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Shao X, Lu X, Sun X, Jiang H, Chen Y. Preliminary studies on the molecular mechanism of intramuscular fat deposition in the longest dorsal muscle of sheep. BMC Genomics 2024; 25:592. [PMID: 38867146 PMCID: PMC11167792 DOI: 10.1186/s12864-024-10486-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: 03/13/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Intramuscular fat content is an important index reflecting the quality of mutton, which directly affects the flavor and tenderness of mutton. Livestock and poultry intramuscular fat content is influenced by genetics, nutritional level, and environmental factors. Key regulatory factors play a crucial role in intramuscular fat deposition. However, there is a limited amount of research on the identification and function of key genes involved in intramuscular fat content deposition specifically in sheep. RESULTS Histological differences in the longest dorsal muscle of the small-tailed frigid sheep increased in diameter and decreased in several muscle fibers with increasing monthly age; The intramuscular fat content of the longest dorsal muscle of the small-tailed cold sheep varied with age, with a minimum of 1 month of age, a maximum of 6 months of age, and a minimum of 12 months of age. Transcriptomic sequencing and bioinformatics analysis revealed a large number of differential genes in the longest dorsal muscles of little-tailed billy goats of different months of age, which were enriched in multiple GO entries and KEGG pathways. Among them, the pathway associated with intramuscular fat was the AMPK signaling pathway, and the related genes were PPARGC1A and ADIPOQ; Immunohistochemical studies showed that PPARGC1A and ADIPOQ proteins were expressed in connective tissues, cell membranes, and, to a lesser extent, the cytoplasm of the longest dorsal muscle of the little-tailed frigid sheep; Real-time PCR and Western Blot validation showed that PPARGC1A and ADIPOQ were both expressed in the longest dorsal muscle of the little-tailed frigid sheep at different ages, and there were age differences in the amount of expression. The ADIPOQ gene was negatively correlated with the intramuscular fat content of the longest dorsal muscle, and the PPARGC1A gene was positively correlated with the intramuscular fat content of the longest dorsal muscle; As inferred from the above results, the ADIPOQ gene was negatively correlated with the intramuscular fat content of the longest dorsal muscle (r = -0.793, P < 0.05); and the PPARGC1A gene was positively correlated with the intramuscular fat content of the longest dorsal muscle r = 0.923, P < 0.05). CONCLUSIONS Based on the above results, it can be inferred that the ADIPOQ gene is negatively correlated with the intramuscular fat content of the longest back muscle (r = -0.793, P < 0.05); the PPARGC1A gene is positively correlated with the intramuscular fat content of the longest back muscle (r = 0.923, P < 0.05).
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Affiliation(s)
- Xuwen Shao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
- Key Laboratory of Livestock and Poultry Resources (Sheep & Goat) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changchun, China
| | - Xintan Lu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
- Key Laboratory of Livestock and Poultry Resources (Sheep & Goat) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changchun, China
| | - Xinming Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
- Key Laboratory of Livestock and Poultry Resources (Sheep & Goat) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changchun, China
| | - Huaizhi Jiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China.
- Key Laboratory of Livestock and Poultry Resources (Sheep & Goat) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changchun, China.
| | - Yang Chen
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China.
- Key Laboratory of Livestock and Poultry Resources (Sheep & Goat) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changchun, China.
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Wang J, Chen H, Zhang Y, Shen H, Zeng X. Long non-coding RNA Loc105611671 promotes the proliferation of ovarian granulosa cells and steroid hormone production upregulation of CDC42. Front Vet Sci 2024; 11:1366759. [PMID: 38500606 PMCID: PMC10944914 DOI: 10.3389/fvets.2024.1366759] [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: 01/07/2024] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Granulosa cells (GCs) are essential for follicular development, and long non-coding RNAs (LncRNAs) are known to support the maintenance of this process and hormone synthesis in mammals. Nevertheless, the regulatory roles of these lncRNAs within sheep follicular GCs remain largely unexplored. This study delved into the influence of a Loc105611671, on the proliferation and steroid hormone synthesis of sheep ovarian GCs and the associated target genes in vitro. Cell Counting Kit-8 (CCK-8) gain-of-function experiments indicated that overexpression of Loc105611671 significantly boosted GCs proliferation, along with estrogen (E2) and progesterone (P4) levels. Further mechanistic scrutiny revealed that Loc105611671 is primarily localized within the cytoplasm of ovarian granulosa cells and engages in molecular interplay with CDC42. This interaction results in the upregulation of CDC42 protein expression. Moreover, it was discerned that increased CDC42 levels contribute to augmented proliferation of follicular granulosa cells and the secretion of E2 and P4. Experiments involving co-transfection elucidated that the concurrent overexpression of CDC42 and Loc105611671 acted synergistically to potentiate these effects. These findings provide insights into the molecular underpinnings of fecundity in ovine species and may inform future strategies for enhancing reproductive outcomes.
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Affiliation(s)
- Jinglei Wang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Hanying Chen
- School of Pharmacy, Shihezi University, Shihezi, Xinjiang, China
| | - Yongsheng Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Hong Shen
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Xiancun Zeng
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
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Wu C, Liu H, Zhan Z, Zhang X, Zhang M, You J, Ma J. Unveiling dysregulated lncRNAs and networks in non-syndromic cleft lip with or without cleft palate pathogenesis. Sci Rep 2024; 14:1047. [PMID: 38200098 PMCID: PMC10781966 DOI: 10.1038/s41598-024-51747-8] [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: 09/20/2023] [Accepted: 01/09/2024] [Indexed: 01/12/2024] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital facial malformation with a complex, incompletely understood origin. Long noncoding RNAs (lncRNAs) have emerged as pivotal regulators of gene expression, potentially shedding light on NSCL/P's etiology. This study aimed to identify critical lncRNAs and construct regulatory networks to unveil NSCL/P's underlying molecular mechanisms. Integrating gene expression profiles from the Gene Expression Omnibus (GEO) database, we pinpointed 30 dysregulated NSCL/P-associated lncRNAs. Subsequent analyses enabled the creation of competing endogenous RNA (ceRNA) networks, lncRNA-RNA binding protein (RBP) interaction networks, and lncRNA cis and trans regulation networks. RT-qPCR was used to examine the regulatory networks of lncRNA in vivo and in vitro. Furthermore, protein levels of lncRNA target genes were validated in human NSCL/P tissue samples and murine palatal shelves. Consequently, two lncRNAs and three mRNAs: FENDRR (log2FC = - 0.671, P = 0.040), TPT1-AS1 (log2FC = 0.854, P = 0.003), EIF3H (log2FC = - 1.081, P = 0.041), RBBP6 (log2FC = 0.914, P = 0.037), and SRSF1 (log2FC = 0.763, P = 0.026) emerged as potential contributors to NSCL/P pathogenesis. Functional enrichment analyses illuminated the biological functions and pathways associated with these lncRNA-related networks in NSCL/P. In summary, this study comprehensively delineates the dysregulated transcriptional landscape, identifies associated lncRNAs, and reveals pivotal sub-networks relevant to NSCL/P development, aiding our understanding of its molecular progression and setting the stage for further exploration of lncRNA and mRNA regulation in NSCL/P.
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Affiliation(s)
- Caihong Wu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
- Stomatological Hospital affiliated Suzhou Vocational Health College, Suzhou, China
| | - Haojie Liu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Zhuorong Zhan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Xinyu Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Mengnan Zhang
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Jiawen You
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Junqing Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.
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Zheng X, Zheng D, Zhang C, Guo H, Zhang Y, Xue X, Shi Z, Zhang X, Zeng X, Wu Y, Gao W. A cuproptosis-related lncRNA signature predicts the prognosis and immune cell status in head and neck squamous cell carcinoma. Front Oncol 2023; 13:1055717. [PMID: 37538124 PMCID: PMC10394648 DOI: 10.3389/fonc.2023.1055717] [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: 09/28/2022] [Accepted: 06/29/2023] [Indexed: 08/05/2023] Open
Abstract
Introduction The incidence of head and neck squamous cell carcinoma (HNSCC), one of the most prevalent tumors, is increasing rapidly worldwide. Cuproptosis, as a new copper-dependent cell death form, was proposed recently. However, the prognosis value and immune effects of cuproptosis-related lncRNAs (CRLs) have not yet been elucidated in HNSCC. Methods In the current study, the expression pattern, differential profile, clinical correlation, DNA methylation, functional enrichment, univariate prognosis factor, and the immune effects of CRLs were analyzed. A four-CRL signature was constructed using the least absolute shrinkage and selection operator (LASSO) algorithm. Results Results showed that 20 CRLs had significant effects on the stage progression of HNSCC. Sixteen CRLs were tightly correlated with the overall survival (OS) of HNSCC patients. Particularly, lnc-FGF3-4 as a single risk factor was upregulated in HNSCC tissues and negatively impacted the prognosis of HNSCC. DNA methylation probes of cg02278768 (MIR9-3HG), cg07312099 (ASAH1-AS1), and cg16867777 (TIAM1-AS1) were also correlated with the prognosis of HNSCC. The four-CRL signature that included MAP4K3-DT, lnc-TCEA3-1, MIR9-3HG, and CDKN2A-DT had a significantly negative effect on the activation of T cells follicular helper and OS probability of HNSCC. Functional analysis revealed that cell cycle, DNA replication, and p53 signal pathways were enriched. Discussion A novel CRL-related signature has the potential of prognosis prediction in HNSCC. Targeting CRLs may be a promising therapeutic strategy for HNSCC.
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Affiliation(s)
- Xiwang Zheng
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Defei Zheng
- Department of Hematology/Oncology, Children’s Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chunming Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Huina Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yuliang Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xuting Xue
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zhaohui Shi
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
| | - Xiangmin Zhang
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
| | - Xianhai Zeng
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
| | - Yongyan Wu
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
| | - Wei Gao
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
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Yousuf S, Malik WA, Feng H, Liu T, Xie L, Miao X. Genome wide identification and characterization of fertility associated novel CircRNAs as ceRNA reveal their regulatory roles in sheep fecundity. J Ovarian Res 2023; 16:115. [PMID: 37340323 DOI: 10.1186/s13048-023-01178-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/29/2023] [Indexed: 06/22/2023] Open
Abstract
Reproductive traits play a vital role in determining the production efficiency of sheep. Maximizing the production is of paramount importance for breeders worldwide due to the growing population. Circular RNAs (circRNAs) act as miRNA sponges by absorbing miRNA activity through miRNA response elements (MREs) and participate in ceRNA regulatory networks (ceRNETs) to regulate mRNA expression. Despite of extensive research on role of circRNAs as miRNA sponges in various species, their specific regulatory roles and mechanism in sheep ovarian tissue are still not well understood. In this study, we performed whole genome sequencing of circRNAs, miRNA and mRNA employing bioinformatic techniques on ovine tissues of two contrasting sheep breeds "Small tail Han (X_LC) and Dolang sheep (D_LC)", which results into identification of 9,878 circRNAs with a total length of 23,522,667 nt and an average length of 2,381.32 nt. Among them, 44 differentially expressed circRNAs (DECs) were identified. Moreover, correlation between miRNA-mRNA and lncRNA-miRNA provided us with to prediction of miRNA binding sites on nine differentially expressed circRNAs and 165 differentially expressed mRNAs using miRanda. miRNA-mRNA and lncRNA-miRNA pairs with negative correlation were selected to determine the ceRNA score along with positively correlated pairs from lncRNA and mRNA network. Integration of ceRNA score and positively correlated pairs exhibit a significant ternary relationship among circRNAs-miRNA-mRNA demonestrated by ceRNA, comprising of 50 regulatory pairs sharring common nodes and predicted potential differentially expressed circRNAs-miRNAs-mRNAs regulatory axis. Based on functional enrichment analysis shortlisted key ceRNA regulatory pairs associated with reproduction including circRNA_3257-novel579_mature-EPHA3, circRNA_8396-novel130_mature-LOC101102473, circRNA_4140- novel34_mature > novel661_mature-KCNK9, and circRNA_8312-novel339_mature-LOC101110545. Furthermore, expression profiling, functional enrichments and qRT-PCR analysis of key target genes infer their implication in reproduction and metabolism. ceRNA target mRNAs evolutionary trajectories, expression profiling, functional enrichments, subcellular localizations following genomic organizations will provide new insights underlying molecular mechanisms of reproduction, and establish a solid foundation for future research. Graphical abstract summarizing the scheme of study.
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Affiliation(s)
- Salsabeel Yousuf
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Waqar Afzal Malik
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hui Feng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tianyi Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lingli Xie
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangyang Miao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Alonso-García M, Suárez-Vega A, Fonseca PAS, Marina H, Pelayo R, Mateo J, Arranz JJ, Gutiérrez-Gil B. Transcriptome analysis of perirenal fat from Spanish Assaf suckling lamb carcasses showing different levels of kidney knob and channel fat. Front Vet Sci 2023; 10:1150996. [PMID: 37255997 PMCID: PMC10225515 DOI: 10.3389/fvets.2023.1150996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/19/2023] [Indexed: 06/01/2023] Open
Abstract
Introduction Suckling lamb meat is highly appreciated in European Mediterranean countries because of its mild flavor and soft texture. In suckling lamb carcasses, perirenal and pelvic fat depots account for a large fraction of carcass fat accumulation, and their proportions are used as an indicator of carcass quality. Material and Methods This study aimed to characterize the genetic mechanisms that regulate fat deposition in suckling lambs by evaluating the transcriptomic differences between Spanish Assaf lambs with significantly different proportions of kidney knob and channel fat (KKCF) depots in their carcasses (4 High-KKCF lambs vs. 4 Low-KKCF lambs). Results The analyzed fat tissue showed overall dominant expression of white adipose tissue gene markers, although due to the young age of the animals (17-36 days), the expression of some brown adipose tissue gene markers (e.g., UCP1, CIDEA) was still identified. The transcriptomic comparison between the High-KKCF and Low-KKCF groups revealed a total of 80 differentially expressed genes (DEGs). The enrichment analysis of the 49 DEGs with increased expression levels in the Low-KKCF lambs identified significant terms linked to the biosynthesis of lipids and thermogenesis, which may be related to the higher expression of the UCP1 gene in this group. In contrast, the enrichment analysis of the 31 DEGs with increased expression in the High-KKCF lambs highlighted angiogenesis as a key biological process supported by the higher expression of some genes, such as VEGF-A and THBS1, which encode a major angiogenic factor and a large adhesive extracellular matrix glycoprotein, respectively. Discussion The increased expression of sestrins, which are negative regulators of the mTOR complex, suggests that the preadipocyte differentiation stage is being inhibited in the High-KKCF group in favor of adipose tissue expansion, in which vasculogenesis is an essential process. All of these results suggest that the fat depots of the High-KKCF animals are in a later stage of development than those of the Low-KKCF lambs. Further genomic studies based on larger sample sizes and complementary analyses, such as the identification of polymorphisms in the DEGs, should be designed to confirm these results and achieve a deeper understanding of the genetic mechanisms underlying fat deposition in suckling lambs.
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Affiliation(s)
- María Alonso-García
- Departemento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Aroa Suárez-Vega
- Departemento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Pablo A. S. Fonseca
- Departemento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Héctor Marina
- Departemento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Rocío Pelayo
- Departemento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Javier Mateo
- Departamento de Higiene y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Juan-José Arranz
- Departemento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Beatriz Gutiérrez-Gil
- Departemento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
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