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Wang J, Zhang C, Zhang L, Yao HJ, Liu X, Shi Y, Zhao J, Bo X, Chen H, Li L. Comparative study on genomic and epigenomic profiles of retinoblastoma or tuberous sclerosis complex via nanopore sequencing and a joint screening framework. Cancer Gene Ther 2024; 31:439-453. [PMID: 38146007 DOI: 10.1038/s41417-023-00714-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/27/2023]
Abstract
Recurrence and extraocular metastasis in advanced intraocular retinoblastoma (RB) are still major obstacles for successful treatment of Chinese children. Tuberous sclerosis complex (TSC) is a very rare, multisystemic genetic disorder characterized by hamartomatous growth. In this study, we aimed to compare genomic and epigenomic profiles with human RB or TSC using recently developed nanopore sequencing, and to identify disease-associated variations or genes. Peripheral blood samples were collected from either RB or RB/TSC patients plus their normal siblings, followed by nanopore sequencing and identification of disease-specific structural variations (SVs) and differentially methylated regions (DMRs) by a systematic biology strategy named as multiomics-based joint screening framework. In total, 316 RB- and 1295 TSC-unique SVs were identified, as well as 1072 RB- and 1114 TSC-associated DMRs, respectively. We eventually identified 6 key genes for RB for further functional validation. Knockdown of CDK19 with specific siRNAs significantly inhibited Y79 cellular proliferation and increased sensitivity to carboplatin, whereas downregulation of AHNAK2 promoted the cell growth as well as drug resistance. Those two genes might serve as potential diagnostic markers or therapeutic targets of RB. The systematic biology strategy combined with functional validation might be an effective approach for rare pediatric malignances with limited samples and challenging collection process.
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Affiliation(s)
- Junting Wang
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, P.R. China
| | - Chengyue Zhang
- Department of Ophthalmology, Beijing Children's Hospital affiliated with Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
| | - Li Zhang
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
| | - Hong-Juan Yao
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
| | - Xiaohong Liu
- Guang'anmen Hospital, Chinese Academy of Chinese Medical Sciences, No.5 BeiXianGe St., Beijing, 100053, China
| | - Yuchen Shi
- Dongzhimen Hospital, Beijing University of Chinese Medicine, No.5 Haiyuncang, Beijing, 100700, China
| | - Junyang Zhao
- Department of Ophthalmology, Beijing Children's Hospital affiliated with Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, P.R. China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, P.R. China.
| | - Liang Li
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China.
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Jin C, Wang T, Yang Y, Zhou P, Li J, Wu W, Lv X, Ma G, Wang A. Rational targeting of autophagy in colorectal cancer therapy: From molecular interactions to pharmacological compounds. ENVIRONMENTAL RESEARCH 2023; 227:115721. [PMID: 36965788 DOI: 10.1016/j.envres.2023.115721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/13/2023] [Accepted: 03/18/2023] [Indexed: 05/08/2023]
Abstract
The abnormal progression of tumors has been a problem for treatment of cancer and therapeutic should be directed towards targeting main mechanisms involved in tumorigenesis in tumors. The genomic mutations can result in changes in biological mechanisms in human cancers. Colorectal cancer is one of the most malignant tumors of gastrointestinal tract and its treatment has been faced some difficulties due to development of resistance in tumor cells and also, their malignant behavior. Hence, new therapeutic modalities for colorectal cancer are being investigated. Autophagy is a "self-digestion" mechanism that is responsible for homeostasis preserving in cells and its aberrant activation/inhibition can lead to tumorigenesis. The current review focuses on the role of autophagy mechanism in colorectal cancer. Autophagy may be associated with increase/decrease in progression of colorectal cancer due to mutual function of this molecular mechanism. Pro-survival autophagy inhibits apoptosis to increase proliferation and survival rate of colorectal tumor cells and it is also involved in cancer metastasis maybe due to EMT induction. In contrast, pro-death autophagy decreases growth and invasion of colorectal tumor cells. The status of autophagy (upregulation and down-regulation) is a determining factor for therapy response in colorectal tumor cells. Therefore, targeting autophagy can increase sensitivity of colorectal tumor cells to chemotherapy and radiotherapy. Interestingly, nanoparticles can be employed for targeting autophagy in cancer therapy and they can both induce/suppress autophagy in tumor cells. Furthermore, autophagy modulators can be embedded in nanostructures in improving tumor suppression and providing cancer immunotherapy.
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Affiliation(s)
- Canhui Jin
- Department of Gastrointestinal Surgery, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, PR China
| | - Tianbao Wang
- Department of Gastrointestinal Surgery, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, PR China
| | - Yanhui Yang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, 471003, China
| | - Pin Zhou
- Department of Gastrointestinal Surgery, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, PR China
| | - Juncheng Li
- Department of Gastrointestinal Surgery, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, PR China
| | - Wenhao Wu
- Department of Gastrointestinal Surgery, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, PR China
| | - Xin Lv
- Department of Gastrointestinal Surgery, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, PR China
| | - Guoqing Ma
- Department of Gastrointestinal Surgery, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, PR China
| | - Aihong Wang
- Department of Gastrointestinal Surgery, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, PR China.
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Khakurel A, Lupashin VV. Role of GARP Vesicle Tethering Complex in Golgi Physiology. Int J Mol Sci 2023; 24:6069. [PMID: 37047041 PMCID: PMC10094427 DOI: 10.3390/ijms24076069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 04/14/2023] Open
Abstract
The Golgi associated retrograde protein complex (GARP) is an evolutionarily conserved component of Golgi membrane trafficking machinery that belongs to the Complexes Associated with Tethering Containing Helical Rods (CATCHR) family. Like other multisubunit tethering complexes such as COG, Dsl1, and Exocyst, the GARP is believed to function by tethering and promoting fusion of the endosome-derived small trafficking intermediate. However, even twenty years after its discovery, the exact structure and the functions of GARP are still an enigma. Recent studies revealed novel roles for GARP in Golgi physiology and identified human patients with mutations in GARP subunits. In this review, we summarized our knowledge of the structure of the GARP complex, its protein partners, GARP functions related to Golgi physiology, as well as cellular defects associated with the dysfunction of GARP subunits.
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Affiliation(s)
| | - Vladimir V. Lupashin
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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Zhang Y, Li H, Lv L, Lu K, Li H, Zhang W, Cui T. Autophagy: Dual roles and perspective for clinical treatment of colorectal cancer. Biochimie 2023; 206:49-60. [PMID: 36244578 DOI: 10.1016/j.biochi.2022.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/29/2022] [Accepted: 10/09/2022] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) raises concerns to people because of its high recurrence and metastasis rate, diagnosis challenges, and poor prognosis. Various studies have shown the association of altered autophagy with tumorigenesis, tumor-stroma interactions, and resistance to cancer therapy in CRC. Autophagy is a highly conserved cytosolic catabolic process in eukaryotes that plays distinct roles in CRC occurrence and progression. In early tumorigenesis, autophagy may inhibit tumor growth through diverse mechanisms, whereas it exhibits a tumor promoting function in CRC progression. This different functions of autophagy in CRC occurrence and progression make developing therapies targeting autophagy complicated. In this review, we discuss the classification and process of autophagy as well as its dual roles in CRC, functions in the tumor microenvironment, cross-talk with apoptosis, and potential usefulness as a CRC therapeutic target.
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Affiliation(s)
- Yabin Zhang
- West China Second University Hospital, State Key Laboratory of Biotherapy, Laboratory of Metabolomics and Gynecological Disease Research and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China
| | - Haiyan Li
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Liang Lv
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Huihui Li
- West China Second University Hospital, State Key Laboratory of Biotherapy, Laboratory of Metabolomics and Gynecological Disease Research and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China
| | - Wenli Zhang
- Department of Orthopedics, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Tao Cui
- West China Second University Hospital, State Key Laboratory of Biotherapy, Laboratory of Metabolomics and Gynecological Disease Research and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China.
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Tan Y, He Q, Chan KHK. Identification of shared genetic architecture between non-alcoholic fatty liver disease and type 2 diabetes: A genome-wide analysis. Front Endocrinol (Lausanne) 2023; 14:1050049. [PMID: 37033223 PMCID: PMC10073682 DOI: 10.3389/fendo.2023.1050049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND The incidence of complications of non-alcoholic fatty liver disease (NAFLD) and type 2 diabetes (T2D) has been increasing. METHOD In order to identify the shared genetic architecture of the two disease phenotypes of NAFLD and T2D, a European population-based GWAS summary and a cross-trait meta-analysis was used to identify significant shared genes for NAFLD and T2D. The enrichment of shared genes was then determined through the use of functional enrichment analysis to investigate the relationship between genes and phenotypes. Additionally, differential gene expression analysis was performed, significant differentially expressed genes in NAFLD and T2D were identified, genes that overlapped between those that were differentially expressed and cross-trait results were reported, and enrichment analysis was performed on the core genes that had been obtained in this way. Finally, the application of a bidirectional Mendelian randomization (MR) approach determined the causal link between NAFLD and T2D. RESULT A total of 115 genes were discovered to be shared between NAFLD and T2D in the GWAS analysis. The enrichment analysis of these genes showed that some were involved in the processes such as the decomposition and metabolism of lipids, phospholipids, and glycerophospholipids. Additionally, through the use of differential gene expression analysis, 15 core genes were confirmed to be linked to both T2D and NAFLD. They were correlated with carcinoma cells and inflammation. Furthermore, the bidirectional MR identified a positive causal relationship between NAFLD and T2D. CONCLUSION Our study determined the genetic structure shared between NAFLD and T2D, offering a new reference for the genetic pathogenesis and mechanism of NAFLD and T2D comorbidities.
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Affiliation(s)
- Yajing Tan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Qian He
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Kei Hang Katie Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Epidemiology, Center for Global Cardiometabolic Health, Brown University, Providence, RI, United States
- *Correspondence: Kei Hang Katie Chan,
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Proteomic Analysis Reveals Molecular Differences in the Development of Gastric Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:8266544. [PMID: 35958927 PMCID: PMC9357686 DOI: 10.1155/2022/8266544] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/18/2022] [Accepted: 06/23/2022] [Indexed: 02/08/2023]
Abstract
Gastric cancer (GC) is the 3rd leading cause of death from cancer and the 5th most common cancer worldwide. The detection rate of GC among Tibetans is significantly higher than that in Han Chinese, probably due to differences in their living habits, dietary structure, and environment. Despite such a high disease burden, the epidemiology of gastric cancer has not been studied in this population. Molecular markers are required to aid the diagnosis and treatment of GC. In this study, we collected gastric tissue samples from patients in Tibet with chronic nonatrophic gastritis (CNAG) (n = 6), chronic atrophic gastritis (CAG) (n = 7), gastric intraepithelial neoplasia (GIN) (n = 4), and GC (n = 5). The proteins in each group were analyzed using coupled label-free mass spectrometry. In addition, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein interaction networks were used to analyze the differentially expressed proteins (DEPs) among groups. DEPs were quantified in comparisons of GC versus CNAG (223), GC versus GIN (100), and GIN versus CNAG (341). GO and KEGG analyses showed that the DEPs were mainly associated with immunity (GC versus CNAG) and cancer proliferation and metastasis (GC versus GIN, and GIN versus CNAG). Furthermore, the expression levels of cell proliferation and cytoskeleton-related proteins increased consistently during cancer development, such as ITGA4, DDC, and CPT1A; thus, they are potential diagnostic markers. These results obtained by proteomics analysis could improve our understanding of cancer biology in GC and provide a rich resource for data mining and discovering potential immunotherapy targets.
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Spano D, Colanzi A. Golgi Complex: A Signaling Hub in Cancer. Cells 2022; 11:1990. [PMID: 35805075 PMCID: PMC9265605 DOI: 10.3390/cells11131990] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 02/01/2023] Open
Abstract
The Golgi Complex is the central hub in the endomembrane system and serves not only as a biosynthetic and processing center but also as a trafficking and sorting station for glycoproteins and lipids. In addition, it is an active signaling hub involved in the regulation of multiple cellular processes, including cell polarity, motility, growth, autophagy, apoptosis, inflammation, DNA repair and stress responses. As such, the dysregulation of the Golgi Complex-centered signaling cascades contributes to the onset of several pathological conditions, including cancer. This review summarizes the current knowledge on the signaling pathways regulated by the Golgi Complex and implicated in promoting cancer hallmarks and tumor progression.
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Affiliation(s)
- Daniela Spano
- Institute of Biochemistry and Cell Biology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Antonino Colanzi
- Institute for Endocrinology and Experimental Oncology “G. Salvatore”, National Research Council, 80131 Naples, Italy;
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