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Mares-Quiñones MD, Galán-Vásquez E, Pérez-Rueda E, Pérez-Ishiwara DG, Medel-Flores MO, Gómez-García MDC. Identification of modules and key genes associated with breast cancer subtypes through network analysis. Sci Rep 2024; 14:12350. [PMID: 38811600 PMCID: PMC11137066 DOI: 10.1038/s41598-024-61908-4] [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: 07/13/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Breast cancer is the most common malignancy in women around the world. Intratumor and intertumoral heterogeneity persist in mammary tumors. Therefore, the identification of biomarkers is essential for the treatment of this malignancy. This study analyzed 28,143 genes expressed in 49 breast cancer cell lines using a Weighted Gene Co-expression Network Analysis to determine specific target proteins for Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes. Sixty-five modules were identified, of which five were characterized as having a high correlation with breast cancer subtypes. Genes overexpressed in the tumor were found to participate in the following mechanisms: regulation of the apoptotic process, transcriptional regulation, angiogenesis, signaling, and cellular survival. In particular, we identified the following genes, considered as hubs: IFIT3, an inhibitor of viral and cellular processes; ETS1, a transcription factor involved in cell death and tumorigenesis; ENSG00000259723 lncRNA, expressed in cancers; AL033519.3, a hypothetical gene; and TMEM86A, important for regulating keratinocyte membrane properties, considered as a key in Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes, respectively. The modules and genes identified in this work can be used to identify possible biomarkers or therapeutic targets in different breast cancer subtypes.
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Affiliation(s)
- María Daniela Mares-Quiñones
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Mexico
| | - D Guillermo Pérez-Ishiwara
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Olivia Medel-Flores
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Del Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico.
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Li P, Jin Q, Zeng K, Niu C, Xie Q, Dong T, Huang Z, Dou X, Feng C. Amino acid-based supramolecular chiral hydrogels promote osteogenesis of human dental pulp stem cells via the MAPK pathway. Mater Today Bio 2024; 25:100971. [PMID: 38347936 PMCID: PMC10859303 DOI: 10.1016/j.mtbio.2024.100971] [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: 11/25/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/15/2024] Open
Abstract
Critical-size defects (CSDs) of the craniofacial bones cause aesthetic and functional complications that seriously impact the quality of life. The transplantation of human dental pulp stem cells (hDPSCs) is a promising strategy for bone tissue engineering. Chirality is commonly observed in natural biomolecules, yet its effect on stem cell differentiation is seldom studied, and little is known about the underlying mechanism. In this study, supramolecular chiral hydrogels were constructed using L/d-phenylalanine (L/D-Phe) derivatives. The results of alkaline phosphatase expression analysis, alizarin red S assay, as well as quantitative real-time polymerase chain reaction and western blot analyses suggest that right-handed D-Phe hydrogel fibers significantly promoted osteogenic differentiation of hDPSCs. A rat model of calvarial defects was created to investigate the regulation of chiral nanofibers on the osteogenic differentiation of hDPSCs in vivo. The results of the animal experiment demonstrated that the D-Phe group exhibited greater and faster bone formation on hDPSCs. The results of RNA sequencing, vinculin immunofluorescence staining, a calcium fluorescence probe assay, and western blot analysis indicated that L-Phe significantly promoted adhesion of hDPSCs, while D-Phe nanofibers enhanced osteogenic differentiation of hDPSCs by facilitating calcium entry into cells and activate the MAPK pathway. These results of chirality-dependent osteogenic differentiation offer a novel therapeutic strategy for the treatment of CSDs by optimising the differentiation of hDPSCs into chiral nanofibers.
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Affiliation(s)
- Peilun Li
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Qiaoqiao Jin
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Kangrui Zeng
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Chenguang Niu
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Qianyang Xie
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Ting Dong
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Zhengwei Huang
- Department of Endodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Xiaoqiu Dou
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chuanliang Feng
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
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Chen C, Ren H, Li H, Deng Y, Cui Q, Zhu J, Zhang S, Yu J, Wang H, Yu X, Yang S, Hu X, Peng Y. Identification of crucial modules and genes associated with backfat tissue development by WGCNA in Ningxiang pigs. Front Genet 2023; 14:1234757. [PMID: 37662841 PMCID: PMC10469685 DOI: 10.3389/fgene.2023.1234757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Fat deposition is an economically important trait in pigs. Ningxiang pig, one of the four famous indigenous breeds in China, is characterized by high fat content. The underlying gene expression pattern in different developmental periods of backfat tissue remains unclear, and the purpose of this investigation is to explore the potential molecular regulators of backfat tissue development in Ningxiang pigs. Backfat tissue (three samples for each stage) was initially collected from different developmental stages (60, 120, 180, 240, 300, and 360 days after birth), and histological analysis and RNA sequencing (RNA-seq) were then conducted. Fragments per kilobase of transcript per million (FPKM) method was used to qualify gene expressions, and differentially expressed genes (DEGs) were identified. Furthermore, strongly co-expressed genes in modules, which were named by color, were clustered by Weighted gene co-expression network analysis (WGCNA) based on dynamic tree cutting algorithm. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment were subsequently implemented, and hub genes were described in each module. Finally, QPCR analysis was employed to validate RNA-seq data. The results showed that adipocyte area increased and adipocyte number decreased with development of backfat tissue. A total of 1,024 DEGs were identified in five comparison groups (120 days vs. 60 days, 180 days vs. 120 days, 240 days vs. 180 days, 300 days vs. 240 days, and 360 days vs. 300 days). The turquoise, red, pink, paleturquoise, darkorange, and darkgreen module had the highest correlation coefficient with 60, 120, 180, 240, 300, and 360 days developmental stage, while the tan, black and turquoise module had strong relationship with backfat thickness, adipocyte area, and adipocyte number, respectively. Thirteen hub genes (ACSL1, ACOX1, FN1, DCN, CHST13, COL1A1, COL1A2, COL6A3, COL5A1, COL14A1, OAZ3, DNM1, and SELP) were recognized. ACSL1 and ACOX1 might perform function in the early developmental stage of backfat tissue (60 days), and FN1, DCN, COL1A1, COL1A2, COL5A1, COL6A3, and COL14A1 have unignorable position in backfat tissue around 120 days developmental stage. Besides, hub genes SELP and DNM1 in modules significantly associated with backfat thickness and adipocyte area might be involved in the process of backfat tissue development. These findings contribute to understand the integrated mechanism underlying backfat tissue development and promote the progress of genetic improvement in Ningxiang pigs.
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Affiliation(s)
- Chen Chen
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Huibo Ren
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Huali Li
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Yuan Deng
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Qingming Cui
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Ji Zhu
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Siyang Zhang
- Hunan Liushahe Ecological Animal Husbandry Co, Ltd., Changsha, China
| | - Jine Yu
- Hunan Liushahe Ecological Animal Husbandry Co, Ltd., Changsha, China
| | - Huiming Wang
- Hunan Liushahe Ecological Animal Husbandry Co, Ltd., Changsha, China
| | - Xiaodan Yu
- Hunan Liushahe Ecological Animal Husbandry Co, Ltd., Changsha, China
| | - Shiliu Yang
- Hunan Liushahe Ecological Animal Husbandry Co, Ltd., Changsha, China
| | - Xionggui Hu
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Yinglin Peng
- Department of Pig Breeding, Key Laboratory of Conservation and Genetic Analysis of Indigenous Pigs, Hunan Institute of Animal and Veterinary Science, Changsha, China
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
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Mlera L, Collins-McMillen D, Zeltzer S, Buehler JC, Moy M, Zarrella K, Caviness K, Cicchini L, Tafoya DJ, Goodrum F. Liver X Receptor-Inducible Host E3 Ligase IDOL Targets a Human Cytomegalovirus Reactivation Determinant. J Virol 2023; 97:e0075823. [PMID: 37338407 PMCID: PMC10373547 DOI: 10.1128/jvi.00758-23] [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: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023] Open
Abstract
Liver X receptor (LXR) signaling broadly restricts virus replication; however, the mechanisms of restriction are poorly defined. Here, we demonstrate that the cellular E3 ligase LXR-inducible degrader of low-density lipoprotein receptor (IDOL) targets the human cytomegalovirus (HMCV) UL136p33 protein for turnover. UL136 encodes multiple proteins that differentially impact latency and reactivation. UL136p33 is a determinant of reactivation. UL136p33 is targeted for rapid turnover by the proteasome, and its stabilization by mutation of lysine residues to arginine results in a failure to quiet replication for latency. We show that IDOL targets UL136p33 for turnover but not the stabilized variant. IDOL is highly expressed in undifferentiated hematopoietic cells where HCMV establishes latency but is sharply downregulated upon differentiation, a stimulus for reactivation. We hypothesize that IDOL maintains low levels of UL136p33 for the establishment of latency. Consistent with this hypothesis, knockdown of IDOL impacts viral gene expression in wild-type (WT) HCMV infection but not in infection where UL136p33 has been stabilized. Furthermore, the induction of LXR signaling restricts WT HCMV reactivation from latency but does not affect the replication of a recombinant virus expressing a stabilized variant of UL136p33. This work establishes the UL136p33-IDOL interaction as a key regulator of the bistable switch between latency and reactivation. It further suggests a model whereby a key viral determinant of HCMV reactivation is regulated by a host E3 ligase and acts as a sensor at the tipping point between the decision to maintain the latent state or exit latency for reactivation. IMPORTANCE Herpesviruses establish lifelong latent infections, which pose an important risk for disease particularly in the immunocompromised. Our work is focused on the betaherpesvirus human cytomegalovirus (HCMV) that latently infects the majority of the population worldwide. Defining the mechanisms by which HCMV establishes latency or reactivates from latency is important for controlling viral disease. Here, we demonstrate that the cellular inducible degrader of low-density lipoprotein receptor (IDOL) targets a HCMV determinant of reactivation for degradation. The instability of this determinant is important for the establishment of latency. This work defines a pivotal virus-host interaction that allows HCMV to sense changes in host biology to navigate decisions to establish latency or to replicate.
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Affiliation(s)
- Luwanika Mlera
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Donna Collins-McMillen
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Sebastian Zeltzer
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Jason C. Buehler
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Melissa Moy
- Graduate Interdisciplinary Program in Cancer Biology, University of Arizona, Tucson, Arizona, USA
| | - Kristen Zarrella
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Katie Caviness
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Graduate Interdisciplinary Program in Genetics, University of Arizona, Tucson, Arizona, USA
| | - Louis Cicchini
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - David J. Tafoya
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Felicia Goodrum
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Graduate Interdisciplinary Program in Cancer Biology, University of Arizona, Tucson, Arizona, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
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Ye J, Yang K, Li Y, Xu F, Cheng S, Zhang W, Liao Y, Yang X, Wang L, Wang Q. Genome-wide transcriptome analysis reveals the regulatory network governing terpene trilactones biosynthesis in Ginkgo biloba. TREE PHYSIOLOGY 2022; 42:2068-2085. [PMID: 35532090 DOI: 10.1093/treephys/tpac051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Ginkgo biloba L. is currently the only remaining gymnosperm of the Ginkgoaceae Ginkgo genus, and its history can be traced back to the Carboniferous 200 million years ago. Terpene trilactones (TTLs) are one of the main active ingredients in G. biloba, including ginkgolides and bilobalide. They have a good curative effect on cardiovascular and cerebrovascular diseases because of their special antagonistic effect on platelet-activating factors. Therefore, it is necessary to deeply mine genes related to TTLs and to analyze their transcriptional regulation mechanism, which will hold vitally important scientific and practical significance for quality improvement and regulation of G. biloba. In this study, we performed RNA-Seq on the root, stem, immature leaf, mature leaf, microstrobilus, ovulate strobilus, immature fruit and mature fruit of G. biloba. The TTL regulatory network of G. biloba in different organs was revealed by different transcriptomic analysis strategies. Weighted gene co-expression network analysis (WGCNA) revealed that the five modules were closely correlated with organs. The 12 transcription factors, 5 structural genes and 24 Cytochrome P450 (CYP450) were identified as candidate regulators for TTL accumulation by WGCNA and cytoscape visualization. Finally, 6 APETALA2/ethylene response factors, 2 CYP450s and bHLH were inferred to regulate the metabolism of TTLs by correlation analysis. This study is the comprehensive in authenticating transcription factors, structural genes and CYP450 involved in TTL biosynthesis, thereby providing molecular evidence for revealing the comprehensive regulatory network involved in TTL metabolism in G. biloba.
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Affiliation(s)
- Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Ke Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Yuting Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Shuiyuan Cheng
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan 430023, China
- National Selenium Rich Product Quality Supervision and Inspection Center, Enshi, Hubei 445000, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Xiaoyan Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Lina Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
| | - Qijian Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei 434025, China
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Najjar D, Chikhaoui A, Zarrouk S, Azouz S, Kamoun W, Nassib N, Bouchoucha S, Yacoub-Youssef H. Combining Gene Mutation with Expression of Candidate Genes to Improve Diagnosis of Escobar Syndrome. Genes (Basel) 2022; 13:genes13101748. [PMID: 36292632 PMCID: PMC9601381 DOI: 10.3390/genes13101748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/24/2022] Open
Abstract
Escobar syndrome is a rare, autosomal recessive disorder that affects the musculoskeletal system and the skin. Mutations in the CHRNG and TPM2 genes are associated with this pathology. In this study, we conducted a clinical and genetic investigation of five patients and also explored via in silico and gene expression analysis their phenotypic variability. In detail, we identified a patient with a novel composite heterozygous variant of the CHRNG gene and two recurrent mutations in both CHRNG and TPM2 in the rest of the patients. As for the clinical particularities, we reported a list of modifier genes in a patient suffering from myopathy. Moreover, we identified decreased expression of IGF-1, which could be related to the short stature of Escobar patients, and increased expression of POLG1 specific to patients with TPM2 mutation. Through this study, we identified the genetic spectrum of Escobar syndrome in the Tunisian population, which will allow setting up genetic counseling and prenatal diagnosis for families at risk. In addition, we highlighted relevant biomarkers that could differentiate between patients with different genetic defects.
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Affiliation(s)
- Dorra Najjar
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Asma Chikhaoui
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Sinda Zarrouk
- Genomics Platform, Institut Pasteur de Tunis (IPT), Tunis-Belvédère, Tunis 1002, Tunisia
| | - Saifeddine Azouz
- Genomics Platform, Institut Pasteur de Tunis (IPT), Tunis-Belvédère, Tunis 1002, Tunisia
| | - Wafa Kamoun
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Nabil Nassib
- Service Orthopédie Pédiatrique, Hôpital d’Enfant Béchir Hamza, Tunis 1000, Tunisia
| | - Sami Bouchoucha
- Service Orthopédie Pédiatrique, Hôpital d’Enfant Béchir Hamza, Tunis 1000, Tunisia
| | - Houda Yacoub-Youssef
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
- Correspondence:
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Xu Y, Wang Z, Wang Y, Huang Q, Ren C, Sun L, Wang Q, Li M, Liu H, Li Z, Zhang K, Ma T, Lu Y. Identification of differentially expressed autophagy genes associated with osteogenic differentiation in human bone marrow mesenchymal stem cells. Am J Transl Res 2022; 14:5326-5342. [PMID: 36105058 PMCID: PMC9452348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Mesenchymal stem cells derived from human tissues have been widely used for tissue regeneration because of their strong self-renewal capacity and multi-potential properties. Autophagy plays a vital role in maintaining bone homeostasis. However, the mechanism underlying this role for autophagy in the osteogenic differentiation of mesenchymal stem cells remains to be elucidated. METHODS Two microarray datasets were downloaded from the GEO database. Fourteen bone marrow mesenchymal stem cell samples comprising control and induction groups were selected to identify differentially expressed autophagy-related genes via multiple bioinformatics approaches, followed by functional analysis. Interactions among differentially expressed autophagy genes, miRNAs, and transcription factors were analyzed and visualized using Cytoscape software. The association between hub differentially expressed genes and autophagy was validated by qRT-PCR. RESULTS Ten autophagy-related genes (including VPS8, NDRG4, and CYBB) were identified as osteogenic hub genes. Correlation analysis revealed that CYBB was highly correlated with the sensitivity to multiple drugs, such as imexon, megestrol acetate, and isotretinoin. The regulatory network displayed a complex connection among miRNAs, transcription factors, and differentially expressed autophagy genes. Friends' analysis showed that NDRG4 was highly closely related to other hub genes (P < 0.05). Furthermore, NDRG4 expression was downregulated in the induction group (P < 0.01). NDRG4 was significantly correlated with infiltrating immune cells, including monocytes, eosinophils, type 17 T helper cells, neutrophils, activated CD8 T cells, and immature B cells. Levels of the 10 autophagy-related genes (including VPS8, NDRG4, and CYBB) were successfully validated based on in vitro experiments. CONCLUSION We identified candidate molecules to further investigate their functions in osteogenesis, providing novel insights into the role of autophagy in mesenchymal stem cell differentiation.
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Affiliation(s)
- Yibo Xu
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
- Bioinspired Engineering and Biomechanics Center (BEBC), School of Life Science and Technology, Xi′an Jiaotong UniversityXi’an 710049, Shaan’xi Province, China
| | - Zhimeng Wang
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
| | - Yakang Wang
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
| | - Qiang Huang
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
| | - Cheng Ren
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
- Bioinspired Engineering and Biomechanics Center (BEBC), School of Life Science and Technology, Xi′an Jiaotong UniversityXi’an 710049, Shaan’xi Province, China
| | - Liang Sun
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
| | - Qian Wang
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
| | - Ming Li
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
| | - Hongliang Liu
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
| | - Zhong Li
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
| | - Kun Zhang
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
| | - Teng Ma
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
- Bioinspired Engineering and Biomechanics Center (BEBC), School of Life Science and Technology, Xi′an Jiaotong UniversityXi’an 710049, Shaan’xi Province, China
| | - Yao Lu
- Department of Orthopaedic Surgery, Honghui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaan’xi Province, China
- Bioinspired Engineering and Biomechanics Center (BEBC), School of Life Science and Technology, Xi′an Jiaotong UniversityXi’an 710049, Shaan’xi Province, China
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Chen H, Chen X, Zeng F, Fu A, Huang M. Prognostic value of SOX9 in cervical cancer: Bioinformatics and experimental approaches. Front Genet 2022; 13:939328. [PMID: 36003340 PMCID: PMC9394184 DOI: 10.3389/fgene.2022.939328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Among gynecological cancers, cervical cancer is a common malignancy and remains the leading cause of cancer-related death for women. However, the exact molecular pathogenesis of cervical cancer is not known. Hence, understanding the molecular mechanisms underlying cervical cancer pathogenesis will aid in the development of effective treatment modalities. In this research, we attempted to discern candidate biomarkers for cervical cancer by using multiple bioinformatics approaches. First, we performed differential expression analysis based on cervical squamous cell carcinoma and endocervical adenocarcinoma data from The Cancer Genome Atlas database, then used differentially expressed genes for weighted gene co-expression network construction to find the most relevant gene module for cervical cancer. Next, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed on the module genes, followed by using protein–protein interaction network analysis and Cytoscape to find the key gene. Finally, we validated the key gene by using multiple online sites and experimental methods. Through weighted gene co-expression network analysis, we found the turquoise module was the highest correlated module with cervical cancer diagnosis. The biological process of the module genes focused on cell proliferation, cell adhesion, and protein binding processes, while the Kyoto Encyclopedia of Genes and Genomes pathway of the module significantly enriched pathways related to cancer and cell circle. Among the module genes, SOX9 was identified as the hub gene, and its expression was associated with cervical cancer prognosis. We found the expression of SOX9 correlates with cancer-associated fibroblast immune infiltration in immune cells by Timer2.0. Furthermore, cancer-associated fibroblast infiltration is linked to cervical cancer patients’ prognosis. Compared to those in normal adjacent, immunohistochemical and real-time quantitative polymerase chain reaction (qPCR) showed that the protein and mRNA expression of SOX9 in cervical cancer were higher. Therefore, the SOX9 gene acts as an oncogene in cervical cancer, interactive with immune infiltration of cancer-associated fibroblasts, thereby affecting the prognosis of patients with cervical cancer.
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Affiliation(s)
- Huan Chen
- Department of Obstetrics and Gynecology, Zhu Zhou Central Hospital, Zhuzhou, Hunan China
| | - Xupeng Chen
- Laboratory Medicine Center, Zhu Zhou Central Hospital, Zhuzhou, Hunan China
| | - Fanhua Zeng
- Department of Obstetrics and Gynecology, Zhu Zhou Central Hospital, Zhuzhou, Hunan China
| | - Aizhen Fu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Meiyuan Huang
- Department of Pathology, Zhu Zhou Central Hospital, Zhuzhou, Hunan China
- *Correspondence: Meiyuan Huang,
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