comprehensive overview of these proteins. Here, we describe TFCheckpoint 2.0 (https://www.tfcheckpoint.org/index.php), comprising 13 collections of dbTFs, coTFs and GTFs. TFCheckpoint 2.0 provides an easy and versatile cross-referencing system for users to view and download collections that may otherwise be cumbersome to find, compare and retrieve.
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Affiliation(s)
- Marcio L Acencio
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Miguel Vazquez
- Barcelona Supercomputing Center, Barcelona, 08034, Spain
| | - Konika Chawla
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
- Bioinformatics Core Facility, St. Olavs hospital HF, Trondheim, NO-7491, Norway
| | - Astrid Lægreid
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Martin Kuiper
- Department of Biology, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
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Shao F, Van Otterloo E, Cao H. Computational identification of key transcription factors for embryonic and postnatal Sox2+ dental epithelial stem cell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573158. [PMID: 38187542 PMCID: PMC10769342 DOI: 10.1101/2023.12.22.573158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
While many reptiles can replace their tooth throughout life, human loss the tooth replacement capability after formation of the permanent teeth. It was thought that the difference in tooth regeneration capability depends on the persistence of a specialized dental epithelial structure, the dental lamina that contains dental epithelial stem cells (DESC). Currently, we know very little about DESC such as what genes are expressed or its chromatin accessibility profile. Multiple markers of DESC have been proposed such as Sox2 and Lgr5 . Few single cell RNA-seq experiments have been performed previously, but no obvious DESC cluster was identified in these scRNA-seq datasets, possible due to that the expression level of DESC markers such as Sox2 and Lgr5 is too low or the percentage of DESC is too low in whole tooth. We utilize a mouse line Sox2-GFP to enrich Sox2+ DESC and use Smart-Seq2 protocol and ATAC-seq protocol to generate transcriptome profile and chromatin accessibility profile of P2 Sox2+ DESC. Additionally, we generate transcriptome profile and chromatin accessibility profile of E11.5 Sox2+ dental lamina cells. With transcriptome profile and chromatin accessibility profile, we systematically identify potential key transcription factors for E11.5 Sox2+ cells and P2 Sox2+ cells. We identified transcription factors including Pitx2, Id3, Pitx1, Tbx1, Trp63, Nkx2-3, Grhl3, Dlx2, Runx1, Nfix, Zfp536 , etc potentially formed the core transcriptional regulatory networks of Sox2+ DESC in both embryonic and postnatal stages.
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Al-Obaide MA, Islam S, Al-Obaidi I, Vasylyeva TL. Novel enhancer mediates the RPL36A-HNRNPH2 readthrough loci and GLA gene expressions associated with fabry disease. Front Genet 2023; 14:1229088. [PMID: 38155709 PMCID: PMC10753776 DOI: 10.3389/fgene.2023.1229088] [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: 05/25/2023] [Accepted: 11/10/2023] [Indexed: 12/30/2023] Open
Abstract
Fabry disease (FD) is a rare genetic condition caused by mutations in the GLA gene, located on the X chromosome in the RPL36-HNRNPH2 readthrough genomic region. This gene produces an enzyme called alpha-galactosidase A (α-Gal A). When the enzyme does not function properly due to the mutations, it causes harmful substances called globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3) to build up in the body's lysosomes. This accumulation can damage the kidneys, heart, eyes, and nervous system. Recent studies have shown that the RPL36A-HNRNPH2 readthrough loci, which include RPL36A and HNRNPH2 genes, as well as the regulatory sequence known as the GLA-HNRNPH2 bidirectional promoter, may also play a role in FD. However, the involvement of enhancer RNAs (eRNAs) in FD is still poorly understood despite their known role in various diseases. To investigate this further, we studied an RPL36A enhancer called GH0XJ101390 and showed its genomic setting in the RPL36-HNRNPH2 readthrough region; the eRNA is rich in Homotypic Clusters of TFBSs (HCTs) type and hosts a CpG Island (CGI). To test the functional correlation further with GLA, RPL36A, and HNRNPH2, we used siRNAs to knock down GH0XJ101390 in human kidney embryonic cells 293T. The results showed a significant decrease in RPL36A and GLA expression and a non-significant decrease in HNRNPH2 expression. These findings could have important implications for understanding the regulatory mechanisms of GH0XJ101390 and its potential role in FD. A better understanding of these mechanisms may improve diagnostic and therapeutic methods for FD, which could ultimately benefit patients with this rare condition.
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Affiliation(s)
| | | | | | - Tetyana L. Vasylyeva
- Department of Pediatrics, Texas Tech University Health Sciences Center, Amarillo, TX, United States
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Fu C, Yang Y. iCAZyGFADB: an insect CAZyme and gene function annotation database. Database (Oxford) 2023; 2023:baad086. [PMID: 38015957 PMCID: PMC10684042 DOI: 10.1093/database/baad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023]
Abstract
With the continuous upgrading of high-throughput sequencing technology, a large amount of biological genome data has been deciphered and published. The research on functional genes of biological genomes urgently needs a collection of service websites with user-friendly and full annotation functions for a variety of gene function annotation tools. In this study, iCAZyGFADB, which is a database website integrating nine gene function annotation tools, was perfectly developed to meet the needs of biological genome functional annotation. Its nine gene function annotation tools were Carbohydrate-Active Enzymes (CAZyme) annotation, Gene Ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation, Cluster of Orthologous Gene (COG) annotation, Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (eggNOG) annotation, SwissProt annotation, Pfam annotation, KOG annotation and Animal Transcription Factor DataBase (AnimalTFDB) annotation. It has three advantages. First, it is superior to gene function annotation of other biological cloud analysis platforms and runs very fast. Second, all gene annotation functions of the website are free and open to users. Third, it can annotate eight gene functions (GO, KEGG, COG, eggNOG, SwissProt, Pfam, KOG and AnimalTFDB annotation) of a single species at the same time, while other cloud platforms do not have the ability or need to charge to open for users to complete the annotation of eight gene functions at the same time. Moreover, the development and operation of our database will provide great help for gene function annotation research and significantly improve the efficiency of genome function research and reduce the cost of bioinformatics analysis. Genomic functional annotation researchers can access this database through the following website: http://www.icazygfadb.org.cn/. Database URL: http://www.icazygfadb.org.cn/.
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Affiliation(s)
- Chun Fu
- Key Laboratory of Sichuan Province for Bamboo Pests Control and Resource Development, Leshan Normal University, No. 778 Binhe Road, Shizhong District, Leshan, Sichuan 614000, China
| | - YaoJun Yang
- Key Laboratory of Sichuan Province for Bamboo Pests Control and Resource Development, Leshan Normal University, No. 778 Binhe Road, Shizhong District, Leshan, Sichuan 614000, China
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Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ. Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. eLife 2023; 12:RP89993. [PMID: 37938195 PMCID: PMC10631760 DOI: 10.7554/elife.89993] [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] [Indexed: 11/09/2023] Open
Abstract
Neuronal and behavioral adaptations to novel stimuli are regulated by temporally dynamic waves of transcriptional activity, which shape neuronal function and guide enduring plasticity. Neuronal activation promotes expression of an immediate early gene (IEG) program comprised primarily of activity-dependent transcription factors, which are thought to regulate a second set of late response genes (LRGs). However, while the mechanisms governing IEG activation have been well studied, the molecular interplay between IEGs and LRGs remain poorly characterized. Here, we used transcriptomic and chromatin accessibility profiling to define activity-driven responses in rat striatal neurons. As expected, neuronal depolarization generated robust changes in gene expression, with early changes (1 hr) enriched for inducible transcription factors and later changes (4 hr) enriched for neuropeptides, synaptic proteins, and ion channels. Remarkably, while depolarization did not induce chromatin remodeling after 1 hr, we found broad increases in chromatin accessibility at thousands of sites in the genome at 4 hr after neuronal stimulation. These putative regulatory elements were found almost exclusively at non-coding regions of the genome, and harbored consensus motifs for numerous activity-dependent transcription factors such as AP-1. Furthermore, blocking protein synthesis prevented activity-dependent chromatin remodeling, suggesting that IEG proteins are required for this process. Targeted analysis of LRG loci identified a putative enhancer upstream of Pdyn (prodynorphin), a gene encoding an opioid neuropeptide implicated in motivated behavior and neuropsychiatric disease states. CRISPR-based functional assays demonstrated that this enhancer is both necessary and sufficient for Pdyn transcription. This regulatory element is also conserved at the human PDYN locus, where its activation is sufficient to drive PDYN transcription in human cells. These results suggest that IEGs participate in chromatin remodeling at enhancers and identify a conserved enhancer that may act as a therapeutic target for brain disorders involving dysregulation of Pdyn.
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Affiliation(s)
- Robert A Phillips
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Ethan Wan
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Jennifer J Tuscher
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - David Reid
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Olivia R Drake
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
| | - Lara Ianov
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
- Civitan International Research Center, University of Alabama at BirminghamBirminghamUnited States
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at BirminghamBirminghamUnited States
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Wang M, Liang AM, Zhou ZZ, Pang TL, Fan YJ, Xu YZ. Deletions of singular U1 snRNA gene significantly interfere with transcription and 3'-end mRNA formation. PLoS Genet 2023; 19:e1011021. [PMID: 37917726 PMCID: PMC10645366 DOI: 10.1371/journal.pgen.1011021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 11/14/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Small nuclear RNAs (snRNAs) are structural and functional cores of the spliceosome. In metazoan genomes, each snRNA has multiple copies/variants, up to hundreds in mammals. However, the expressions and functions of each copy/variant in one organism have not been systematically studied. Focus on U1 snRNA genes, we investigated all five copies in Drosophila melanogaster using two series of constructed strains. Analyses of transgenic flies that each have a U1 promoter-driven gfp revealed that U1:21D is the major and ubiquitously expressed copy, and the other four copies have specificities in developmental stages and tissues. Mutant strains that each have a precisely deleted copy of U1-gene exhibited various extents of defects in fly morphology or mobility, especially deletion of U1:82Eb. Interestingly, splicing was changed at limited levels in the deletion strains, while large amounts of differentially-expressed genes and alternative polyadenylation events were identified, showing preferences in the down-regulation of genes with 1-2 introns and selection of proximal sites for 3'-end polyadenylation. In vitro assays suggested that Drosophila U1 variants pulled down fewer SmD2 proteins compared to the canonical U1. This study demonstrates that all five U1-genes in Drosophila have physiological functions in development and play regulatory roles in transcription and 3'-end formation.
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Affiliation(s)
- Mei Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China, University of Chinese Academy of Sciences, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
- Shanghai Institute of Biological Products, Shanghai, China
| | - An-Min Liang
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
| | - Zhen-Zhen Zhou
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
| | - Ting-Lin Pang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China, University of Chinese Academy of Sciences, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
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Paré L, Bideau L, Baduel L, Dalle C, Benchouaia M, Schneider SQ, Laplane L, Clément Y, Vervoort M, Gazave E. Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii. BMC Genomics 2023; 24:583. [PMID: 37784028 PMCID: PMC10546743 DOI: 10.1186/s12864-023-09602-z] [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: 05/25/2023] [Accepted: 08/18/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Restorative regeneration, the capacity to reform a lost body part following amputation or injury, is an important and still poorly understood process in animals. Annelids, or segmented worms, show amazing regenerative capabilities, and as such are a crucial group to investigate. Elucidating the molecular mechanisms that underpin regeneration in this major group remains a key goal. Among annelids, the nereididae Platynereis dumerilii (re)emerged recently as a front-line regeneration model. Following amputation of its posterior part, Platynereis worms can regenerate both differentiated tissues of their terminal part as well as a growth zone that contains putative stem cells. While this regeneration process follows specific and reproducible stages that have been well characterized, the transcriptomic landscape of these stages remains to be uncovered. RESULTS We generated a high-quality de novo Reference transcriptome for the annelid Platynereis dumerilii. We produced and analyzed three RNA-sequencing datasets, encompassing five stages of posterior regeneration, along with blastema stages and non-amputated tissues as controls. We included two of these regeneration RNA-seq datasets, as well as embryonic and tissue-specific datasets from the literature to produce a Reference transcriptome. We used this Reference transcriptome to perform in depth analyzes of RNA-seq data during the course of regeneration to reveal the important dynamics of the gene expression, process with thousands of genes differentially expressed between stages, as well as unique and specific gene expression at each regeneration stage. The study of these genes highlighted the importance of the nervous system at both early and late stages of regeneration, as well as the enrichment of RNA-binding proteins (RBPs) during almost the entire regeneration process. CONCLUSIONS In this study, we provided a high-quality de novo Reference transcriptome for the annelid Platynereis that is useful for investigating various developmental processes, including regeneration. Our extensive stage-specific transcriptional analysis during the course of posterior regeneration sheds light upon major molecular mechanisms and pathways, and will foster many specific studies in the future.
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Affiliation(s)
- Louis Paré
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Loïc Bideau
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Loeiza Baduel
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Caroline Dalle
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Médine Benchouaia
- Département de biologie, GenomiqueENS, Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Stephan Q Schneider
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Lucie Laplane
- Université Paris I Panthéon-Sorbonne, CNRS UMR 8590 Institut d'Histoire et de Philosophie des Sciences et des Techniques (IHPST), Paris, France
- Gustave Roussy, UMR 1287, Villejuif, France
| | - Yves Clément
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Michel Vervoort
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Eve Gazave
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France.
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Liu Z, Fu S, He X, Dai L, Liu X, Narisu, Shi C, Gu M, Wang Y, Manda, Guo L, Bao Y, Baiyinbatu, Chang C, Liu Y, Zhang W. Integrated Multi-Tissue Transcriptome Profiling Characterizes the Genetic Basis and Biomarkers Affecting Reproduction in Sheep ( Ovis aries). Genes (Basel) 2023; 14:1881. [PMID: 37895230 PMCID: PMC10606288 DOI: 10.3390/genes14101881] [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: 08/26/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
The heritability of litter size in sheep is low and controlled by multiple genes, but the research on its related genes is not sufficient. Here, to explore the expression pattern of multi-tissue genes in Chinese native sheep, we selected 10 tissues of the three adult ewes with the highest estimated breeding value in the early study of the prolific Xinggao sheep population. The global gene expression analysis showed that the ovary, uterus, and hypothalamus expressed the most genes. Using the Uniform Manifold Approximation and Projection (UMAP) cluster analysis, these samples were clustered into eight clusters. The functional enrichment analysis showed that the genes expressed in the spleen, uterus, and ovary were significantly enriched in the Ataxia Telangiectasia Mutated Protein (ATM) signaling pathway, and most genes in the liver, spleen, and ovary were enriched in the immune response pathway. Moreover, we focus on the expression genes of the hypothalamic-pituitary-ovarian axis (HPO) and found that 11,016 genes were co-expressed in the three tissues, and different tissues have different functions, but the oxytocin signaling pathway was widely enriched. To further explore the differences in the expression genes (DEGs) of HPO in different sheep breeds, we downloaded the transcriptome data in the public data, and the analysis of DEGs (Xinggao sheep vs. Sunite sheep in Hypothalamus, Xinggao sheep vs. Sunite sheep in Pituitary, and Xinggao sheep vs. Suffolk sheep in Ovary) revealed the neuroactive ligand-receptor interactions. In addition, the gene subsets of the transcription factors (TFs) of DEGs were identified. The results suggest that 51 TF genes and the homeobox TF may play an important role in transcriptional variation across the HPO. Altogether, our study provided the first fundamental resource to investigate the physiological functions and regulation mechanisms in sheep. This important data contributes to improving our understanding of the reproductive biology of sheep and isolating effecting molecular markers that can be used for genetic selection in sheep.
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Affiliation(s)
- Zaixia Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Shaoyin Fu
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (S.F.); (X.H.)
| | - Xiaolong He
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China; (S.F.); (X.H.)
| | - Lingli Dai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- Veterinary Research Institute, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Xuewen Liu
- Animal Husbandry and Bioengineering, College of Agronomy, Xing’an Vocational and Technical College, Ulanhot 137400, China;
| | - Narisu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Caixia Shi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
| | - Mingjuan Gu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Yu Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China;
| | - Manda
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
| | - Lili Guo
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- School of Life Science, Inner Mongolia University, Hohhot 010021, China;
| | - Yanchun Bao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Baiyinbatu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Chencheng Chang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Yongbin Liu
- School of Life Science, Inner Mongolia University, Hohhot 010021, China;
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Z.L.); (L.D.); (N.); (C.S.); (M.G.); (M.); (L.G.); (Y.B.); (B.); (C.C.)
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, China
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Lu M, Feng R, Zhang C, Xiao Y, Yin C. Identifying Novel Drug Targets for Epilepsy Through a Brain Transcriptome-Wide Association Study and Protein-Wide Association Study with Chemical-Gene-Interaction Analysis. Mol Neurobiol 2023; 60:5055-5066. [PMID: 37246165 PMCID: PMC10415436 DOI: 10.1007/s12035-023-03382-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/04/2023] [Indexed: 05/30/2023]
Abstract
Epilepsy is a severe neurological condition affecting 50-65 million individuals worldwide that can lead to brain damage. Nevertheless, the etiology of epilepsy remains poorly understood. Meta-analyses of genome-wide association studies involving 15,212 epilepsy cases and 29,677 controls of the ILAE Consortium cohort were used to conduct transcriptome-wide association studies (TWAS) and protein-wide association studies (PWAS). Furthermore, a protein-protein interaction (PPI) network was generated using the STRING database, and significant epilepsy-susceptible genes were verified using chip data. Chemical-related gene set enrichment analysis (CGSEA) was performed to determine novel drug targets for epilepsy. TWAS analysis identified 21,170 genes, of which 58 were significant (TWASfdr < 0.05) in ten brain regions, and 16 differentially expressed genes were verified based on mRNA expression profiles. The PWAS identified 2249 genes, of which 2 were significant (PWASfdr < 0.05). Through chemical-gene set enrichment analysis, 287 environmental chemicals associated with epilepsy were identified. We identified five significant genes (WIPF1, IQSEC1, JAM2, ICAM3, and ZNF143) that had causal relationships with epilepsy. CGSEA identified 159 chemicals that were significantly correlated with epilepsy (Pcgsea < 0.05), such as pentobarbital, ketone bodies, and polychlorinated biphenyl. In summary, we performed TWAS, PWAS (for genetic factors), and CGSEA (for environmental factors) analyses and identified several epilepsy-associated genes and chemicals. The results of this study will contribute to our understanding of genetic and environmental factors for epilepsy and may predict novel drug targets.
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Affiliation(s)
- Mengnan Lu
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China
| | - Ruoyang Feng
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China
| | - Chenglin Zhang
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China
| | - Yanfeng Xiao
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China.
| | - Chunyan Yin
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China.
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Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ. Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543489. [PMID: 37333110 PMCID: PMC10274686 DOI: 10.1101/2023.06.02.543489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Neuronal and behavioral adaptations to novel stimuli are regulated by temporally dynamic waves of transcriptional activity, which shape neuronal function and guide enduring plasticity. Neuronal activation promotes expression of an immediate early gene (IEG) program comprised primarily of activity-dependent transcription factors, which are thought to regulate a second set of late response genes (LRGs). However, while the mechanisms governing IEG activation have been well studied, the molecular interplay between IEGs and LRGs remain poorly characterized. Here, we used transcriptomic and chromatin accessibility profiling to define activity-driven responses in rat striatal neurons. As expected, neuronal depolarization generated robust changes in gene expression, with early changes (1 h) enriched for inducible transcription factors and later changes (4 h) enriched for neuropeptides, synaptic proteins, and ion channels. Remarkably, while depolarization did not induce chromatin remodeling after 1 h, we found broad increases in chromatin accessibility at thousands of sites in the genome at 4 h after neuronal stimulation. These putative regulatory elements were found almost exclusively at non-coding regions of the genome, and harbored consensus motifs for numerous activity-dependent transcription factors such as AP-1. Furthermore, blocking protein synthesis prevented activity-dependent chromatin remodeling, suggesting that IEG proteins are required for this process. Targeted analysis of LRG loci identified a putative enhancer upstream of Pdyn (prodynorphin), a gene encoding an opioid neuropeptide implicated in motivated behavior and neuropsychiatric disease states. CRISPR-based functional assays demonstrated that this enhancer is both necessary and sufficient for Pdyn transcription. This regulatory element is also conserved at the human PDYN locus, where its activation is sufficient to drive PDYN transcription in human cells. These results suggest that IEGs participate in chromatin remodeling at enhancers and identify a conserved enhancer that may act as a therapeutic target for brain disorders involving dysregulation of Pdyn.
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Affiliation(s)
- Robert A Phillips
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ethan Wan
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jennifer J Tuscher
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David Reid
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Olivia R Drake
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lara Ianov
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Wu J, Tian Z, Zhuang X, Chen Y, Fan T, Li J, Wang X. Dynamic alterations in metabolomics and transcriptomics associated with intestinal fibrosis in a 2,4,6-trinitrobenzene sulfonic acid-induced murine model. J Transl Med 2023; 21:554. [PMID: 37592304 PMCID: PMC10436422 DOI: 10.1186/s12967-023-04392-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/28/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND & AIMS Intestinal fibrosis is a common and severe complication of inflammatory bowel disease without clear pathogenesis. Abnormal expression of host genes and metabolic perturbations might associate with the onset of intestinal fibrosis. In this study, we aimed to investigate the relationship between the development of intestinal fibrosis and the dynamic alterations in both fecal metabolites and host gene expression. METHODS We induced intestinal fibrosis in a murine model using 2,4,6-trinitrobenzene sulfonic acid (TNBS). TNBS-treated or control mice were sacrificed after 4 and 6 weeks of intervention; alterations in colonic genes and fecal metabolites were determined by transcriptomics and metabolomics, respectively. Differential, tendency, enrichment, and correlation analyses were performed to assess the relationship between host genes and fecal metabolites. RESULTS RNA-sequencing analysis revealed that 679 differential genes with enduring changes were mainly enriched in immune response-related signaling pathways and metabolism-related biological processes. Among them, 15 lipid metabolism-related genes were closely related to the development of intestinal fibrosis. Moreover, the fecal metabolic profile was significantly altered during intestinal fibrosis development, especially the lipid metabolites. Particularly, dynamic perturbations in lipids were strongly associated with alterations in lipid metabolism-related genes expression. Additionally, six dynamically altered metabolites might serve as biomarkers to identify colitis-related intestinal fibrosis in the murine model. CONCLUSIONS Intestinal fibrosis in colitis mice might be related to dynamic changes in gene expression and metabolites. These findings could provide new insights into the pathogenesis of intestinal fibrosis.
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Affiliation(s)
- Jinzhen Wu
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, No.253, Industrial Avenue, Haizhu District, Guangzhou, 510000, Guangdong, People's Republic of China
| | - Zhenyi Tian
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, No.253, Industrial Avenue, Haizhu District, Guangzhou, 510000, Guangdong, People's Republic of China
| | - Xiaoduan Zhuang
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, No.253, Industrial Avenue, Haizhu District, Guangzhou, 510000, Guangdong, People's Republic of China
| | - Yiru Chen
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, No.253, Industrial Avenue, Haizhu District, Guangzhou, 510000, Guangdong, People's Republic of China
| | - Tingting Fan
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, No.253, Industrial Avenue, Haizhu District, Guangzhou, 510000, Guangdong, People's Republic of China
| | - Jiayun Li
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, No.253, Industrial Avenue, Haizhu District, Guangzhou, 510000, Guangdong, People's Republic of China
| | - Xinying Wang
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, No.253, Industrial Avenue, Haizhu District, Guangzhou, 510000, Guangdong, People's Republic of China.
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Wei X, Xu D, Liu Z, Liu Q, Zhuo Z. SMRT Sequencing Technology Was Used to Construct the Batocera horsfieldi (Hope) Transcriptome and Reveal Its Features. INSECTS 2023; 14:625. [PMID: 37504630 PMCID: PMC10380457 DOI: 10.3390/insects14070625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023]
Abstract
Batocera horsfieldi (Hope) (Coleoptera: Cerambycidae) is an important forest pest in China that mainly infests timber and economic forests. This pest primarily causes plant tissue to necrotize, rot, and eventually die by feeding on the woody parts of tree trunks. To gain a deeper understanding of the genetic mechanism of B. horsfieldi, this study employed single-molecule real-time sequencing (SMRT) and Illumina RNA-seq technologies to conduct full-length transcriptome sequencing of the insect. Total RNA extracted from male and female adults was mixed and subjected to SMRT sequencing, generating a complete transcriptome. Transcriptome analysis, prediction of long non-coding RNA (lncRNA), coding sequences (CDs), analysis of simple sequence repeats (SSR), prediction of transcription factors, and functional annotation of transcripts were performed in this study. The collective 20,356,793 subreads (38.26 G, clean reads) were generated, including 432,091 circular consensus sequences and 395,851 full-length non-chimera reads. The full-length non-chimera reads (FLNC) were clustered and redundancies were removed, resulting in 39,912 consensus reads. SSR and ANGEL software v3.0 were used for predicting SSR and CDs. In addition, four tools were used for annotating 6058 lncRNAs, identifying 636 transcription factors. Furthermore, a total of 84,650 transcripts were functionally annotated in seven different databases. This is the first time that the full-length transcriptome of B. horsfieldi has been obtained using SMRT sequencing. This provides an important foundation for investigating the gene regulation underlying the interaction between B. horsfieldi and its host plants through gene editing in the future and provides a scientific basis for the prevention and control of B. horsfieldi.
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Affiliation(s)
- Xinju Wei
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Danping Xu
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Zhiqian Liu
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Quanwei Liu
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Zhihang Zhuo
- College of Life Science, China West Normal University, Nanchong 637002, China
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