1
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Wilson MP, Kentache T, Althoff CR, Schulz C, de Bettignies G, Mateu Cabrera G, Cimbalistiene L, Burnyte B, Yoon G, Costain G, Vuillaumier-Barrot S, Cheillan D, Rymen D, Rychtarova L, Hansikova H, Bury M, Dewulf JP, Caligiore F, Jaeken J, Cantagrel V, Van Schaftingen E, Matthijs G, Foulquier F, Bommer GT. A pseudoautosomal glycosylation disorder prompts the revision of dolichol biosynthesis. Cell 2024; 187:3585-3601.e22. [PMID: 38821050 PMCID: PMC11250103 DOI: 10.1016/j.cell.2024.04.041] [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: 07/12/2023] [Revised: 02/21/2024] [Accepted: 04/29/2024] [Indexed: 06/02/2024]
Abstract
Dolichol is a lipid critical for N-glycosylation as a carrier for activated sugars and nascent oligosaccharides. It is commonly thought to be directly produced from polyprenol by the enzyme SRD5A3. Instead, we found that dolichol synthesis requires a three-step detour involving additional metabolites, where SRD5A3 catalyzes only the second reaction. The first and third steps are performed by DHRSX, whose gene resides on the pseudoautosomal regions of the X and Y chromosomes. Accordingly, we report a pseudoautosomal-recessive disease presenting as a congenital disorder of glycosylation in patients with missense variants in DHRSX (DHRSX-CDG). Of note, DHRSX has a unique dual substrate and cofactor specificity, allowing it to act as a NAD+-dependent dehydrogenase and as a NADPH-dependent reductase in two non-consecutive steps. Thus, our work reveals unexpected complexity in the terminal steps of dolichol biosynthesis. Furthermore, we provide insights into the mechanism by which dolichol metabolism defects contribute to disease.
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Affiliation(s)
- Matthew P Wilson
- Laboratory for Molecular Diagnosis, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Takfarinas Kentache
- Metabolic Research Group, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium; WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Charlotte R Althoff
- Laboratory for Molecular Diagnosis, Center for Human Genetics, KU Leuven, Leuven, Belgium; Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Céline Schulz
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Geoffroy de Bettignies
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Gisèle Mateu Cabrera
- Laboratory for Molecular Diagnosis, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Loreta Cimbalistiene
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Birute Burnyte
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Grace Yoon
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada; Division of Neurology, Hospital for Sick Children, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada; Department of Paediatrics, University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sandrine Vuillaumier-Barrot
- AP-HP, Biochimie Métabolique et Cellulaire and Département de Génétique, Hôpital Bichat-Claude Bernard, and Université de Paris, Faculté de Médecine Xavier Bichat, INSERM U1149, CRI, Paris, France
| | - David Cheillan
- Service Biochimie et Biologie Moléculaire - Hospices Civils de Lyon; Laboratoire Carmen - Inserm U1060, INRAE UMR1397, Université Claude Bernard Lyon 1, Lyon, France
| | - Daisy Rymen
- Department of Pediatrics, Center for Metabolic Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Lucie Rychtarova
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Hana Hansikova
- Laboratory for Study of Mitochondrial Disorders, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine and General University Hospital in Prague, Charles University, Prague, Czechia
| | - Marina Bury
- Metabolic Research Group, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium; WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Joseph P Dewulf
- Metabolic Research Group, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium; WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Francesco Caligiore
- Metabolic Research Group, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium; WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Jaak Jaeken
- Department of Pediatrics, Center for Metabolic Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Vincent Cantagrel
- Developmental Brain Disorders Laboratory, Université Paris Cité, INSERM UMR1163, Imagine Institute, Paris, France
| | - Emile Van Schaftingen
- Metabolic Research Group, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium; WELBIO Department, WEL Research Institute, Wavre, Belgium.
| | - Gert Matthijs
- Laboratory for Molecular Diagnosis, Center for Human Genetics, KU Leuven, Leuven, Belgium.
| | - François Foulquier
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France.
| | - Guido T Bommer
- Metabolic Research Group, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium; WELBIO Department, WEL Research Institute, Wavre, Belgium.
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2
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Li X, Huang Z, Zhu L, Lai W, Li Y, Chen H, Liu D, Huang J, Zhou D, Li Y, Weng W, Xu H, Xu L, Luo Z, Fang J. The potential role of RNA sequencing in diagnosing unexplained insensitivity to conventional chemotherapy in pediatric patients with B-cell acute lymphoblastic leukemia. BMC Med Genomics 2024; 17:149. [PMID: 38811988 PMCID: PMC11137891 DOI: 10.1186/s12920-024-01892-w] [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: 12/24/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Pediatric B-cell acute lymphoblastic leukemia (B-ALL) is a highly heterogeneous disease. According to large-scale RNA sequencing (RNA-seq) data, B-ALL patients can be divided into more than 10 subgroups. However, many genomic defects associated with resistance mechanisms have not yet been identified. As an individual clinical tool for molecular diagnostic risk classification, RNA-seq and gene expression pattern-based therapy could be potential upcoming strategies. In this study, we retrospectively analyzed the RNA-seq gene expression profiles of 45 children whose molecular diagnostic classifications were inconsistent with the response to chemotherapy. The relationship between the transcriptome and chemotherapy response was analyzed. Fusion gene identification was conducted for the included patients who did not have known high-risk associated fusion genes or gene mutations. The most frequently detected fusion gene pair in the high-risk group was the DHRSX duplication, which is a novel finding. Fusions involving ABL1, LMNB2, NFATC1, PAX5, and TTYH3 at onset were more frequently detected in the high-risk group, while fusions involving LFNG, TTYH3, and NFATC1 were frequently detected in the relapse group. According to the pathways involved, the underlying drug resistance mechanism is related to DNA methylation, autophagy, and protein metabolism. Overall, the implementation of an RNA-seq diagnostic system will identify activated markers associated with chemotherapy response, and guide future treatment adjustments.
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Affiliation(s)
- Xinyu Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Zaoli Huang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Liwen Zhu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Weixin Lai
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Yunyao Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Han Chen
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Diandian Liu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Dunhua Zhou
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Yang Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Wenjun Weng
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Honggui Xu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Luhong Xu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China.
| | - Zhenhua Luo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China.
| | - Jianpei Fang
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China.
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3
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Zhao H, Wei Y, Zhang J, Zhang K, Tian L, Liu Y, Zhang S, Zhou Y, Wang Z, Shi S, Fu Z, Fu J, Zhao J, Li X, Zhang L, Zhao L, Liu K. HPV16 infection promotes the malignant transformation of the esophagus and progression of esophageal squamous cell carcinoma. J Med Virol 2023; 95:e29132. [PMID: 37792307 DOI: 10.1002/jmv.29132] [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: 06/06/2023] [Revised: 07/27/2023] [Accepted: 09/05/2023] [Indexed: 10/05/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) may be correlated with HPV infection, and the mechanism underlying the ESCC formation induced by HPV16 infection remains elusive. Here, we overexpressed HPV16 E6 and E7 and coordinated the overexpression of these two genes in EPC2 and ESCC cells. We found that E7 and coordinated expression of E6 and E7 promoted the proliferation of EPC2 cells, and upregulation of shh was responsible for cell proliferation since the use of vismodegib led to the failure of organoid formation. Meanwhile, overexpression of E6 and E7 in ESCC cells promoted cell proliferation, migration, and invasion in vitro. Importantly, E6 and E7 coordinately increased the capability of tumor growth in nude mice, while vismodegib slowed the growth of tumors in NCG mice. Moreover, a series of genes and proteins changed in cell lines after overexpression of the E6 and E7 genes, the potential biological processes and pathways were systematically analyzed using a bioinformatics assay. Together, these findings suggest that the activation of the hedgehog pathway induced by HPV16 infection may initially transform basal cells in the esophagus and promote following malignant processes in ESCC cells. The application of hedgehog inhibitors may represent a therapeutic avenue for ESCC treatment.
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Affiliation(s)
- Hongzhou Zhao
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
- School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Yuxuan Wei
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
- School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Jiaying Zhang
- School of Life Science, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Kun Zhang
- Department of General Surgery, The First Hospital of Fuzhou, Fuzhou, Fujian, People's Republic of China
| | - Liming Tian
- Department of Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yongpan Liu
- School of Life Science, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Shihui Zhang
- Centre for Translational Stem Cell Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Yijian Zhou
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
- School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Zhuo Wang
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
- School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Songlin Shi
- School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Zhichao Fu
- Department of Radiotherapy, 900 Hospital of the Joint Logistics Team (Dongfang Hospital, Xiamen University), Fuzhou, Fujian, People's Republic of China
| | - Jianqian Fu
- Department of Medical Oncology, The Fifth Hospital of Xiamen, Xiamen, Fujian, People's Republic of China
| | - Jing Zhao
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
- School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Xinxin Li
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
- School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Lijia Zhang
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Liran Zhao
- School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Kuancan Liu
- Central Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
- School of Medicine, Xiamen University, Xiamen, Fujian, People's Republic of China
- School of Life Science, Nanchang Normal University, Nanchang, Jiangxi, People's Republic of China
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4
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Jima DD, Skaar DA, Planchart A, Motsinger-Reif A, Cevik SE, Park SS, Cowley M, Wright F, House J, Liu A, Jirtle RL, Hoyo C. Genomic map of candidate human imprint control regions: the imprintome. Epigenetics 2022; 17:1920-1943. [PMID: 35786392 PMCID: PMC9665137 DOI: 10.1080/15592294.2022.2091815] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Imprinted genes – critical for growth, metabolism, and neuronal function – are expressed from one parental allele. Parent-of-origin-dependent CpG methylation regulates this expression at imprint control regions (ICRs). Since ICRs are established before tissue specification, these methylation marks are similar across cell types. Thus, they are attractive for investigating the developmental origins of adult diseases using accessible tissues, but remain unknown. We determined genome-wide candidate ICRs in humans by performing whole-genome bisulphite sequencing (WGBS) of DNA derived from the three germ layers and from gametes. We identified 1,488 hemi-methylated candidate ICRs, including 19 of 25 previously characterized ICRs (https://humanicr.org/). Gamete methylation approached 0% or 100% in 332 ICRs (178 paternally and 154 maternally methylated), supporting parent-of-origin-specific methylation, and 65% were in well-described CTCF-binding or DNaseI hypersensitive regions. This draft of the human imprintome will allow for the systematic determination of the role of early-acquired imprinting dysregulation in the pathogenesis of human diseases and developmental and behavioural disorders.
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Affiliation(s)
- Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - David A Skaar
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Antonio Planchart
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Sebnem E Cevik
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Sarah S Park
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.,Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Michael Cowley
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Fred Wright
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - John House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Andy Liu
- Department of Neurology, Duke University, School of Medicine, Durham, NC, USA
| | - Randy L Jirtle
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
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5
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Li J, Yu C, Ni S, Duan Y. Identification of Core Genes and Screening of Potential Targets in Intervertebral Disc Degeneration Using Integrated Bioinformatics Analysis. Front Genet 2022; 13:864100. [PMID: 35711934 PMCID: PMC9196128 DOI: 10.3389/fgene.2022.864100] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/22/2022] [Indexed: 12/27/2022] Open
Abstract
Background: Intervertebral disc degeneration (IDD), characterized by diverse pathological changes, causes low back pain (LBP). However, prophylactic and delaying treatments for IDD are limited. The aim of our study was to investigate the gene network and biomarkers of IDD and suggest potential therapeutic targets. Methods: Differentially expressed genes (DEGs) associated with IDD were identified by analyzing the mRNA, miRNA, and lncRNA expression profiles of IDD cases from the Gene Expression Omnibus (GEO). The protein–protein interaction (PPI) network, Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis as well as miRNA–lncRNA–mRNA networks were conducted. Moreover, we obtained 71 hub genes and performed a comprehensive analysis including GO, KEGG, gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), Disease Ontology (DO), methylation analysis, receiver operating characteristic (ROC) curve analysis, immune infiltration analysis, and potential drug identification. We finally used qRT-PCR to verify 13 significant DEGs in normal and degenerative nucleus pulposus cells (NPCs). Results: We identified 305 DEGs closely related to IDD. The GO and KEGG analyses indicated that changes in IDD are significantly associated with enrichment of the inflammatory and immune response. GSEA analysis suggested that cell activation involved in the inflammatory immune response amide biosynthetic process was the key for the development of IDD. The GSVA suggested that DNA repair, oxidative phosphorylation, peroxisome, IL-6-JAK-STAT3 signaling, and apoptosis were crucial in the development of IDD. Among the 71 hub genes, the methylation levels of 11 genes were increased in IDD. A total of twenty genes showed a high functional similarity and diagnostic value in IDD. The result of the immune cell infiltration analysis indicated that seven genes were closely related to active natural killer cells. The most relevant targeted hub genes for potential drug or molecular compounds were MET and PIK3CD. Also, qRT-PCR results showed that ARHGAP27, C15orf39, DEPDC1, DHRSX, MGAM, SLC11A1, SMC4, and LINC00887 were significantly downregulated in degenerative NPCs; H19, LINC00685, mir-185-5p, and mir-4306 were upregulated in degenerative NPCs; and the expression level of mir-663a did not change significantly in normal and degenerative NPCs. Conclusion: Our findings may provide new insights into the functional characteristics and mechanism of IDD and aid the development of IDD therapeutics.
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Affiliation(s)
- Jianjun Li
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Cheng Yu
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Songjia Ni
- Department of Orthopaedic Trauma, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yang Duan
- Department of Spine Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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6
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Touati R, Tajouri A, Mesaoudi I, Oueslati AE, Lachiri Z, Kharrat M. New methodology for repetitive sequences identification in human X and Y chromosomes. Biomed Signal Process Control 2021; 64:102207. [PMID: 33101452 PMCID: PMC7572123 DOI: 10.1016/j.bspc.2020.102207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 07/23/2020] [Accepted: 09/01/2020] [Indexed: 11/24/2022]
Abstract
Repetitive DNA sequences occupy the major proportion of DNA in the human genome and even in the other species' genomes. The importance of each repetitive DNA type depends on many factors: structural and functional roles, positions, lengths and numbers of these repetitions are clear examples. Conserving such DNA sequences or not in different locations in the chromosome remains a challenge for researchers in biology. Detecting their location despite their great variability and finding novel repetitive sequences remains a challenging task. To side-step this problem, we developed a new method based on signal and image processing tools. In fact, using this method we could find repetitive patterns in DNA images regardless of the repetition length. This new technique seems to be more efficient in detecting new repetitive sequences than bioinformatics tools. In fact, the classical tools present limited performances especially in case of mutations (insertion or deletion). However, modifying one or a few numbers of pixels in the image doesn't affect the global form of the repetitive pattern. As a consequence, we generated a new repetitive patterns database which contains tandem and dispersed repeated sequences. The highly repetitive sequences, we have identified in X and Y chromosomes, are shown to be located in other human chromosomes or in other genomes. The data we have generated is then taken as input to a Convolutional neural network classifier in order to classify them. The system we have constructed is efficient and gives an average of 94.4% as recognition score.
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Affiliation(s)
- Rabeb Touati
- University of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis (FMT), Tunisia
- University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, Le Belvédère, 1002, Tunis, Tunisia
| | - Asma Tajouri
- University of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis (FMT), Tunisia
| | - Imen Mesaoudi
- University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, Le Belvédère, 1002, Tunis, Tunisia
| | - Afef Elloumi Oueslati
- University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, Le Belvédère, 1002, Tunis, Tunisia
| | - Zied Lachiri
- University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, Le Belvédère, 1002, Tunis, Tunisia
| | - Maher Kharrat
- University of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis (FMT), Tunisia
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7
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Dai C, Xu P, Liu S, Xu S, Xu J, Fu Z, Cao J, Lv M, Zhou J, Liu G, Zhang H, Jia X. Long noncoding RNA ZEB1-AS1 affects paclitaxel and cisplatin resistance by regulating MMP19 in epithelial ovarian cancer cells. Arch Gynecol Obstet 2020; 303:1271-1281. [PMID: 33151424 DOI: 10.1007/s00404-020-05858-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/21/2020] [Indexed: 01/27/2023]
Abstract
PURPOSE The long noncoding RNA (lncRNA) ZEB1-AS1 is reported overexpressed in sensitive ovarian cancer cells A2780 compared with paclitaxel (PTX)-and cisplatin (DDP)- resistant. However, the function and mechanism of ZEB1-AS1 in EOC cells still unknown. METHODS We used quantitative real-time PCR (qPCR) to detect ZEB1-AS1 expression in A2780 and A2780/R cells. A combination of siRNA, plasmids, CCK8 and flow cytometry was used to detect the effect of ZEB1-AS1 on ovarian cancer cell A2780 PTX and DDP resistance. Transcriptome sequencing, qPCR, and western blot were used for further mechanistic studies. RESULTS ZEB1-AS1 depletion using siRNA in chemosensitive A2780 cells significantly increased PTX and DDP resistance. In contrast, ZEB1-AS1 overexpression in PTX- and DDP-resistant A2780/resistant (A2780/R) cells reversed the observed drug resistance. Thus, ZEB1-AS1 plays an important role in PTX and DDP resistance in EOC cells. However, quantitative real-time PCR (qPCR) and western blot results suggested that ZEB1-AS1 did not regulate chemoresistance through regulation of ZEB1 protein. We used sequencing to detect mRNA expression changes in A2780 cells after ZEB1-AS1 silencing. The results indicated that MMP19 was the likely downstream factor of ZEB1-AS1. We further examined whether ZEB1-AS1 played an important role in chemoresistance by silencing MMP19 in ZEB1-AS1-overexpressing cells. CCK8 assay results suggested that MMP19 knockdown promoted ZEB1-AS1-induced chemoresistance to PTX and DDP in A2780 cells. CONCLUSION This study is the first to reveal that ZEB1-AS1 plays a pivotal role in cancer chemoresistance.
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Affiliation(s)
- Chencheng Dai
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China.,Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Pengfei Xu
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Siyu Liu
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China.,Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Sujuan Xu
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Juan Xu
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China.,Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Ziyi Fu
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Jian Cao
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Mingming Lv
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Juan Zhou
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Guangquan Liu
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China.,Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Huilin Zhang
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Xuemei Jia
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China.
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8
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Tower J, Pomatto LCD, Davies KJA. Sex differences in the response to oxidative and proteolytic stress. Redox Biol 2020; 31:101488. [PMID: 32201219 PMCID: PMC7212483 DOI: 10.1016/j.redox.2020.101488] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 02/20/2020] [Accepted: 02/29/2020] [Indexed: 12/16/2022] Open
Abstract
Sex differences in diseases involving oxidative and proteolytic stress are common, including greater ischemic heart disease, Parkinson disease and stroke in men, and greater Alzheimer disease in women. Sex differences are also observed in stress response of cells and tissues, where female cells are generally more resistant to heat and oxidative stress-induced cell death. Studies implicate beneficial effects of estrogen, as well as cell-autonomous effects including superior mitochondrial function and increased expression of stress response genes in female cells relative to male cells. The p53 and forkhead box (FOX)-family genes, heat shock proteins (HSPs), and the apoptosis and autophagy pathways appear particularly important in mediating sex differences in stress response.
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Affiliation(s)
- John Tower
- Molecular and Computational Biology Program, Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA; Leonard Davis School of Gerontology, Ethel Percy Andrus Gerontology Center, University of Southern California, Los Angeles, CA90089, USA.
| | - Laura C D Pomatto
- National Institute on General Medical Sciences, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kelvin J A Davies
- Molecular and Computational Biology Program, Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA; Leonard Davis School of Gerontology, Ethel Percy Andrus Gerontology Center, University of Southern California, Los Angeles, CA90089, USA; Department of Biochemistry & Molecular Medicine, Keck School of Medicine of USC, University of Southern California, USA
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9
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Abou-Fadel J, Vasquez M, Grajeda B, Ellis C, Zhang J. Systems-wide analysis unravels the new roles of CCM signal complex (CSC). Heliyon 2019; 5:e02899. [PMID: 31872111 PMCID: PMC6909108 DOI: 10.1016/j.heliyon.2019.e02899] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/17/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022] Open
Abstract
Cerebral cavernous malformations (CCMs) are characterized by abnormally dilated intracranial capillaries that result in increased susceptibility to stroke. Three genes have been identified as causes of CCMs; KRIT1 (CCM1), MGC4607 (CCM2) and PDCD10 (CCM3); one of them is disrupted in most CCM cases. It was demonstrated that both CCM1 and CCM3 bind to CCM2 to form a CCM signaling complex (CSC) to modulate angiogenesis. In this report, we deployed both RNA-seq and proteomic analysis of perturbed CSC after depletion of one of three CCM genes to generate interactomes for system-wide studies. Our results demonstrated a unique portrait detailing alterations in angiogenesis and vascular integrity. Interestingly, only in-direct overlapped alterations between RNA and protein levels were detected, supporting the existence of multiple layers of regulation in CSC cascades. Notably, this is the first report identifying that both β4 integrin and CAV1 signaling are downstream of CSC, conveying the angiogenic signaling. Our results provide a global view of signal transduction modulated by the CSC, identifies novel regulatory signaling networks and key cellular factors associated with CSC.
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Affiliation(s)
- Johnathan Abou-Fadel
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, TX, 79905, USA
| | - Mariana Vasquez
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, TX, 79905, USA
| | - Brian Grajeda
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, TX, 79905, USA
| | - Cameron Ellis
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, TX, 79905, USA
| | - Jun Zhang
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, El Paso, TX, 79905, USA
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10
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Weng S, Stoner SA, Zhang DE. Sex chromosome loss and the pseudoautosomal region genes in hematological malignancies. Oncotarget 2018; 7:72356-72372. [PMID: 27655702 PMCID: PMC5342167 DOI: 10.18632/oncotarget.12050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/07/2016] [Indexed: 11/25/2022] Open
Abstract
Cytogenetic aberrations, such as chromosomal translocations, aneuploidy, and amplifications, are frequently detected in hematological malignancies. For many of the common autosomal aberrations, the mechanisms underlying their roles in cancer development have been well-characterized. On the contrary, although loss of a sex chromosome is observed in a broad range of hematological malignancies, how it cooperates in disease development is less understood. Nevertheless, it has been postulated that tumor suppressor genes reside on the sex chromosomes. Although the X and Y sex chromosomes are highly divergent, the pseudoautosomal regions are homologous between both chromosomes. Here, we review what is currently known about the pseudoautosomal region genes in the hematological system. Additionally, we discuss implications for haploinsufficiency of critical pseudoautosomal region sex chromosome genes, driven by sex chromosome loss, in promoting hematological malignancies. Because mechanistic studies on disease development rely heavily on murine models, we also discuss the challenges and caveats of existing models, and propose alternatives for examining the involvement of pseudoautosomal region genes and loss of a sex chromosome in vivo. With the widespread detection of loss of a sex chromosome in different hematological malignances, the elucidation of the role of pseudoautosomal region genes in the development and progression of these diseases would be invaluable to the field.
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Affiliation(s)
- Stephanie Weng
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Samuel A Stoner
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Dong-Er Zhang
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.,Department of Pathology and Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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