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Gu S, Huang Q, Jie Y, Sun C, Wen C, Yang N. Transcriptomic and epigenomic landscapes of muscle growth during the postnatal period of broilers. J Anim Sci Biotechnol 2024; 15:91. [PMID: 38961455 PMCID: PMC11223452 DOI: 10.1186/s40104-024-01049-w] [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: 02/04/2024] [Accepted: 05/12/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Broilers stand out as one of the fastest-growing livestock globally, making a substantial contribution to animal meat production. However, the molecular and epigenetic mechanisms underlying the rapid growth and development of broiler chickens are still unclear. This study aims to explore muscle development patterns and regulatory networks during the postnatal rapid growth phase of fast-growing broilers. We measured the growth performance of Cornish (CC) and White Plymouth Rock (RR) over a 42-d period. Pectoral muscle samples from both CC and RR were randomly collected at day 21 after hatching (D21) and D42 for RNA-seq and ATAC-seq library construction. RESULTS The consistent increase in body weight and pectoral muscle weight across both breeds was observed as they matured, with CC outpacing RR in terms of weight at each stage of development. Differential expression analysis identified 398 and 1,129 genes in the two dimensions of breeds and ages, respectively. A total of 75,149 ATAC-seq peaks were annotated in promoter, exon, intron and intergenic regions, with a higher number of peaks in the promoter and intronic regions. The age-biased genes and breed-biased genes of RNA-seq were combined with the ATAC-seq data for subsequent analysis. The results spotlighted the upregulation of ACTC1 and FDPS at D21, which were primarily associated with muscle structure development by gene cluster enrichment. Additionally, a noteworthy upregulation of MUSTN1, FOS and TGFB3 was spotted in broiler chickens at D42, which were involved in cell differentiation and muscle regeneration after injury, suggesting a regulatory role of muscle growth and repair. CONCLUSIONS This work provided a regulatory network of postnatal broiler chickens and revealed ACTC1 and MUSTN1 as the key responsible for muscle development and regeneration. Our findings highlight that rapid growth in broiler chickens triggers ongoing muscle damage and subsequent regeneration. These findings provide a foundation for future research to investigate the functional aspects of muscle development.
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Affiliation(s)
- Shuang Gu
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
| | - Qiang Huang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
| | - Yuchen Jie
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
| | - Congjiao Sun
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Hainan, 572025, China
| | - Chaoliang Wen
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Hainan, 572025, China
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China.
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Hainan, 572025, China.
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Feng H, Xu D, Jiang C, Chen Y, Wang J, Ren Z, Li X, Zhang XD, Cang S. LINC01559 promotes lung adenocarcinoma metastasis by disrupting the ubiquitination of vimentin. Biomark Res 2024; 12:19. [PMID: 38311781 PMCID: PMC10840222 DOI: 10.1186/s40364-024-00571-3] [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: 09/19/2023] [Accepted: 01/24/2024] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND Distant metastasis is the major cause of lung adenocarcinoma (LUAD)-associated mortality. However, molecular mechanisms involved in LUAD metastasis remain to be fully understood. While the role of long non-coding RNAs (lncRNAs) in cancer development, progression, and treatment resistance is being increasingly appreciated, the list of dysregulated lncRNAs that contribute to LUAD pathogenesis is also rapidly expanding. METHODS Bioinformatics analysis was conducted to interrogate publicly available LUAD datasets. In situ hybridization and qRT-PCR assays were used to test lncRNA expression in human LUAD tissues and cell lines, respectively. Wound healing as well as transwell migration and invasion assays were employed to examine LUAD cell migration and invasion in vitro. LUAD metastasis was examined using mouse models in vivo. RNA pulldown and RNA immunoprecipitation were carried out to test RNA-protein associations. Cycloheximide-chase assays were performed to monitor protein turnover rates and Western blotting was employed to test protein expression. RESULTS The expression of the lncRNA LINC01559 was commonly upregulated in LUADs, in particular, in those with distant metastasis. High LINC01559 expression was associated with poor outcome of LUAD patients and was potentially an independent prognostic factor. Knockdown of LINC01559 diminished the potential of LUAD cell migration and invasion in vitro and reduced the formation of LUAD metastatic lesions in vivo. Mechanistically, LINC01559 binds to vimentin and prevents its ubiquitination and proteasomal degradation, leading to promotion of LUAD cell migration, invasion, and metastasis. CONCLUSION LINC01559 plays an important role in LUAD metastasis through stabilizing vimentin. The expression of LINC01559 is potentially an independent prognostic factor of LUAD patients, and LINC01559 targeting may represent a novel avenue for the treatment of late-stage LUAD.
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Affiliation(s)
- Hao Feng
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-Coding RNA Translational Research, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Dengfei Xu
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-Coding RNA Translational Research, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Chenyang Jiang
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-Coding RNA Translational Research, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Yuming Chen
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-Coding RNA Translational Research, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Junru Wang
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-Coding RNA Translational Research, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Zirui Ren
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-Coding RNA Translational Research, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Xiang Li
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-Coding RNA Translational Research, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Xu Dong Zhang
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia.
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-Coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-Coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, 450003, China.
| | - Shundong Cang
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-Coding RNA Translational Research, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China.
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Li Q, Wang X, Xu S, Chen B, Wu T, Liu J, Zhao G, Wu L. Remodeling of Chromatin Accessibility Regulates the Radiological Responses of NSCLC A549 Cells to High-LET Carbon Ions. Radiat Res 2023; 200:474-488. [PMID: 37815204 DOI: 10.1667/rade-23-00097.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]
Abstract
Carbon-ion radiation therapy (CIRT) may offer remarkable advantages in cancer treatment with its unique physical and biological characteristics. However, the underlying epigenetic regulatory mechanisms of cancer response to CIRT remain to be identified. In this study, we showed consistent but different degrees of biological effects induced in NSCLC A549 cells by carbon ions of different LET. The genome-wide chromatin accessibility and transcriptional profiles of carbon ion-treated A549 cells were performed using transposase-accessible chromatin sequencing (ATAC-seq) and RNA-seq, respectively, and further gene regulatory network analysis was performed by integrating the two sets of genomic data. Alterations in chromatin accessibility by carbon ions of different LET predominantly occurred in intron, distal intergenic and promoter regions of differential chromatin accessibility regions. The transcriptional changes were mainly regulated by proximal chromatin accessibility. Notably, CCCTC-binding factor (CTCF) was identified as a key transcription factor in the cellular response to carbon ions. The target genes regulated by CTCF in response to carbon ions were found to be closely associated with the LET of carbon ions, particularly in the regulation of gene transcription within the DNA replication- and metabolism-related signaling pathways. This study provides a regulatory profile of genes involved in key signaling pathways and highlighted key regulatory elements in NSCLC A549 cells during CIRT, which expands our understanding of the epigenetic mechanisms of carbon ion-induced biological effects and reveals an important role for LET in the regulation of changes in chromatin accessibility, although further research is needed.
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Affiliation(s)
- Qian Li
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Xiaofei Wang
- School of Biology, Food and Environment, Hefei University, Hefei 230601, P. R. China
| | - Shengmin Xu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Biao Chen
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Tao Wu
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Jie Liu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Guoping Zhao
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Lijun Wu
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
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Zhou A, Zhang D, Kang X, Brooks JD. Identification of age- and immune-related gene signatures for clinical outcome prediction in lung adenocarcinoma. Cancer Med 2023; 12:17475-17490. [PMID: 37434467 PMCID: PMC10501266 DOI: 10.1002/cam4.6330] [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: 03/23/2023] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND The understanding of the factors causing decreased overall survival (OS) in older patients compared to younger patients in lung adenocarcinoma (LUAD) remains. METHODS Gene expression profiles of LUAD were obtained from publicly available databases by Kaplan-Meier analysis was performed to determine whether age was associated with patient OS. The immune cell composition in the tumor microenvironment (TME) was evaluated using CIBERSORT. The fraction of stromal and immune cells in tumor samples were also using assessed using multiple tools including ESTIMATE, EPIC, and TIMER. Differentially expressed genes (DEGs) from the RNA-Seq data that were associated with age and immune cell composition were identified using the R package DEGseq. A 22-gene signature composed of DEGs associated with age and immune cell composition that predicted OS were constructed using Least Absolute Shrinkage and Selection Operator (LASSO). RESULTS In The Cancer Genome Atlas (TCGA)-LUAD dataset, we found that younger patients (≤70) had a significant better OS compared to older patients (>70). In addition, older patients had significantly higher expression of immune checkpoint proteins including inhibitory T cell receptors and their ligands. Moreover, analyses using multiple bioinformatics tools showed increased immune infiltration, including CD4+ T cells, in older patients compared to younger patients. We identified a panel of genes differentially expressed between patients >70 years compared to those ≤70 years, as well as between patients with high or low immune scores and selected 84 common genes to construct a prognostic gene signature. A risk score calculated based on 22 genes selected by LASSO predicted 1, 3, and 5-year OS, with an area under the curve (AUC) of 0.72, 0.72, 0.69, receptively, in TCGA-LUAD dataset and an independent validation dataset available from the European Genome-phenome Archive (EGA). CONCLUSION Our results demonstrate that age contributes to OS of LUAD patients atleast in part through its association with immune infiltration in the TME.
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Affiliation(s)
- Andrew Zhou
- Department of UrologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Dalin Zhang
- Department of UrologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Xiaoman Kang
- Department of OncologyStanford University School of MedicineStanfordCaliforniaUSA
| | - James D. Brooks
- Department of UrologyStanford University School of MedicineStanfordCaliforniaUSA
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Minnai F, Noci S, Chierici M, Cotroneo CE, Bartolini B, Incarbone M, Tosi D, Mattioni G, Jurman G, Dragani TA, Colombo F. Genetic predisposition to lung adenocarcinoma outcome is a feature already present in patients' noninvolved lung tissue. Cancer Sci 2022; 114:281-294. [PMID: 36114746 PMCID: PMC9807507 DOI: 10.1111/cas.15591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/23/2022] [Accepted: 09/12/2022] [Indexed: 01/07/2023] Open
Abstract
Emerging evidence suggests that the prognosis of patients with lung adenocarcinoma can be determined from germline variants and transcript levels in nontumoral lung tissue. Gene expression data from noninvolved lung tissue of 483 lung adenocarcinoma patients were tested for correlation with overall survival using multivariable Cox proportional hazard and multivariate machine learning models. For genes whose transcript levels are associated with survival, we used genotype data from 414 patients to identify germline variants acting as cis-expression quantitative trait loci (eQTLs). Associations of eQTL variant genotypes with gene expression and survival were tested. Levels of four transcripts were inversely associated with survival by Cox analysis (CLCF1, hazard ratio [HR] = 1.53; CNTNAP1, HR = 2.17; DUSP14, HR = 1.78; and MT1F: HR = 1.40). Machine learning analysis identified a signature of transcripts associated with lung adenocarcinoma outcome that was largely overlapping with the transcripts identified by Cox analysis, including the three most significant genes (CLCF1, CNTNAP1, and DUSP14). Pathway analysis indicated that the signature is enriched for ECM components. We identified 32 cis-eQTLs for CNTNAP1, including 6 with an inverse correlation and 26 with a direct correlation between the number of minor alleles and transcript levels. Of these, all but one were prognostic: the six with an inverse correlation were associated with better prognosis (HR < 1) while the others were associated with worse prognosis. Our findings provide supportive evidence that genetic predisposition to lung adenocarcinoma outcome is a feature already present in patients' noninvolved lung tissue.
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Affiliation(s)
- Francesca Minnai
- Institute for Biomedical TechnologiesNational Research CouncilSegrateItaly
| | - Sara Noci
- Department of ResearchFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Marco Chierici
- Data Science for Health Research UnitBruno Kessler FoundationTrentoItaly
| | | | - Barbara Bartolini
- Department of ResearchFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | | | - Davide Tosi
- Thoracic Surgery and Lung Transplantation UnitFondazione IRCCS Cà Granda Ospedale Maggiore PoliclinicoMilanItaly
| | - Giovanni Mattioni
- Thoracic Surgery and Lung Transplantation UnitFondazione IRCCS Cà Granda Ospedale Maggiore PoliclinicoMilanItaly
| | - Giuseppe Jurman
- Data Science for Health Research UnitBruno Kessler FoundationTrentoItaly
| | - Tommaso A. Dragani
- Department of ResearchFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Francesca Colombo
- Institute for Biomedical TechnologiesNational Research CouncilSegrateItaly
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