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Du Q, Zhang M, Gao A, He T, Guo M. Epigenetic silencing ZSCAN23 promotes pancreatic cancer growth by activating Wnt signaling. Cancer Biol Ther 2024; 25:2302924. [PMID: 38226836 PMCID: PMC10793710 DOI: 10.1080/15384047.2024.2302924] [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: 11/06/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most malignant tumor. Zinc finger and SCAN domain-containing protein 23 (ZSCAN23) is a new member of the SCAN domain family. The expression regulation and biological function remain to be elucidated. In this study, we explored the epigenetic regulation and the function of ZSCAN23 in PDAC. ZSCAN23 was methylated in 60.21% (171/284) of PDAC and its expression was regulated by promoter region methylation. The expression of ZSCAN23 inhibited cell proliferation, colony formation, migration, invasion, and induced apoptosis and G1/S phase arrest. ZSCAN23 suppressed Panc10.05 cell xenograft growth in mice. Mechanistically, ZSCAN23 inhibited Wnt signaling by interacting with myosin heavy chain 9 (MYH9) in pancreatic cancer cells. ZSCAN23 is frequently methylated in PDAC and may serve as a detective marker. ZSCAN23 suppresses PDAC cell growth both in vitro and in vivo.
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Affiliation(s)
- Qian Du
- Department of Gastroenterology and Hepatology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, People's Republic of China
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Meiying Zhang
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Aiai Gao
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Tao He
- Department of Pathology, Characteristic Medical Center of the Chinese People's Armed Police Force, Tianjin, People's Republic of China
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
- National Key Laboratory of Kidney Diseases, the First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
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Zhang H, Han B, Tian S, Gong Y, Liu L. ZNF740 facilitates the malignant progression of hepatocellular carcinoma via the METTL3/HIF‑1A signaling axis. Int J Oncol 2024; 65:105. [PMID: 39301659 PMCID: PMC11436261 DOI: 10.3892/ijo.2024.5693] [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: 01/25/2024] [Accepted: 07/11/2024] [Indexed: 09/22/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the second leading cause of cancer‑related death, and efficient treatments to facilitate recovery and enhance long‑term outcomes are lacking. Zinc finger proteins (ZNFs), known as the largest group of transcription factors, have gained interest for their roles in HCC by stimulating the transcription of well‑known tumor‑causing genes. However, the specific roles and molecular mechanisms of ZNF740 in HCC remain unknown. The present study performed bioinformatics analysis and RNA‑sequencing analysis of differentially expressed genes in HCC, detected ZNF740 expression levels in HCC using reverse transcription‑quantitative PCR, western blotting and immunohistochemistry, and explored the effects of ZNF740 on the progression of liver cancer in vitro and in vivo using cellular functionality assays and cell‑derived xenografts. In addition, a dual‑luciferase reporter assay was performed to analyze the binding of ZNF740 with the METTL3 promoter. Furthermore, cell functionality experiments were performed to analyze whether ZNF740 promotes the proliferation of liver cancer cells in a METTL3‑dependent manner. Bioinformatics and immunoprecipitation assays were further used to analyze the molecular mechanism of ZNF740 in liver cancer. The present study demonstrated that ZNF740 expression was upregulated in HCC. Mechanistically, overexpressed ZNF740 interacted with the methyltransferase‑like 3 (METTL3) promoter and increased METTL3 expression, leading to the stabilization of hypoxia‑inducible factor‑1A (HIF1A) mRNA in an N6‑methyladenosine/YTH N6‑methyladenosine RNA‑binding protein 1‑dependent manner. Eventually, the ZNF740/METTL3/HIF1A signaling axis may facilitate the proliferation, invasion and metastasis of liver cancer via METTL3/HIF‑1A signaling. The present findings revealed the important role of ZNF740 and suggested a potential therapeutic approach that might improve clinical therapies for liver cancer.
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Affiliation(s)
- Hao Zhang
- College of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 561113, P.R. China
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550000, P.R. China
| | - Bing Han
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, Guizhou 561113, P.R. China
| | - She Tian
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550000, P.R. China
| | - Yongjun Gong
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550000, P.R. China
| | - Li Liu
- School of Public Health, Guizhou Medical University, Guiyang, Guizhou 561113, P.R. China
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Xie W, Bao Z, Yao D, Yang Y. Overexpression of ZFP69B promotes hepatocellular carcinoma growth by upregulating the expression of TLX1 and TRAPPC9. Cell Div 2024; 19:27. [PMID: 39261946 PMCID: PMC11391796 DOI: 10.1186/s13008-024-00131-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 08/29/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND T-cell leukemia homeobox protein 1 (TLX1) has been revealed as a hub transcription factor in leukemia, while its function in hepatocellular carcinoma (HCC) has not been well described. Here, we investigated the regulation and function of TLX1 in HCC. METHODS TLX1 and its possible upstream and downstream molecules in HCC were identified using bioinformatics tools, which were then verified by RT-qPCR assay. CCK-8, wound healing, and Transwell invasion assays were performed to detect the effects of TLX1 knockdown on HCC cells. The interactions between TLX1 and trafficking protein particle complex subunit 9 (TRAPPC9) or Zinc finger protein 69 homolog B (ZFP69B) were further probed by ChIP and luciferase reporter assays. Rescue experiments were finally conducted in vitro and in vivo. RESULTS TLX1 was highly expressed in HCC cells, and the knockdown of TLX1 led to reduced malignant biological behavior of HCC cells. TLX1 bound to the promoter region of TRAPPC9, thereby promoting TRAPPC9 expression. Overexpression of TRAPPC9 attenuated the effect of TLX1 reduction on suppressing malignant behavior of HCC cells. ZFP69B was also highly expressed in HCC cells and bound to the promoter region of TLX1 to induce TLX1 expression. Knockdown of ZFP69B inhibited the viability and mobility of HCC cells in vitro and tumor growth in vivo, and overexpression of TLX1 rescued this inhibition. CONCLUSION These findings suggest that ZFP69B promotes the proliferation of HCC cells by directly upregulating the expression of TLX1 and the ensuing TRAPPC9.
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Affiliation(s)
- Wei Xie
- Department of General Surgery, Jurong Hospital Affiliated to Jiangsu University, Zhenjiang, Jiangsu, 212400, P.R. China
| | - Zhongming Bao
- Department of Hepatobiliary Surgery, Huai'an Fifth People's Hospital, Huaiyin, Jiangsu, 223300, P.R. China
| | - Dan Yao
- Department of Gastrointestinal Surgery, Huai'an Second People's Hospital (Huai'an Hospital Affiliated to Xuzhou Medical University), Huai'an, Jiangsu, 223001, P.R. China
| | - Yong Yang
- Department of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Xuzhou Medical University, No. 99, Huaihai West Road, Quanshan District, Xuzhou, Jiangsu, 221000, P.R. China.
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4
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Wu M, Li B, Shi L, Yang L, Liang C, Wang T, Sheng X. RNA sequencing and multiplexed immunohistochemistry reveal the factors for postoperative recurrence of stage IB-IIA cervical squamous cell carcinoma. Discov Oncol 2024; 15:422. [PMID: 39254825 PMCID: PMC11387578 DOI: 10.1007/s12672-024-01283-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024] Open
Abstract
BACKGROUND Stage IB-IIA Cervical Squamous Cell Carcinoma (CSCC) presents diverse clinical outcomes, the mechanisms that cause recurrence in CC patients remain unclear. The goal of this study was to identify predictive biomarkers leading to tumor recurrence in IB-IIA CSCC after surgical treatment by comparing the transcriptional and immune landscape between the recurrence and non-recurrence group. METHODS We performed mRNA sequencing and multiplexed immunohistochemistry (mIHC) analysis among stage IB-IIA patients with or without recurrence after surgical resection and were followed-up for a median of three years. RESULTS Integrated analysis indicates that the upregulated gene expression in zinc finger proteins, the activation of the PI3K/Akt pathway, and the low infiltration level of T follicular helper cells and B-cells may serve as potential recurrent biomarkers for CSCC. We also observed significant differences in the immune and genomic landscape between two groups. CONCLUSIONS These findings provide new insights into the relapse mechanisms of CSCC, which could potentially guide clinical exploration of drug targets.
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Affiliation(s)
- Meiyao Wu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China
- Department of Gynecologic Oncology Research Office, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China
- Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Baixue Li
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China
- Department of Gynecologic Oncology Research Office, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China
- Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China
| | - Lina Shi
- Medical Department, Nanjing Geneseeq Technology Inc., Nanjing, 211899, China
| | - Lingling Yang
- Medical Department, Nanjing Geneseeq Technology Inc., Nanjing, 211899, China
| | - Chuqiao Liang
- Medical Department, Nanjing Geneseeq Technology Inc., Nanjing, 211899, China
| | - Tianhong Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China.
- Department of Gynecologic Oncology Research Office, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China.
- Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China.
| | - Xiujie Sheng
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China.
- Department of Gynecologic Oncology Research Office, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China.
- Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China.
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China.
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Feng H, Liu J, Jia H, Bu X, Yang W, Su P. Cancer-associated fibroblasts-derived exosomal ZNF250 promotes the proliferation, migration, invasion, and immune escape of hepatocellular carcinoma cells by transcriptionally activating PD-L1. J Biochem Mol Toxicol 2024; 38:e23778. [PMID: 39252517 DOI: 10.1002/jbt.23778] [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: 04/28/2024] [Revised: 06/18/2024] [Accepted: 07/14/2024] [Indexed: 09/11/2024]
Abstract
Hepatocellular carcinoma (HCC) is a lethal form of liver cancer, and the tumor microenvironment, particularly cancer-associated fibroblasts (CAFs), plays a critical role in its progression. This study aimed to elucidate the mechanism by which CAF-derived exosomes regulate the development of HCC. The study employed quantitative real-time polymerase chain reaction for mRNA expression analysis and western blot analysis for protein expression detection. Chromatin immunoprecipitation assay and dual-luciferase reporter assay were performed to investigate the relationship between zinc finger protein 250 (ZNF250) and programmed cell death 1 ligand 1 (PD-L1). Transmission electron microscopy and western blot analysis were used to characterize the isolated exosomes. The transferability of CAF-derived exosomes and normal fibroblasts (NFs)-derived exosomes into HCC cells was analyzed using a green fluorescent labeling dye PKH67. Cell proliferation was assessed via a 5-Ethynyl-2'-deoxyuridine assay, while Transwell assays were conducted to evaluate cell migration and invasion. Flow cytometry was performed to measure cell apoptosis, while enzyme-linked immunosorbent assays were used to assess the levels of tumor necrosis factor-α and perforin. Finally, a xenograft mouse model was constructed to examine the effects of exosomes derived from ZNF250-deficient CAFs on the tumor properties of HCC cells. The study revealed increased expression of ZNF250 in HCC tissues and cells, with ZNF250 transcriptionally activating PD-L1 in HCC cells. ZNF250 expression was associated with HbsAg, clinical stage and tumor size of HCC patients. CAF-derived exosomal ZNF250 can regulate PD-L1 expression in HCC cells. Furthermore, exosomes derived from ZNF250-deficient CAFs inhibited the proliferation, migration, invasion, and immune escape of HCC cells by downregulating PD-L1 expression. Moreover, CAF-derived exosomal ZNF250 promoted tumor formation in vivo. These findings provide insights into the role of CAF-derived exosomes in the suppression of HCC development, highlighting the significance of ZNF250 and PD-L1 regulation in tumor progression.
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Affiliation(s)
- Huizhi Feng
- Department of Gastroenterology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jingmei Liu
- Department of Gastroenterology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Haixia Jia
- Department of Scientific Research, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Xiaoqian Bu
- Department of Digestive System Cancer Center, Shanxi Bethune Hospital, Taiyuan, China
| | - Wenhui Yang
- Department of Gastroenterology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Peng Su
- Department of Medical Service, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
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Badhe MR, Das P, Sahoo S, Paul A, Sahoo PK, Reddy RRK, Suryawanshi AR, Nandanpawar PC, Das Mahapatra K, Nagpure NS, Goswami M, Mohanty J. Physiological Responses to Acute Heat Stress in Rohu, Labeo rohita: Insights from Liver Proteomics. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10360-6. [PMID: 39207653 DOI: 10.1007/s10126-024-10360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Heat stress is a major problem in aquaculture species, causing changes in physiology such as decreased feed intake, growth rate, reproduction, and internal cellular damage, thereby affecting fish's health. The effects of an acute heat stress simulating a daily rise and fall in temperature on summer days were evaluated in the liver proteome of rohu (Labeo rohita) fingerlings in the present study. The fish maintained at 30 °C were gradually exposed to a higher temperature of 36 °C at an increment rate of 1 °C per 1.5 h, and after 3 h at that temperature, it was gradually reduced to 30 °C. The liver tissue samples were collected at 5 am, 5 pm, and 5 am the next day from the exposed and control fish. Protein samples were prepared from the liver tissues, and the extracted proteins were compared using 2-dimensional (2D) gel electrophoresis (2DGE) and mass spectrometry (MS) using a MALDI-TOF/TOF mass spectrometer. A total of 44 differentially expressed protein spots were visualized in 2D gel analysis from heat stress exposed fish at three time points, out of which 21 proteins including one hypothetical protein could be identified by MS. The abundance of five selected differentially expressed proteins (DEPs) was validated using qPCR. The majority of DEPs were found to be involved primarily in lipid, protein and energy metabolism, immune system regulation, cytoskeletal stability, and ROS management. The findings of this study would help in the development of strategies to mitigate heat stress in L. rohita.
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Affiliation(s)
- Mohan R Badhe
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Priyanka Das
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Sonalina Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Anirban Paul
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Pramoda Kumar Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | | | | | | | - Kanta Das Mahapatra
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Naresh S Nagpure
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, India
| | - Mukunda Goswami
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, India
| | - Jyotirmaya Mohanty
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India.
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Zhu J, Qiu X, Jin X, Nie X, Ou S, Wu G, Shen J, Zhang R. ZNF468-mediated epigenetic upregulation of VEGF-C facilitates lymphangiogenesis and lymphatic metastasis in ESCC via PI3K/Akt and ERK1/2 signaling pathways. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00976-0. [PMID: 39141315 DOI: 10.1007/s13402-024-00976-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 08/15/2024] Open
Abstract
PURPOSE Dysfunctional lymphangiogenesis is pivotal for various pathological processes including tumor lymph node metastasis which is a crucial cause of therapeutic failure for ESCC. In this study, we aim to elucidate the molecular mechanisms and clinical relevance of Zinc-finger protein ZNF468 in lymphangiogenesis and lymphatic metastasis in ESCC. METHODS Immunohistochemistry, Western blot, Kaplan-Meier plotter analysis and Gene Set Enrichment Analysis were preformed to detect the association of ZNF468 with lymphangiogenesis and poor prognosis in ESCC patients. Foot-pads lymph node metastasis model, tube formation assay, 3D-culture assay and invasion assay were preformed to verify the effect of ZNF468 on lymphangiogenesis and lymph node metastasis. CUT&Tag analysis, immunoprecipitation and mass spectrometry analysis and ChIP-PCR assay were preformed to study the molecular mechanisms of ZNF468 in lymphangiogenesis. RESULTS We found that ectopic expression of ZNF468 was correlated with higher microlymphatic vessel density in ESCC tissues, leading to poorer prognosis of ESCC patients. ZNF468 enhanced the capacity of lymphangiogenesis and promoted lymphatic metastasis in ESCC both in vitro and in vivo. However, silencing ZNF468 reversed these phenotypes in ESCC. Mechanically, we demonstrated that ZNF468 recruits the histone modification factors (PRMT1/HAT1) to increase the levels of H4R2me2a and H3K9ac, which then leads to the recruitment of the transcription initiation complex on the VEGF-C promoter, ultimately promoting the upregulation of VEGF-C transcription. Strikingly, the promoting effect of lymphatic metastasis induced by ZNF468 in ESCC was abrogated by targeting PRMT1 using Arginine methyltransferase inhibitor-1 or silencing VEGF-C. Furthermore, we found that the activation of PI3K/AKT and ERK1/2 signaling is required for ZNF468-medicated lymphatic metastasis in ESCC. Importantly, the clinical relevance between ZNF468 and VEGF-C were confirmed not only in ESCC samples and but also in multiple cancer types. CONCLUSION Our results identified a precise mechanism underlying ZNF468-induced epigenetic upregulation of VEGF-C in facilitating lymphangiogenesis and lymph node metastasis of ESCC, which might provide a novel prognostic biomarker and potential therapeutic for ESCC patients.
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Affiliation(s)
- Jinrong Zhu
- Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiangyu Qiu
- Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xin Jin
- Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaoya Nie
- Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, China
| | - Shengming Ou
- Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, China
| | - Geyan Wu
- Biomedicine Research Centre, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provicial Clinical Research Center for Obsterics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Jianfei Shen
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Taizhou, China.
| | - Rongxin Zhang
- Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, China.
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Park JE, Patnaik BB, Sang MK, Song DK, Jeong JY, Hong CE, Kim YT, Shin HJ, Ziwei L, Patnaik HH, Hwang HJ, Park SY, Kang SW, Ko JH, Lee JS, Park HS, Jo YH, Han YS, Lee YS. Transcriptome sequencing of the endangered land snail Karaftohelix adamsi from the Island Ulleung: De novo assembly, annotation, valuation of fitness genes and SSR markers. Genes Genomics 2024; 46:851-870. [PMID: 38809491 DOI: 10.1007/s13258-024-01511-z] [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: 06/12/2023] [Accepted: 03/08/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND The Bradybaenidae snail Karaftohelix adamsi is endemic to Korea, with the species tracked from Island Ulleung in North Gyeongsang Province of South Korea. K. adamsi has been classified under the Endangered Wildlife Class II species of Korea and poses a severe risk of extinction following habitat disturbances. With no available information at the DNA (genome) or mRNA (transcriptome) level for the species, conservation by utilizing informed molecular resources seems difficult. OBJECTIVE In this study, we used the Illumina short-read sequencing and Trinity de novo assembly to draft the reference transcriptome of K. adamsi. RESULTS After assembly, 13,753 unigenes were obtained of which 10,511 were annotated to public databases (a maximum of 10,165 unigenes found homologs in PANM DB). A total of 6,351, 3,535, 358, and 3,407 unigenes were ascribed to the functional categories under KOG, GO, KEGG, and IPS, respectively. The transcripts such as the HSP 70, aquaporin, TLR, and MAPK, among others, were screened as putative functional resources for adaptation. DNA transposons were found to be thickly populated in comparison to retrotransposons in the assembled unigenes. Further, 2,164 SSRs were screened with the promiscuous presence of dinucleotide repeats such as AC/GT and AG/CT. CONCLUSION The transcriptome-guided discovery of molecular resources in K. adamsi will not only serve as a basis for functional genomics studies but also provide sustainable tools to be utilized for the protection of the species in the wild. Moreover, the development of polymorphic SSRs is valuable for the identification of species from newer habitats and cross-species genotyping.
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Affiliation(s)
- Jie Eun Park
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Bharat Bhusan Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
- PG Department of Biosciences and Biotechnology, Fakir Mohan University, Nuapadhi, Balasore, Odisha, 756089, India
| | - Min Kyu Sang
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Dae Kwon Song
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Jun Yang Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Chan Eui Hong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Yong Tae Kim
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Hyeon Jun Shin
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Liu Ziwei
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Hongray Howrelia Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- PG Department of Zoology, BJB Autonomous College, Bhubaneswar, Odisha, 751014, India
| | - Hee Ju Hwang
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - So Young Park
- Biodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, South Korea
| | - Se Won Kang
- Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, South Korea
| | - Jung Ho Ko
- Police Science Institute, Korean National Police University, Asan, 31539, Chungnam, Korea
| | - Jun Sang Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD, 621-6 Banseok-Dong, Yuseong-Gu, Daejeon, 34069, Korea
| | - Yong Hun Jo
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-Ro, Buk-Gu, Gwangju, 61186, South Korea
| | - Yong Seok Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea.
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea.
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9
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Zhou H, Liu L, Pang Y, Xu Y, Wu J, Ma F, Jin P, Zhou X. Relish-mediated C2H2 zinc finger protein IMZF restores Drosophila immune homeostasis via inhibiting the transcription of Imd/Tak1. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 170:104138. [PMID: 38762126 DOI: 10.1016/j.ibmb.2024.104138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 05/20/2024]
Abstract
The dysregulation of intensity and duration in innate immunity can result in detrimental effects on the body, emphasizing the crucial need for precise regulation. However, the intricate and accurate nature of innate immunity implies the existence of numerous undiscovered innate immunomodulators, particularly transcription factors. In this study, we have identified a Drosophila C2H2 zinc finger protein CG18262, named Immune-mediated Zinc Finger protein (IMZF), capable of suppressing immune responses of Imd pathway. Mechanistically, IMZF serves as a transcription factor that represses the expression of Imd and Tak1. Intriguingly, our findings also reveal that Relish, an NF-κB transcription factor, positively regulates the expression of IMZF, consequently inhibiting the activation of Imd and Tak1 to prevent an exaggerated immune response. Additionally, we have elucidated the pivotal role played by the Relish-IMZF-Imd/Tak1 axis in restoring immune homeostasis of Drosophila Imd pathway. In summary, our findings not only unveil a novel C2H2 zinc finger immunoregulatory transcription factor, IMZF, along with its specific mechanism of immune regulation, but also shed light on the dual functionality of Relish in different stages of the immune response by modulating distinct effectors. This discovery provides new insights and enlightenment into the complex regulation of Drosophila innate immunity.
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Affiliation(s)
- Hongjian Zhou
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Li Liu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Yujia Pang
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Yina Xu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Jing Wu
- Department of Psychology, College of Victoria College, University of Toronto, Toronto, ON, M5R 0A3, Canada
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Xue Zhou
- School of Chemistry and Biological Engineering, Nanjing Normal University Taizhou College, Taizhou, 225300, China.
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10
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Zhang J, Wang Y, Hou S, Chi X, Ding D, Xue M, Zhang M, Wang J, Shuai J, Sun H, Gao Q, Kang C. Overexpression of ZNF169 promotes the growth and proliferation of colorectal cancer cells via the upregulation of ANKZF1. Oncol Rep 2024; 51:82. [PMID: 38666541 PMCID: PMC11063753 DOI: 10.3892/or.2024.8741] [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: 09/11/2023] [Accepted: 04/05/2024] [Indexed: 05/01/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies worldwide. The 5‑year survival rate of patients diagnosed with the early stages of the disease is markedly higher than that of patients in the advanced stages. Therefore, identifying novel biomarkers and drug targets for CRC is critical for clinical practice. Zinc finger protein 169 (ZNF169) is a crucial transcription factor, and its role in CRC remains to be explored. The present study aimed to investigate the clinical relevance, function and underlying mechanisms of ZNF169 in CRC growth and proliferation. The Cancer Genome Atlas (TCGA) database was utilized to analyze the clinical relevance of ZNF169 in patients with CRC. Immunohistochemical staining was performed on tissue samples from patients with CRC to detect the expression of ZNF169. The HCT‑116, HT‑29 and RKO cell lines were employed for in vitro experiments. The overexpression and knockdown of ZNF169 were achieved by transfecting the cells with lentivirus and small interfering RNAs, respectively. Cell Counting Kit‑8, colony formation and EdU staining assays were applied to investigate the function of ZNF169 in CRC cells. Dual luciferase activity and chromatin immunoprecipitation (ChIP)‑quantitative PCR (qPCR) assays were performed to identify the regulatory effects of ZNF169 on the ankyrin repeat and zinc‑finger domain‑containing 1 (ANKZF1; also known as ZNF744) gene. Reverse transcription‑quantitative PCR and western blot analysis were performed to measure mRNA and protein expression, respectively. The analysis of TCGA data revealed a positive correlation between ZNF169 and ANKZF1, with the overexpression of ANKZF1 being associated with a poor prognosis of patients with CRC. The experimental results demonstrated that ZNF169 was expression upregulated in CRC tissue compared with that in normal colon tissue. Gain‑of‑function and loss‑of‑function experiments revealed that ZNF169 enhanced the intensity of EdU staining, promoting the growth and proliferation of CRC cells. Furthermore, the overexpression of ZNF169 potentiated the transcriptional activity of the ANKZF1 gene, while the knockdown of ZNF169 produced the opposite results. ChIP‑qPCR confirmed the interaction between ZNF169 and the promoter sequence of ANKZF1. Rescue experiments revealed that ZNF169 accelerated CRC cell growth and proliferation through the upregulation of ANKZF1. Furthermore, there was a positive correlation identified between ZNF169 and ANKZF1, and upregulation of ANKZF1 expression was associated with the poor prognosis of patients with CRC. On the whole, the present study demonstrates that ZNF169 contributes to CRC malignancy by potentiating the expression of ANKZF1. Thus, the regulation of ZNF169 and/or ANKZF1 expression may represent a viable strategy for the treatment patients with CRC with a high expression of ZNF169.
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Affiliation(s)
- Jie Zhang
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Ye Wang
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Shiyang Hou
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Xiaoqian Chi
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Danyang Ding
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Mei Xue
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Mengqiao Zhang
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Jing Wang
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Junfang Shuai
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Haiying Sun
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Qiang Gao
- Department of Gastroenterology and Hepatology, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
| | - Chunbo Kang
- Department of Surgery, Center of Gastrointestinal Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, P.R. China
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11
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Zhang J, Chen C, Geng Q, Li H, Wu M, Chan B, Wang S, Sheng W. ZNF263 cooperates with ZNF31 to promote the drug resistance and EMT of pancreatic cancer through transactivating RNF126. J Cell Physiol 2024; 239:e31259. [PMID: 38515383 DOI: 10.1002/jcp.31259] [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: 12/08/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/23/2024]
Abstract
The poor prognosis of pancreatic ductal adenocarcinoma (PDAC) is attribute to the aggressive local invasion, distant metastasis and drug resistance of PDAC patients, which was strongly accelerated by epithelial-mesenchymal transition (EMT). In current study, we systematically investigate the role of ZNF263/RNF126 axis in the initiation of EMT in PDAC in vitro and vivo. ZNF263 is firstly identified as a novel transactivation factor of RNF126. Both ZNF263 and RNF126 were overexpressed in PDAC tissues, which were associated with multiple advanced clinical stages and poor prognosis of PDAC patients. ZNF263 overexpression promoted cell proliferation, drug resistance and EMT in vitro via activating RNF126 following by the upregulation of Cyclin D1, N-cad, and MMP9, and the downregulation of E-cad, p21, and p27. ZNF263 silencing contributed to the opposite phenotype. Mechanistically, ZNF263 transactivated RNF126 via binding to its promoter. Further investigations revealed that ZNF263 interacted with ZNF31 to coregulate the transcription of RNF126, which in turn promoted ubiquitination-mediated degradation of PTEN. The downregulation of PTEN activated AKT/Cyclin D1 and AKT/GSK-3β/β-catenin signaling, thereby promoting the malignant phenotype of PDAC. Finally, the coordination of ZNF263 and RNF126 promotes subcutaneous tumor size and distant liver metastasis in vivo. ZNF263, as an oncogene, promotes proliferation, drug resistance and EMT of PDAC through transactivating RNF126.
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Affiliation(s)
- Jiawei Zhang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Chuanping Chen
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Qilong Geng
- Department of Clinical Medicine, The First Clinical College, Anhui Medical University, Hefei, Anhui, China
| | - Haoyu Li
- Department of Clinical Medicine, The First Clinical College, Anhui Medical University, Hefei, Anhui, China
| | - Mengcheng Wu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Boyuan Chan
- Department of Clinical Medicine, The First Clinical College, Anhui Medical University, Hefei, Anhui, China
| | - Shiyang Wang
- Department of Geriatric Surgery, The First Hospital, China Medical University, Shenyang, China
| | - Weiwei Sheng
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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12
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Teng Y, Xu J, Wang Y, Wen N, Ye H, Li B. Combining a glycolysis‑related prognostic model based on scRNA‑Seq with experimental verification identifies ZFP41 as a potential prognostic biomarker for HCC. Mol Med Rep 2024; 29:78. [PMID: 38516783 PMCID: PMC10975023 DOI: 10.3892/mmr.2024.13203] [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: 10/23/2023] [Accepted: 02/27/2024] [Indexed: 03/23/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a common malignancy with a poor prognosis, and its heterogeneity affects the response to clinical treatments. Glycolysis is highly associated with HCC therapy and prognosis. The present study aimed to identify a novel biomarker for HCC by exploring the heterogeneity of glycolysis in HCC. The intersection of both marker genes of glycolysis‑related cell clusters from single‑cell RNA sequencing analysis and mRNA data of liver HCC from The Cancer Genome Atlas were used to construct a prognostic model through Cox proportional hazard regression and the least absolute shrinkage and selection operator Cox regression. Data from the International Cancer Genome Consortium were used to validate the results of the analysis. Immune status analysis was then conducted. A significant gene in the prognostic model was identified as a potential biomarker and was verified through in vitro experiments. The results revealed that the glycolysis‑related prognostic model divided patients with HCC into high‑ and low‑risk groups. A nomogram combining the model and clinical features exhibited accurate predictive ability, with an area under the curve of 0.763 at 3 years. The high‑risk group exhibited a higher expression of checkpoint genes and lower tumor immune dysfunction and exclusion scores, suggesting that this group may be more likely to benefit from immunotherapy. The tumor tissues had a higher zinc finger protein (ZFP)41 mRNA and protein expression compared with the adjacent tissues. In vitro analyses revealed that ZFP41 played a crucial role in cell viability, proliferation, migration, invasion and glycolysis. On the whole, the present study demonstrates that the glycolysis‑related prognostic gene, ZFP41, is a potential prognostic biomarker and therapeutic target, and may play a crucial role in glycolysis and malignancy in HCC.
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Affiliation(s)
- Yu Teng
- West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jianrong Xu
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yaoqun Wang
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Division of Biliary Tract Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ningyuan Wen
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Division of Biliary Tract Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Hui Ye
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Division of Biliary Tract Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Bei Li
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Division of Biliary Tract Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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13
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St. Peter C, Hossain WA, Lovell S, Rafi SK, Butler MG. Mowat-Wilson Syndrome: Case Report and Review of ZEB2 Gene Variant Types, Protein Defects and Molecular Interactions. Int J Mol Sci 2024; 25:2838. [PMID: 38474085 PMCID: PMC10932183 DOI: 10.3390/ijms25052838] [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: 11/21/2023] [Revised: 01/12/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Mowat-Wilson syndrome (MWS) is a rare genetic neurodevelopmental congenital disorder associated with various defects of the zinc finger E-box binding homeobox 2 (ZEB2) gene. The ZEB2 gene is autosomal dominant and encodes six protein domains including the SMAD-binding protein, which functions as a transcriptional corepressor involved in the conversion of neuroepithelial cells in early brain development and as a mediator of trophoblast differentiation. This review summarizes reported ZEB2 gene variants, their types, and frequencies among the 10 exons of ZEB2. Additionally, we summarized their corresponding encoded protein defects including the most common variant, c.2083 C>T in exon 8, which directly impacts the homeodomain (HD) protein domain. This single defect was found in 11% of the 298 reported patients with MWS. This review demonstrates that exon 8 encodes at least three of the six protein domains and accounts for 66% (198/298) of the variants identified. More than 90% of the defects were due to nonsense or frameshift changes. We show examples of protein modeling changes that occurred as a result of ZEB2 gene defects. We also report a novel pathogenic variant in exon 8 in a 5-year-old female proband with MWS. This review further explores other genes predicted to be interacting with the ZEB2 gene and their predicted gene-gene molecular interactions with protein binding effects on embryonic multi-system development such as craniofacial, spine, brain, kidney, cardiovascular, and hematopoiesis.
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Affiliation(s)
- Caroline St. Peter
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, 3901 Rainbow Blvd. MS 4015, Kansas City, KS 66160, USA; (C.S.P.); (W.A.H.); (S.K.R.)
| | - Waheeda A. Hossain
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, 3901 Rainbow Blvd. MS 4015, Kansas City, KS 66160, USA; (C.S.P.); (W.A.H.); (S.K.R.)
| | - Scott Lovell
- Protein Structure Laboratory, University of Kansas, Lawrence, KS 66047, USA;
| | - Syed K. Rafi
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, 3901 Rainbow Blvd. MS 4015, Kansas City, KS 66160, USA; (C.S.P.); (W.A.H.); (S.K.R.)
| | - Merlin G. Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, 3901 Rainbow Blvd. MS 4015, Kansas City, KS 66160, USA; (C.S.P.); (W.A.H.); (S.K.R.)
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14
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Han Y, Jung KJ, Kim U, Jeon CI, Lee K, Jee SH. Non-invasive biomarkers for early diagnosis of pancreatic cancer risk: metabolite genomewide association study based on the KCPS-II cohort. J Transl Med 2023; 21:878. [PMID: 38049855 PMCID: PMC10694897 DOI: 10.1186/s12967-023-04670-x] [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: 08/15/2023] [Accepted: 10/27/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Pancreatic cancer is a lethal disease with a high mortality rate. The difficulty of early diagnosis is one of its primary causes. Therefore, we aimed to discover non-invasive biomarkers that facilitate the early diagnosis of pancreatic cancer risk. METHODS The study subjects were randomly selected from the Korean Cancer Prevention Study-II and matched by age, sex, and blood collection point [pancreatic cancer incidence (n = 128) vs. control (n = 256)]. The baseline serum samples were analyzed by non-targeted metabolomics, and XGBoost was used to select significant metabolites related to pancreatic cancer incidence. Genomewide association study for the selected metabolites discovered valuable single nucleotide polymorphisms (SNPs). Moderation and mediation analysis were conducted to explore the variables related to pancreatic cancer risk. RESULTS Eleven discriminant metabolites were selected by applying a cut-off of 4.0 in XGBoost. Five SNP presented significance in metabolite-GWAS (p ≤ 5 × 10-6) and logistic regression analysis. Among them, the pair metabolite of rs2370981, rs55870181, and rs72805402 displayed a different network pattern with clinical/biochemical indicators on comparison with allelic carrier and non-carrier. In addition, we demonstrated the indirect effect of rs59519100 on pancreatic cancer risk mediated by γ-glutamyl tyrosine, which affects the smoking status. The predictive ability for pancreatic cancer on the model using five SNPs and four pair metabolites with the conventional risk factors was the highest (AUC: 0.738 [0.661-0.815]). CONCLUSIONS Signatures involving metabolites and SNPs discovered in the present research may be closely associated with the pathogenesis of pancreatic cancer and for use as predictive biomarkers allowing early pancreatic cancer diagnosis and therapy.
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Affiliation(s)
- Youngmin Han
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, Republic of Korea
| | - Keum Ji Jung
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, Republic of Korea
| | - Unchong Kim
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, Republic of Korea
| | - Chan Il Jeon
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, Republic of Korea
| | - Kwangbae Lee
- Korea Medical Institute, Seoul, Republic of Korea
| | - Sun Ha Jee
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, Republic of Korea.
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15
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da Silva Lima F, da Silva Gonçalves CE, Fock RA. A review of the role of zinc finger proteins on hematopoiesis. J Trace Elem Med Biol 2023; 80:127290. [PMID: 37659124 DOI: 10.1016/j.jtemb.2023.127290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 09/04/2023]
Abstract
The bone marrow is responsible for producing an incredible number of cells daily in order to maintain blood homeostasis through a process called hematopoiesis. Hematopoiesis is a greatly demanding process and one entirely dependent on complex interactions between the hematopoietic stem cell (HSC) and its surrounding microenvironment. Zinc (Zn2+) is considered an important trace element, playing diverse roles in different tissues and cell types, and zinc finger proteins (ZNF) are proteins that use Zn2+ as a structural cofactor. In this way, the ZNF structure is supported by a Zn2+ that coordinates many possible combinations of cysteine and histidine, with the most common ZNF being of the Cys2His2 (C2H2) type, which forms a family of transcriptional activators that play an important role in different cellular processes such as development, differentiation, and suppression, all of these being essential processes for an adequate hematopoiesis. This review aims to shed light on the relationship between ZNF and the regulation of the hematopoietic tissue. We include works with different designs, including both in vitro and in vivo studies, detailing how ZNF might regulate hematopoiesis.
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Affiliation(s)
- Fabiana da Silva Lima
- Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Ricardo Ambrósio Fock
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
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16
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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17
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Xiao Q, Lan Z, Zhang S, Ren H, Wang S, Wang P, Feng L, Li D, Wang C, Bai X, Zhang J. Overexpression of ZNF488 supports pancreatic cancer cell proliferation and tumorigenesis through inhibition of ferroptosis via regulating SCD1-mediated unsaturated fatty acid metabolism. Biol Direct 2023; 18:77. [PMID: 37986084 PMCID: PMC10658979 DOI: 10.1186/s13062-023-00421-6] [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: 06/28/2023] [Accepted: 10/02/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Pancreatic cancer is a malignancy with high mortality. Once diagnosed, effective treatment strategies are limited and the five-year survival is extremely poor. Recent studies have shown that zinc finger proteins play important roles in tumorigenesis, including pancreatic cancer. However, it remains unknown on the clinical significance, function and underlying mechanisms of zinc finger protein 488 (ZNF488) during the development of pancreatic cancer. METHODS The clinical relevance of ZNF488 and stearoyl-CoA desaturase 1 (SCD1) was examined by analyzing the data from The Cancer Genome Atlas (TCGA) and immunohistochemical staining of the tissue microarray. Gain-of-function and loss-of-function experiments were performed by transfecting the cells with overexpressing lentivirus and siRNAs or shRNA lentivirus, respectively. The function of ZNF488 in pancreatic cancer was assessed by CCK8, colony formation, EdU staining, PI/Annexin V staining and xenografted tumorigenesis. Chip-qPCR assay was conducted to examine the interaction between ZNF488 and the promoter sequence of SCD1. Transcription activity was measured by dual luciferase reporter assay. mRNA and protein expression was detected by qRT-PCR and immunoblotting experiment, respectively. Fatty acid was quantified by gas chromatography mass spectrometry. RESULTS ZNF488 was overexpressed in pancreatic cancer samples compared with normal tissues. High expression of ZNF488 predicted the poor prognosis of the patients. In vitro, ZNF488 upregulation contributed to the EuU cooperation, proliferation and colony formation of MIAPaCa-2 and PANC-1 cells. Based on PI/Annexin V and trypan blue staining results, we showed that ZNF488 suppressed the ferroptosis and apoptosis of pancreatic cancer cells. Mechanistically, ZNF488 directly interacted with the promoter sequence of SCD1 gene and promoted its transcription activity, which resulted in enhanced palmitoleic and oleic acid production, as well as the peroxidation of fatty acid. In vivo, ZNF488 overexpression promoted the xenograted tumorigenesis of PANC-1, which was reversed by SCD1 knockdown. Importantly, combination of erastin and SCD1 inhibitors A939572 completely blunted the growth of ZNF488 overexpressed MIAPaCa-2 and PANC-1 cells. Usage of A939572 or erastin recovered the sensitivity of pancreatic cancer cells to the treatment of gemcitabine. Lastly, we found a positive correlation between ZNF488 and SCD1 in pancreatic cancer patients based on TCGA and immunohistochemical staining results. CONCLUSION Overexpression of ZNF488 suppresses the ferroptosis and apoptosis to support the growth and tumorigenesis of pancreatic cancer through augmentation of SCD1-mediated unsaturated fatty acid metabolism. Combination of SCD1 inhibitors, ferroptosis inducers or gemcitabine could be applied for the treatment of pancreatic cancer with overexpression of ZNF488.
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Affiliation(s)
- Qifeng Xiao
- Pancreatic and gastric surgery department, National Cancer Center/National clinical research center for cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhongmin Lan
- Pancreatic and gastric surgery department, National Cancer Center/National clinical research center for cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shuisheng Zhang
- Pancreatic and gastric surgery department, National Cancer Center/National clinical research center for cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hu Ren
- Pancreatic and gastric surgery department, National Cancer Center/National clinical research center for cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shunda Wang
- Pancreatic and gastric surgery department, National Cancer Center/National clinical research center for cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peng Wang
- Pancreatic and gastric surgery department, National Cancer Center/National clinical research center for cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Dan Li
- State Key Laboratory of Molecular Oncology, Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chengfeng Wang
- Pancreatic and gastric surgery department, National Cancer Center/National clinical research center for cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaofeng Bai
- Pancreatic and gastric surgery department, National Cancer Center/National clinical research center for cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jianwei Zhang
- Pancreatic and gastric surgery department, National Cancer Center/National clinical research center for cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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18
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Jayathirtha M, Jayaweera T, Whitham D, Sullivan I, Petre BA, Darie CC, Neagu AN. Two-Dimensional-PAGE Coupled with nLC-MS/MS-Based Identification of Differentially Expressed Proteins and Tumorigenic Pathways in MCF7 Breast Cancer Cells Transfected for JTB Protein Silencing. Molecules 2023; 28:7501. [PMID: 38005222 PMCID: PMC10673289 DOI: 10.3390/molecules28227501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
The identification of new cancer-associated genes/proteins, the characterization of their expression variation, the interactomics-based assessment of differentially expressed genes/proteins (DEGs/DEPs), and understanding the tumorigenic pathways and biological processes involved in BC genesis and progression are necessary and possible by the rapid and recent advances in bioinformatics and molecular profiling strategies. Taking into account the opinion of other authors, as well as based on our own team's in vitro studies, we suggest that the human jumping translocation breakpoint (hJTB) protein might be considered as a tumor biomarker for BC and should be studied as a target for BC therapy. In this study, we identify DEPs, carcinogenic pathways, and biological processes associated with JTB silencing, using 2D-PAGE coupled with nano-liquid chromatography tandem mass spectrometry (nLC-MS/MS) proteomics applied to a MCF7 breast cancer cell line, for complementing and completing our previous results based on SDS-PAGE, as well as in-solution proteomics of MCF7 cells transfected for JTB downregulation. The functions of significant DEPs are analyzed using GSEA and KEGG analyses. Almost all DEPs exert pro-tumorigenic effects in the JTBlow condition, sustaining the tumor suppressive function of JTB. Thus, the identified DEPs are involved in several signaling and metabolic pathways that play pro-tumorigenic roles: EMT, ERK/MAPK, PI3K/AKT, Wnt/β-catenin, mTOR, C-MYC, NF-κB, IFN-γ and IFN-α responses, UPR, and glycolysis/gluconeogenesis. These pathways sustain cancer cell growth, adhesion, survival, proliferation, invasion, metastasis, resistance to apoptosis, tight junctions and cytoskeleton reorganization, the maintenance of stemness, metabolic reprogramming, survival in a hostile environment, and sustain a poor clinical outcome. In conclusion, JTB silencing might increase the neoplastic phenotype and behavior of the MCF7 BC cell line. The data is available via ProteomeXchange with the identifier PXD046265.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Taniya Jayaweera
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Isabelle Sullivan
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Brîndușa Alina Petre
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
- Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 11, 700506 Iasi, Romania
- Center for Fundamental Research and Experimental Development in Translation Medicine–TRANSCEND, Regional Institute of Oncology, 700483 Iasi, Romania
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I Bvd. No. 22, 700505 Iasi, Romania
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19
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Li M, Li D, Lin L, Wang P, Zhao W. Precise Interference of RNA-Protein Interaction by CRISPR-Cas13-Mediated Peptide Competition. ACS Synth Biol 2023; 12:2827-2833. [PMID: 37708031 DOI: 10.1021/acssynbio.3c00287] [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] [Indexed: 09/16/2023]
Abstract
RNA-protein interactions are essential nodes of cellular regulatory circuits and play critical roles in normal physiology and disease. However, the precise roles of individual RNA-protein interactions remain elusive. Here we report a method for precise interference of endogenous RNA interacting with the RNA binding protein (RBP). TTP is an RBP that recognizes the AU-rich element (ARE) of mRNA via the binding domain TZF and represses gene expression. We engineer Cas13b, a class 2 type VI CRISPR-Cas endonuclease that exclusively targets RNA, to direct the peptide of TZF to the binding site and compete with endogenous TTP. We show that this tool specifically interferes with TTP interacting with the PIM1 and IL-2 3' UTR under the guidance of the gRNA specific for the AREs. Further, precise interference with the TTP-PIM1 interaction exerts a distinct effect on cell proliferation compared to transcriptome-wide interference. Thus, our work establishes a tool for deep understanding of RNA-RBP interactions.
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Affiliation(s)
- Meng Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Dan Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Leiruo Lin
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Panpan Wang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Wenxue Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
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20
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Chiwina K, Xiong H, Bhattarai G, Dickson RW, Phiri TM, Chen Y, Alatawi I, Dean D, Joshi NK, Chen Y, Riaz A, Gepts P, Brick M, Byrne PF, Schwartz H, Ogg JB, Otto K, Fall A, Gilbert J, Shi A. Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection. Int J Mol Sci 2023; 24:15300. [PMID: 37894980 PMCID: PMC10607830 DOI: 10.3390/ijms242015300] [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: 08/29/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The common bean (Phaseolus vulgaris L.) is a globally cultivated leguminous crop. Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. phaseoli (Fop), is a significant disease leading to substantial yield loss in common beans. Disease-resistant cultivars are recommended to counteract this. The objective of this investigation was to identify single nucleotide polymorphism (SNP) markers associated with FW resistance and to pinpoint potential resistant common bean accessions within a core collection, utilizing a panel of 157 accessions through the Genome-wide association study (GWAS) approach with TASSEL 5 and GAPIT 3. Phenotypes for Fop race 1 and race 4 were matched with genotypic data from 4740 SNPs of BARCBean6K_3 Infinium Bea Chips. After ranking the 157-accession panel and revealing 21 Fusarium wilt-resistant accessions, the GWAS pinpointed 16 SNPs on chromosomes Pv04, Pv05, Pv07, Pv8, and Pv09 linked to Fop race 1 resistance, 23 SNPs on chromosomes Pv03, Pv04, Pv05, Pv07, Pv09, Pv10, and Pv11 associated with Fop race 4 resistance, and 7 SNPs on chromosomes Pv04 and Pv09 correlated with both Fop race 1 and race 4 resistances. Furthermore, within a 30 kb flanking region of these associated SNPs, a total of 17 candidate genes were identified. Some of these genes were annotated as classical disease resistance protein/enzymes, including NB-ARC domain proteins, Leucine-rich repeat protein kinase family proteins, zinc finger family proteins, P-loopcontaining nucleoside triphosphate hydrolase superfamily, etc. Genomic prediction (GP) accuracy for Fop race resistances ranged from 0.26 to 0.55. This study advanced common bean genetic enhancement through marker-assisted selection (MAS) and genomic selection (GS) strategies, paving the way for improved Fop resistance.
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Affiliation(s)
- Kenani Chiwina
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Gehendra Bhattarai
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Ryan William Dickson
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Theresa Makawa Phiri
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Yilin Chen
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Ibtisam Alatawi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Derek Dean
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Neelendra K. Joshi
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Yuyan Chen
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Awais Riaz
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Paul Gepts
- Department of Plant Sciences, University of California, 1 Shields Avenue, Davis, CA 95616, USA;
| | - Mark Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Patrick F. Byrne
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Howard Schwartz
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA; (H.S.); (K.O.)
| | - James B. Ogg
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Kristin Otto
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA; (H.S.); (K.O.)
| | - Amy Fall
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Jeremy Gilbert
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
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21
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Mao XC, Shi S, Yan LJ, Wang HC, Ding ZN, Liu H, Pan GQ, Zhang X, Han CL, Tian BW, Wang DX, Tan SY, Dong ZR, Yan YC, Li T. A model based on adipose and muscle-related indicators evaluated by CT images for predicting microvascular invasion in HCC patients. Biomark Res 2023; 11:87. [PMID: 37794517 PMCID: PMC10548702 DOI: 10.1186/s40364-023-00527-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND AND AIM The presence of microvascular invasion (MVI) will impair the surgical outcome of hepatocellular carcinoma (HCC). Adipose and muscle tissues have been confirmed to be associated with the prognosis of HCC. We aimed to develop and validate a nomogram based on adipose and muscle related-variables for preoperative prediction of MVI in HCC. METHODS One hundred fifty-eight HCC patients from institution A (training cohort) and 53 HCC patients from institution B (validation cohort) were included, all of whom underwent preoperative CT scan and curative resection with confirmed pathological diagnoses. Least absolute shrinkage and selection operator (LASSO) logistic regression was applied to data dimensionality reduction and screening. Nomogram was constructed based on the independent variables, and evaluated by external validation, calibration curve, receiver operating characteristic (ROC) curve and decision curve analysis (DCA). RESULTS Histopathologically identified MVI was found in 101 of 211 patients (47.9%). The preoperative imaging and clinical variables associated with MVI were visceral adipose tissue (VAT) density, intramuscular adipose tissue index (IMATI), skeletal muscle (SM) area, age, tumor size and cirrhosis. Incorporating these 6 factors, the nomogram achieved good concordance index of 0.79 (95%CI: 0.72-0.86) and 0.75 (95%CI: 0.62-0.89) in training and validation cohorts, respectively. In addition, calibration curve exhibited good consistency between predicted and actual MVI probabilities. ROC curve and DCA of the nomogram showed superior performance than that of models only depended on clinical or imaging variables. Based on the nomogram score, patients were divided into high (> 273.8) and low (< = 273.8) risk of MVI presence groups. For patients with high MVI risk, wide-margin resection or anatomical resection could significantly improve the 2-year recurrence free survival. CONCLUSION By combining 6 preoperative independently predictive factors of MVI, a nomogram was constructed. This model provides an optimal preoperative estimation of MVI risk in HCC patients, and may help to stratify high-risk individuals and optimize clinical decision making.
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Affiliation(s)
- Xin-Cheng Mao
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Shuo Shi
- Department of Radiology, Qilu Hospital, Shandong University, Jinan, China
| | - Lun-Jie Yan
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Han-Chao Wang
- Institute for Financial Studies, Shandong University, Jinan, 250100, China
| | - Zi-Niu Ding
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Hui Liu
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Guo-Qiang Pan
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Xiao Zhang
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Cheng-Long Han
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Bao-Wen Tian
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Dong-Xu Wang
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Si-Yu Tan
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Zhao-Ru Dong
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Yu-Chuan Yan
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China
| | - Tao Li
- Department of General Surgery, Qilu Hospital, Shandong University, 107 West Wen Hua Road, Jinan, 250012, China.
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22
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He Z, Zhong Y, Hu H, Li F. ZFP64 Promotes Gallbladder Cancer Progression through Recruiting HDAC1 to Activate NOTCH1 Signaling Pathway. Cancers (Basel) 2023; 15:4508. [PMID: 37760477 PMCID: PMC10527061 DOI: 10.3390/cancers15184508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/26/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The lack of meaningful and effective early-stage markers remains the major challenge in the diagnosis of gallbladder cancer (GBC) and a huge barrier to timely treatment. Zinc finger protein 64 (ZFP64), a member of the zinc finger protein family, is considered to be a promising predictor in multiple tumors, but its potential effect in GBC still remains unclear. Here, we identified that ZFP64 was a vital regulatory protein in GBC. We found that ZFP64 expressed higher in GBC gallbladder carcinoma tissues than in normal tissues and was positively correlated with poor prognosis. Furthermore, ZFP64 was responsible for the migration, invasion, proliferation, anti-apoptosis, and epithelial mesenchymal transition (EMT) of GBC cells in vitro and in vivo. Mechanistically, through Co-IP assay, we confirmed that ZFP64 recruits HDAC1 localized to the promoter region of NUMB for deacetylation and therefore inhibits NUMB expression. The downregulation of NUMB enhanced the activation of the Notch1 signaling pathway, which is indispensable for the GBC-promotion effect of ZFP64 on GBC. In conclusion, ZFP64 regulated GBC progression and metastasis through upregulating the Notch1 signaling pathway, and thus ZFP64 is expected to become a new focus for a GBC prognostic marker and targeted therapy.
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Affiliation(s)
- Zhiqiang He
- Department of Biliary Surgery, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Yuhan Zhong
- Laboratory of Liver Transplantation, Key Laboratory of Transplant Engineering and Immunology, National Health Commission (NHC), West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Haijie Hu
- Department of Biliary Surgery, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Fuyu Li
- Department of Biliary Surgery, West China Hospital, Sichuan University, Chengdu 610041, China;
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23
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Stoyanov D, Stoyanov GS, Ivanov MN, Spasov RH, Tonchev AB. Transcription Factor Zbtb20 as a Regulator of Malignancy and Its Practical Applications. Int J Mol Sci 2023; 24:13763. [PMID: 37762065 PMCID: PMC10530547 DOI: 10.3390/ijms241813763] [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: 08/03/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
Zbtb20 (zinc finger and BTB domain-containing protein 20) is a transcription factor with a zinc finger DNA binding domain and a BTB domain responsible for protein-protein interaction. Recently, this TF has received attention because new data showed its pivotal involvement in normal neural development and its regulatory effects on proliferation and differentiation in different tissues. Zbtb20 was shown to increase proliferation and migration and confer resistance to apoptosis in the contexts of many malignant tumors like hepatocellular carcinoma, non-small-cell lung carcinoma, gastric adenocarcinoma, glioblastoma multiforme, breast cancer, and acute myeloid leukemia. The involvement of Zbtb20 in tumor biology is best studied in hepatocellular carcinoma, where it is a promising candidate as an immunohistochemical tumor marker or may be used in patient screening. Here we review the current data connecting Zbtb20 with malignant tumors.
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Affiliation(s)
- Dimo Stoyanov
- Department of Anatomy and Cell Biology, Medical University of Varna, 9000 Varna, Bulgaria
| | - George S. Stoyanov
- Department of Clinical Pathology, Complex Oncology Center, 9700 Shumen, Bulgaria
| | - Martin N. Ivanov
- Department of Anatomy and Cell Biology, Medical University of Varna, 9000 Varna, Bulgaria
- Department of Stem Cell Biology, Research Institute, Medical University of Varna, 9000 Varna, Bulgaria
| | - Radoslav H. Spasov
- Department of Anatomy and Cell Biology, Medical University of Varna, 9000 Varna, Bulgaria
| | - Anton B. Tonchev
- Department of Anatomy and Cell Biology, Medical University of Varna, 9000 Varna, Bulgaria
- Department of Stem Cell Biology, Research Institute, Medical University of Varna, 9000 Varna, Bulgaria
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24
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Zhao J, Wen D, Zhang S, Jiang H, Di X. The role of zinc finger proteins in malignant tumors. FASEB J 2023; 37:e23157. [PMID: 37615242 DOI: 10.1096/fj.202300801r] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/19/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
Zinc finger proteins (ZNFs) are the largest family of transcriptional factors in mammalian cells. Recently, their role in the development, progression, and metastasis of malignant tumors via regulating gene transcription and translation processes has become evident. Besides, their possible involvement in drug resistance has also been found, indicating that ZNFs have the potential to become new biological markers and therapeutic targets. In this review, we summarize the oncogenic and suppressive roles of various ZNFs in malignant tumors, including lung, breast, liver, gastric, colorectal, pancreatic, and other cancers, highlighting their role as prognostic markers, and hopefully provide new ideas for the treatment of malignant tumors in the future.
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Affiliation(s)
- Jia Zhao
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Doudou Wen
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Shubing Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Hao Jiang
- Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China
| | - Xiaotang Di
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
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25
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Luo JY, Shen SQ, Xu HJ, Yang JS, Ma WM. The transcription factor masculinizer in sexual differentiation and achieved full functional sex reversal in prawn. iScience 2023; 26:106968. [PMID: 37534170 PMCID: PMC10391606 DOI: 10.1016/j.isci.2023.106968] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/08/2023] [Accepted: 05/23/2023] [Indexed: 08/04/2023] Open
Abstract
Some Zinc finger (ZnF) proteins are required for masculinization in silkworms. In the present study, a masculinizer gene (Mr-Masc) with multi-tissue expression is identified in the freshwater prawn Macrobrachium rosenbergii. The Mr-Masc is clustered into a separate branch with ZnF proteins from decapoda by phylogenetic tree analysis. Moreover, Mr-Masc silencing in male postlarvae prawn results in functional sex reversal females known as neo-females, which are applied to all-male monosex offspring breeding. This manipulation has been significant in sexually dimorphic cultured species. In addition, several significantly expressed transcripts are enriched and the effects of crucial signal pathways are focused through the comparative transcriptomic analysis in Mr-Masc gene knockdown. The significantly differentially expressed epidermal growth factor, upregulated low-density lipoprotein receptor, flotillin, and sex-lethal unigenes, downregulated heat shock proteins and forkhead box homologs are focused. The finding offers an innovative perspective on Masc proteins' evolution and physiological function.
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Affiliation(s)
- Jing-Yu Luo
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang 315100, People’s Republic of China
| | - Shuai-Qi Shen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang 315100, People’s Republic of China
- College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang 310058, People’s Republic of China
| | - Hai-Jing Xu
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang 315100, People’s Republic of China
| | - Jin-Shu Yang
- College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang 310058, People’s Republic of China
| | - Wen-Ming Ma
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang 315100, People’s Republic of China
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Carotti E, Carducci F, Barucca M, Canapa A, Biscotti MA. Transposable Elements: Epigenetic Silencing Mechanisms or Modulating Tools for Vertebrate Adaptations? Two Sides of the Same Coin. Int J Mol Sci 2023; 24:11591. [PMID: 37511347 PMCID: PMC10380595 DOI: 10.3390/ijms241411591] [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: 07/04/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Transposable elements constitute one of the main components of eukaryotic genomes. In vertebrates, they differ in content, typology, and family diversity and played a crucial role in the evolution of this taxon. However, due to their transposition ability, TEs can be responsible for genome instability, and thus silencing mechanisms were evolved to allow the coexistence between TEs and eukaryotic host-coding genes. Several papers are highlighting in TEs the presence of regulatory elements involved in regulating nearby genes in a tissue-specific fashion. This suggests that TEs are not sequences merely to silence; rather, they can be domesticated for the regulation of host-coding gene expression, permitting species adaptation and resilience as well as ensuring human health. This review presents the main silencing mechanisms acting in vertebrates and the importance of exploiting these mechanisms for TE control to rewire gene expression networks, challenging the general view of TEs as threatening elements.
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Affiliation(s)
| | - Federica Carducci
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (E.C.); (M.B.); (A.C.); (M.A.B.)
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Luo Y, Zhou Y. Identification of novel biomarkers and immune infiltration features of recurrent pregnancy loss by machine learning. Sci Rep 2023; 13:10751. [PMID: 37400532 DOI: 10.1038/s41598-023-38046-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/01/2023] [Indexed: 07/05/2023] Open
Abstract
Recurrent pregnancy loss (RPL) is a complex reproductive disorder. The incompletely understood pathophysiology of RPL makes early detection and exact treatment difficult. The purpose of this work was to discover optimally characterized genes (OFGs) of RPL and to investigate immune cell infiltration in RPL. It will aid in better understanding the etiology of RPL and in the early detection of RPL. The RPL-related datasets were obtained from the Gene Expression Omnibus (GEO), namely GSE165004 and GSE26787. We performed functional enrichment analysis on the screened differentially expressed genes (DEGs). Three machine learning techniques are used to generate the OFGs. A CIBERSORT analysis was conducted to examine the immune infiltration in RPL patients compared with normal controls and to investigate the correlation between OFGs and immune cells. Between the RPL and control groups, 42 DEGs were discovered. These DEGs were found to be involved in cell signal transduction, cytokine receptor interactions, and immunological response, according to the functional enrichment analysis. By integrating OFGs from the LASSO, SVM-REF, and RF algorithms (AUC > 0.880), we screened for three down-regulated genes: ZNF90, TPT1P8, FGF2, and an up-regulated FAM166B. Immune infiltration study revealed that RPL samples had more monocytes (P < 0.001) and fewer T cells (P = 0.005) than controls, which may contribute to RPL pathogenesis. Additionally, all OFGs linked with various invading immune cells to varying degrees. In conclusion, ZNF90, TPT1P8, FGF2, and FAM166B are potential RPL biomarkers, offering new avenues for research into the molecular mechanisms of RPL immune modulation and early detection.
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Affiliation(s)
- Yujia Luo
- Department of NICU, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuanyuan Zhou
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
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Zhu Q, Liu Z, Cheng X, Liang W, Wang H, Li P, Zhang J, Chen Y, Gao Y, Qian R. ZNF480 influences the prognosis, pathogenesis, and immune microenvironment in patients with lower-grade glioma. Heliyon 2023; 9:e18185. [PMID: 37519705 PMCID: PMC10372659 DOI: 10.1016/j.heliyon.2023.e18185] [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: 08/21/2022] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
ZNF480 has not yet attracted attention in the study of malignant tumors. Therefore, this study attempts to explain the significance of ZNF480 in the pathological process of lower-grade gliomas (LGG) based on large-scale samples from public database sources and in vitro experiments. Reverse transcription quantitative real-time polymerase chain reaction and immunohistochemistry confirmed that ZNF480 was highly expressed at both the mRNA and protein levels in LGG. Prognostic correlation analysis confirmed that the high expression of ZNF480, as an independent pathogenic gene, significantly correlates with poor survival in patients. Furthermore, the expression level of ZNF480 was significantly inhibited in SHG-44 cells treated with ademetionine disulfate tosylate. Gene set enrichment analysis showed that ZNF480 exists in multiple tumor-related signaling pathways, including the Notch signaling pathway. Immunological correlation analysis showed that ZNF480 can promote the LGG microenvironment to a high immune state and significantly enhance the infiltration of various immune cells, such as M2 macrophages. Finally, Spearman analysis showed a positive correlation of ZNF480 with many immune checkpoints, such as PD-L1. Overall, this study reveals for the first time the adverse effects of ZNF480 on the prognosis of tumor patients, which expands our understanding of the molecular mechanisms behind the regulation of ZNF480. We believe that the high expression of ZNF480 in LGG may be valuable for molecular targeted therapy or combined immunotherapy.
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Affiliation(s)
- Qingyun Zhu
- People's Hospital of Henan University, Henan Provincial People's Hospital, Microbiome Laboratory, Zhengzhou 450003, Henan Province, China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital; People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 Weiwu Road, Jinshui District, Zhengzhou 450003, Henan Province, China
| | - Xingbo Cheng
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital; People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 Weiwu Road, Jinshui District, Zhengzhou 450003, Henan Province, China
| | - Wenjia Liang
- People's Hospital of Henan University, Henan Provincial People's Hospital, Microbiome Laboratory, Zhengzhou 450003, Henan Province, China
| | - Hongbo Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
| | - Pengxu Li
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital; People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 Weiwu Road, Jinshui District, Zhengzhou 450003, Henan Province, China
| | - Jiangfen Zhang
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital; People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 Weiwu Road, Jinshui District, Zhengzhou 450003, Henan Province, China
| | - Yusheng Chen
- Department of Neurosurgery, Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou 450003, Henan Province, China
| | - Yanzheng Gao
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital; People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 Weiwu Road, Jinshui District, Zhengzhou 450003, Henan Province, China
| | - Rongjun Qian
- Department of Neurosurgery, Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou 450003, Henan Province, China
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Vorel J, Kmentová N, Hahn C, Bureš P, Kašný M. An insight into the functional genomics and species classification of Eudiplozoon nipponicum (Monogenea, Diplozoidae), a haematophagous parasite of the common carp Cyprinus carpio. BMC Genomics 2023; 24:363. [PMID: 37380941 DOI: 10.1186/s12864-023-09461-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/16/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Monogenea (Platyhelminthes, Neodermata) are the most species-rich class within the Neodermata superclass of primarily fish parasites. Despite their economic and ecological importance, monogenean research tends to focus on their morphological, phylogenetic, and population characteristics, while comprehensive omics analyses aimed at describing functionally important molecules are few and far between. We present a molecular characterisation of monogenean representative Eudiplozoon nipponicum, an obligate haematophagous parasite infecting the gills of the common carp. We report its nuclear and mitochondrial genomes, present a functional annotation of protein molecules relevant to the molecular and biochemical aspect of physiological processes involved in interactions with the fish hosts, and re-examinate the taxonomic position of Eudiplozoon species within the Diplozoidae family. RESULTS We have generated 50.81 Gbp of raw sequencing data (Illumina and Oxford Nanopore reads), bioinformatically processed, and de novo assembled them into a genome draft 0.94 Gbp long, consisting of 21,044 contigs (N50 = 87 kbp). The final assembly represents 57% of the estimated total genome size (~ 1.64 Gbp), whereby repetitive and low-complexity regions account for ~ 64% of the assembled length. In total, 36,626 predicted genes encode 33,031 proteins and homology-based annotation of protein-coding genes (PCGs) and proteins characterises 14,785 (44.76%) molecules. We have detected significant representation of functional proteins and known molecular functions. The numbers of peptidases and inhibitors (579 proteins), characterised GO terms (16,016 unique assigned GO terms), and identified KEGG Orthology (4,315 proteins) acting in 378 KEGG pathways demonstrate the variety of mechanisms by which the parasite interacts with hosts on a macromolecular level (immunomodulation, feeding, and development). Comparison between the newly assembled E. nipponicum mitochondrial genome (length of 17,038 bp) and other diplozoid monogeneans confirms the existence of two distinct Eudiplozoon species infecting different fish hosts: Cyprinus carpio and Carassius spp. CONCLUSIONS Although the amount of sequencing data and characterised molecules of monogenean parasites has recently increased, a better insight into their molecular biology is needed. The E. nipponicum nuclear genome presented here, currently the largest described genome of any monogenean parasite, represents a milestone in the study of monogeneans and their molecules but further omics research is needed to understand these parasites' biological nature.
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Affiliation(s)
- Jiří Vorel
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic.
| | - Nikol Kmentová
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Agoralaan Gebouw D, Diepenbeek, B-3590, Belgium
| | - Christoph Hahn
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, A-8010, Austria
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Martin Kašný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
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Bai Y, Xu J, Li D, Zhang X, Chen D, Xie F, Huang L, Yu X, Zhao H, Zhang Y. HepaClear, a blood-based panel combining novel methylated CpG sites and protein markers, for the detection of early-stage hepatocellular carcinoma. Clin Epigenetics 2023; 15:99. [PMID: 37308980 DOI: 10.1186/s13148-023-01508-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/19/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Early screening and detection of hepatocellular carcinoma (HCC) can efficiently improve patient prognosis. We aimed to identify a series of hypermethylated DNA markers and develop a blood-based HCC diagnosis panel containing DNA methylation sites and protein markers with improved sensitivity for early-stage HCC detection. RESULTS Overall, 850K methylation arrays were performed using paired tissue DNA samples from 60 HCC patients. Ten candidate hypermethylated CpG sites were selected for further evaluation by quantitative methylation-specific PCR with 60 pairs of tissue samples. Six methylated CpG sites, along with α-fetoprotein (AFP) and des-gamma-carboxyprothrombin (DCP), were assayed in 150 plasma samples. Finally, an HCC diagnosis panel, named HepaClear, was developed in a cohort consisting of 296 plasma samples and validated in an independent cohort consisting of 198 plasma samples. The HepaClear panel, containing 3 hypermethylated CpG sites (cg14263942, cg12701184, and cg14570307) and 2 protein markers (AFP and DCP), yielded a sensitivity of 82.6% and a specificity of 96.2% in the training set and a sensitivity of 84.7% and a specificity of 92.0% in the validation set. The HepaClear panel had higher sensitivity (72.0%) for early-stage HCC than AFP (≥ 20 ng/mL, 48.0%) and DCP (≥ 40 mAU/mL, 62.0%) and detected 67.5% of AFP-negative HCC patients (AFP ≤ 20 ng/mL). CONCLUSIONS We developed a multimarker HCC detection panel (HepaClear) that shows high sensitivity for early-stage HCC. The HepaClear panel exhibits high potential for HCC screening and diagnosis from an at-risk population.
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Affiliation(s)
- Yi Bai
- Department of Hepatobiliary Surgery, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Juan Xu
- Department of Infectious Diseases, Central Hospital of Shengli Oilfield, Dongying, China
| | - Deqiang Li
- Hangzhou New Horizon Health Technology Co., Ltd, Hangzhou, China
| | - Xiaoyu Zhang
- The First Central Clinical School, Tianjin Medical University, Tianjin, China
| | - Dapeng Chen
- The First Central Clinical School, Tianjin Medical University, Tianjin, China
| | - Fucun Xie
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Longmei Huang
- Hangzhou New Horizon Health Technology Co., Ltd, Hangzhou, China
| | - Xiaotian Yu
- Hangzhou New Horizon Health Technology Co., Ltd, Hangzhou, China
| | - Haitao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yamin Zhang
- Department of Hepatobiliary Surgery, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China.
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Ding H, Liu S, Du W, Su L, Chen J, Tian Y, Pan D, Chen L, Rizzello L, Zheng X, Battaglia G, Luo K, Gong Q, Tian X. Revealing the amyloid β-protein with zinc finger protein of micronucleus during Alzheimer's disease progress by a quaternary ammonium terpyridine probe. Biosens Bioelectron 2023; 236:115446. [PMID: 37290288 DOI: 10.1016/j.bios.2023.115446] [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: 03/10/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Micronucleus (MN) is regarded as an abnormal structure in eukaryotic cells which can be used as a biomarker for genetic instability. However, direct observation of MN in living cells is rarely achieved due to the lack of probes that are capable of distinguishing nuclear- and MN-DNA. Herein, a water-soluble terpyridine organic small molecule (ABT) was designed and employed to recognize Zinc-finger protein (ZF) for imaging intracellular MN. The in vitro experiments suggested ABT has a high affinity towards ZF. Further live cell staining showed that ABT could selectively target MN in HeLa and NSC34 cells when combined with ZF. Importantly, we use ABT to uncover the correlation between neurotoxic amyloid β-protein (Aβ) and MN during Alzheimer's disease (AD) progression. Thus, this study provides profound insight into the relationship between Aβ and genomic disorders, offering a deeper understanding for the diagnosis and treatment of AD.
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Affiliation(s)
- Haitao Ding
- Department of Radiology and National Clinical Research Center for Geriatrics, Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province; Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610000, Sichuan Province, China
| | - Shangke Liu
- Department of Dermatology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Wei Du
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.
| | - Liping Su
- Department of Radiology and National Clinical Research Center for Geriatrics, Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province; Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610000, Sichuan Province, China
| | - Junyang Chen
- Department of Chemistry, University College London, London, United Kingdom
| | - Yupeng Tian
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Hefei, 230039, China
| | - Dayi Pan
- Department of Radiology and National Clinical Research Center for Geriatrics, Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province; Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610000, Sichuan Province, China
| | - Lei Chen
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Hefei, 230039, China.
| | - Loris Rizzello
- Department of Pharmaceutical Sciences - University of Milan, Via G. Balzaretti 9, 20133, Milan, IT, Italy; The National Institute of Molecular Genetics (INGM), Via Francesco Sforza 35, 20122, Milan, IT, Italy
| | - Xiaowei Zheng
- Department of Endocrinology and Metabolism, Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu, China; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Giuseppe Battaglia
- Department of Chemistry, University College London, London, United Kingdom
| | - Kui Luo
- Department of Radiology and National Clinical Research Center for Geriatrics, Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province; Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610000, Sichuan Province, China; Functional and Molecular Imaging Key Laboratory of Sichuan Province, And Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, 610041, China
| | - Qiyong Gong
- Department of Radiology and National Clinical Research Center for Geriatrics, Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province; Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610000, Sichuan Province, China; Functional and Molecular Imaging Key Laboratory of Sichuan Province, And Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, 610041, China; Department of Radiology, West China Xiamen Hospital of Sichuan University, 699 Jinyuan Xi Road, Jimei District, 361021, Xiamen, Fujian, China
| | - Xiaohe Tian
- Department of Radiology and National Clinical Research Center for Geriatrics, Huaxi MR Research Center (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province; Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610000, Sichuan Province, China.
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Iyer VJ, Osman MA. The Antipsychotic Drug Haldol Modulates IQGAP1-Signaling and Inhibits Cell Proliferation in Triple Negative Breast Cancer Cell Lines. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000823. [PMID: 37215640 PMCID: PMC10199339 DOI: 10.17912/micropub.biology.000823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023]
Abstract
The signaling scaffold oncoprotein IQGAP1 was identified as a classification and therapeutic biomarker in triple negative breast cancer (TNBC) cell lines. Here, we report that the antipsychotic drug Haldol induces novel protein-protein interactions with IQGAP1 and inhibits cell proliferation in TNBC cell lines. The identified proteins share known functions of IQGAP1 in secretion, transcription and apoptosis and provide further classification tools and potential precision therapeutic targets for Haldol in TNBC.
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Affiliation(s)
- Varun J. Iyer
- Department of Medicine, Division of Oncology, University of Toledo Medical Center, Toledo, Ohio, 43614 United States
| | - Mahasin A. Osman
- Department of Medicine, Division of Oncology, University of Toledo Medical Center, Toledo, Ohio, 43614 United States
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Liu S, Liu X, Lin X, Chen H. Zinc Finger Proteins in the War on Gastric Cancer: Molecular Mechanism and Clinical Potential. Cells 2023; 12:cells12091314. [PMID: 37174714 PMCID: PMC10177130 DOI: 10.3390/cells12091314] [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: 04/11/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
According to the 2020 global cancer data released by the World Cancer Research Fund (WCRF) International, gastric cancer (GC) is the fifth most common cancer worldwide, with yearly increasing incidence and the second-highest fatality rate in malignancies. Despite the contemporary ambiguous molecular mechanisms in GC pathogenesis, numerous in-depth studies have demonstrated that zinc finger proteins (ZFPs) are essential for the development and progression of GC. ZFPs are a class of transcription factors with finger-like domains that bind to Zn2+ extensively and participate in gene replication, cell differentiation and tumor development. In this review, we briefly outline the roles, molecular mechanisms and the latest advances in ZFPs in GC, including eight principal aspects, such as cell proliferation, epithelial-mesenchymal transition (EMT), invasion and metastasis, inflammation and immune infiltration, apoptosis, cell cycle, DNA methylation, cancer stem cells (CSCs) and drug resistance. Intriguingly, the myeloid zinc finger 1 (MZF1) possesses reversely dual roles in GC by promoting tumor proliferation or impeding cancer progression via apoptosis. Therefore, a thorough understanding of the molecular mechanism of ZFPs on GC progression will pave the solid way for screening the potentially effective diagnostic indicators, prognostic biomarkers and therapeutic targets of GC.
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Affiliation(s)
- Shujie Liu
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
- Medical Department, Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Xingzhu Liu
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
- Medical Department, Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Xin Lin
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
- Medical Department, Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Hongping Chen
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
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Yang H, Sun W, Bi T, Sun J, Lu Z, Li J, Wei H. ZNF8-miR-552-5p Axis Modulates ACSL4-Mediated Ferroptosis in Hepatocellular Carcinoma. DNA Cell Biol 2023. [PMID: 37126948 DOI: 10.1089/dna.2022.0582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a common malignancy that is associated with poor prognosis in humans. Despite the development of targeted drugs, overall survival remains a significant challenge, and new therapeutic strategies are urgently needed. The aim of this study was to investigate the function of miR-552-5p in ferroptosis and the underlying mechanism, as well as to explore novel strategies for HCC treatment. CCK8 assay results showed that the viability of Huh-7 and Hep3B cells decreased significantly after transfection of the miR-552-5p inhibitor. In addition, we found that glutathione levels were depleted, intracellular Fe2+ levels were elevated, and the mean fluorescence intensity of C11-BODIPY was increased after miR-552-5p transfection. Transmission electron microscopy revealed that mitochondria became smaller and mitochondrial membrane intensity was increased in the inhibitor+RSL3 group. Mechanistically, a dual-luciferase reporter assay confirmed that miR-552-5p interacted with the 3' untranslated region (3' UTR) of acyl-CoA synthetase long-chain family member 4 (ACSL4) mRNA. qPCR and Western blotting results verified that miR-552-5p negatively regulated ACSL4 expression. In addition, we found that overexpression of ZNF8, which is a transcription factor, reduced intracellular miR-552-5p levels and enhanced sensitivity to ferroptosis. miR-552-5p reduces sensitivity to ferroptosis by targeting the 3' UTR of ACSL4 in HCC. The ZNF8-miR-552-5p-ACSL4 axis is involved in regulation of ferroptosis in HCC, and these findings may provide a new therapeutic target for treatment of HCC.
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Affiliation(s)
- Hao Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Wensheng Sun
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Tao Bi
- Department of Gastrointestinal Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Jiahao Sun
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Zhihua Lu
- Department of General Surgery, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Jie Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Honglong Wei
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
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Hong K, Yang Q, Yin H, Wei N, Wang W, Yu B. Comprehensive analysis of ZNF family genes in prognosis, immunity, and treatment of esophageal cancer. BMC Cancer 2023; 23:301. [PMID: 37013470 PMCID: PMC10069130 DOI: 10.1186/s12885-023-10779-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND As a common malignant tumor, esophageal carcinoma (ESCA) has a low early diagnosis rate and poor prognosis. This study aimed to construct the prognostic features composed of ZNF family genes to effectively predict the prognosis of ESCA patients. METHODS The mRNA expression matrix and clinical data were downloaded from TCGA and GEO database. Using univariate Cox analysis, lasso regression and multivariate Cox analysis, we screened six prognosis-related ZNF family genes to construct the prognostic model. We then used Kaplan-Meier plot, time-dependent receiver operating characteristic (ROC), multivariable Cox regression analysis of clinical information, and nomogram to evaluate the prognostic value within and across sets, separately and combined. We also validated the prognostic value of the six-gene signature using GSE53624 dataset. The different immune status was observed in the single sample Gene Set Enrichment Analysis (ssGSEA). Finally, real-time quantitative PCR was used to detect the expression of six prognostic ZNF genes in twelve pairs of ESCA and adjacent normal tissues. RESULTS A six prognosis-related ZNF family genes model consisted of ZNF91, ZNF586, ZNF502, ZNF865, ZNF106 and ZNF225 was identified. Multivariable Cox regression analysis revealed that six prognosis-related ZNF family genes were independent prognostic factors for overall survival of ESCA patients in TCGA and GSE53624. Further, a prognostic nomogram including the riskScore, age, gender, T, stage was constructed, and TCGA/GSE53624-based calibration plots indicated its excellent predictive performance. Drug Sensitivity and ssGSEA analysis showed that the six genes model was closely related to immune cells infiltration and could be used as a potential predictor of chemotherapy sensitivity. CONCLUSION We identified six prognosis-related ZNF family genes model of ESCA, which provide evidence for individualized prevention and treatment.
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Affiliation(s)
- Kunqiao Hong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
- Key Laboratory of Hubei Province for Digestive System Disease, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qian Yang
- Department of Gastroenterology, Guizhou Provincial People's Hospital, Guiyang City, Guizhou province, China
- NHC key Laboratory of Pulmonary Immune-related Disease, Guizhou Provincial People's Hospital, Guiyang City, Guizhou province, China
| | - Haisen Yin
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
- Key Laboratory of Hubei Province for Digestive System Disease, Wuhan, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Na Wei
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
- Key Laboratory of Hubei Province for Digestive System Disease, Wuhan, China
| | - Wei Wang
- Department of Gastroenterology, Affiliated Hospital of Hubei, Xiangyang Central Hospital, University of Arts and Science, Hubei, China.
| | - Baoping Yu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.
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Yang W, Zhang Z, Li L, Zhang K, Xu Y, Xia M, Zhou J, Gong Y, Chen J, Gong K. ZNF582 overexpression restrains the progression of clear cell renal cell carcinoma by enhancing the binding of TJP2 and ERK2 and inhibiting ERK2 phosphorylation. Cell Death Dis 2023; 14:212. [PMID: 36966163 PMCID: PMC10039855 DOI: 10.1038/s41419-023-05750-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/27/2023]
Abstract
Recent evidences have suggested that Zinc finger protein 582 (ZNF582) plays different important roles in various tumors, but its clinical role, biological function and regulatory mechanism in clear cell renal cell carcinoma (ccRCC) are still vague. Through analyzing GEO and TCGA-KIRC data and validation with local samples, we identified the low expression pattern of ZNF582 in ccRCC. Decreased ZNF582 expression is correlated with higher tumor stage and grade, distant metastasis and poor prognosis. By analyzing the DNA methylation data of ccRCC in TCGA-KIRC and using Massarray DNA methylation and demethylation analysis, we confirmed the hypermethylation status of ZNF582 in ccRCC and its negative regulation on ZNF582 expression. Using cell phenotype experiments and orthotopic kidney tumor growth models, we determined the inhibitory effect of ZNF582 overexpression on ccRCC growth and metastasis in vivo and in vitro. Mechanistically, using TMT (Tandem mass tags) quantitative proteomics test, Co-IP (Co-immunoprecipitation) and Western Blot experiments, we clarified that ZNF582 binds to TJP2 and up-regulates TJP2 protein expression. Increased TJP2 protein combines with ERK2 to promote ERK2 protein expression and suppresses the phosphorylation of ERK2, thereby inhibiting the growth and metastasis of ccRCC. In general, our findings provide the first solid theoretical rationale for targeting ZNF582/TJP2/ERK2 axis to improve ccRCC treatment.
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Affiliation(s)
- Wuping Yang
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Zedan Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Lei Li
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Kenan Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Yawei Xu
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Mancheng Xia
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Jingcheng Zhou
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China.
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China.
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China.
| | - Jinchao Chen
- Department of Urologic Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, P.R. China.
| | - Kan Gong
- Department of Urology, Peking University First Hospital, Beijing, 100034, P.R. China.
- Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing, 100034, P.R. China.
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, P.R. China.
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Goncharova IA, Zarubin AA, Babushkina NP, Koroleva IA, Nazarenko MS. Changes in DNA methylation profile in liver tissue during progression of HCV-induced fibrosis to hepatocellular carcinoma. Vavilovskii Zhurnal Genet Selektsii 2023; 27:72-82. [PMID: 36923478 PMCID: PMC10009477 DOI: 10.18699/vjgb-23-10] [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: 10/18/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 03/11/2023] Open
Abstract
In this study we compared methylation levels of 27,578 CpG sites between paired samples of the tumor and surrounding liver tissues with various degrees of damage (fibrosis, cirrhosis) in HCV-induced hepatocellular carcinoma (HCC) patients, as well as between tumor and normal tissue in non-viral HCC patients, using GSE73003 and GSE37988 data from GEODataSets (https://www.ncbi.nlm.nih.gov/). A significantly lower number of differentially methylated sites (DMS) were found between HCC of non-viral etiology and normal liver tissue, as well as between HCC and fibrosis (32 and 40), than between HCC and cirrhosis (2450 and 2304, respectively, according to GSE73003 and GSE37988 datasets). As the pathological changes in the tissue surrounding the tumor progress, the ratio of hyper-/hypomethylated DMSs in the tumor decreases. Thus, in tumor tissues compared with normal/fibrosis/cirrhosis of the liver, 75/62.5/47.7 % (GSE73003) and 16 % (GSE37988) of CpG sites are hypermethylated, respectively. Persistent hypermethylation of the ZNF154 and ZNF540 genes, as well as CCL20 hypomethylation, were registered in tumor tissue in relation to both liver fibrosis and liver cirrhosis. Protein products of the EDG4, CCL20, GPR109A, and GRM8 genes, whose CpG sites are characterized by changes in DNA methylation level in tumor tissue in the setting of cirrhosis and fibrosis, belong to "Signaling by G-protein-coupled receptors (GPCRs)" category. However, changes in the methylation level of the "driver" genes for oncopathology (АРС, CDKN2B, GSTP1, ELF4, TERT, WT1) are registered in tumor tissue in the setting of liver cirrhosis but not fibrosis. Among the genes hypermethylated in tumor tissue in the setting of liver cirrhosis, the most represented biological pathways are developmental processes, cell-cell signaling, transcription regulation, Wnt-protein binding. Genes hypomethylated in liver tumor tissue in the setting of liver cirrhosis are related to olfactory signal transduction, neuroactive ligand-receptor interaction, keratinization, immune response, inhibition of serine proteases, and zinc metabolism. The genes hypermethylated in the tumor are located at the 7p15.2 locus in the HOXA cluster region, and the hypomethylated CpG sites occupy extended regions of the genome in the gene clusters of olfactory receptors (11p15.4), keratin and keratin-associated proteins (12q13.13, 17q21.2, and 21q22.11), epidermal differentiation complex (1q21.3), and immune system function loci 9p21.3 (IFNA, IFNB1, IFNW1 cluster) and 19q13.41-19q13.42 (KLK, SIGLEC, LILR, KIR clusters). Among the genes of fibrogenesis or DNA repair, cg14143055 (ADAMDEC1) is located in the binding region of the HOX gene family transcription factors (TFs), while cg05921699 (CD79A), cg06196379 (TREM1) and cg10990993 (MLH1) are located in the binding region of the ZNF protein family transcription factor (TF). Thus, the DNA methylation profile in the liver in HCV-induced HCC is unique and differs depending on the degree of surrounding tissue lesion - liver fibrosis or liver cirrhosis.
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Affiliation(s)
- I A Goncharova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - A A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - N P Babushkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I A Koroleva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - M S Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
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Te L, Liu J, Ma J, Wang S. Correlation between serum zinc and testosterone: A systematic review. J Trace Elem Med Biol 2023; 76:127124. [PMID: 36577241 DOI: 10.1016/j.jtemb.2022.127124] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/11/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Zinc is a vital trace element for normal function of the living system. In male, zinc is involved in various biological processes, an important function of which is as a balancer of hormones such as testosterone. For this purpose, studies related to the influence of zinc on serum testosterone were selected and summarized, including the effect of dietary zinc deficiency and zinc supplementation on testosterone concentrations. After preliminary searching of papers on databases, 38 papers including 8 clinical and 30 animal studies were included in this review. We concluded that zinc deficiency reduces testosterone levels and zinc supplementation improves testosterone levels. Furthermore, the effect degree of zinc on serum testosterone may vary depending on basal zinc and testosterone levels, zinc dosage form, elementary zinc dose, and duration. In conclusion, serum zinc was positively correlated with total testosterone, and moderate supplementation plays an important role in improving androgen.
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Affiliation(s)
- Liger Te
- Graduate School of Hebei Medical University, Shijiazhuang 050017, China
| | - Junsheng Liu
- Graduate School of Hebei Medical University, Shijiazhuang 050017, China
| | - Jing Ma
- Hebei Key Laboratory of Reproductive Medicine, Hebei Institute of Reproductive Health Science and Technology, Shijiazhuang 050071, China
| | - Shusong Wang
- Graduate School of Hebei Medical University, Shijiazhuang 050017, China; Hebei Key Laboratory of Reproductive Medicine, Hebei Institute of Reproductive Health Science and Technology, Shijiazhuang 050071, China.
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Regulation of the tumor immune microenvironment by cancer-derived circular RNAs. Cell Death Dis 2023; 14:132. [PMID: 36797245 PMCID: PMC9935907 DOI: 10.1038/s41419-023-05647-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
Circular RNA (circRNAs) is a covalently closed circular non-coding RNA formed by reverse back-splicing from precursor messenger RNA. It is found widely in eukaryotic cells and can be released to the surrounding environment and captured by other cell types. This, circRNAs serve as connections between different cell types for the mediation of multiple signaling pathways. CircRNAs reshape the tumor microenvironment (TME), a key factor involved in all stages of cancer development, by regulating epithelial-stromal transformation, tumor vascularization, immune cell function, and inflammatory responses. Immune cells are the most abundant cellular TME components, and they have profound toxicity to cancer cells. This review summarizes circRNA regulation of immune cells, including T cells, natural killer cells, and macrophages; highlights the impact of circRNAs on tumor progression, treatment, and prognosis; and indicates new targets for tumor immunotherapy.
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Scherf M, Koy C, Röwer C, Neamtu A, Glocker MO. Characterization of Phosphorylation-Dependent Antibody Binding to Cancer-Mutated Linkers of C 2H 2 Zinc Finger Proteins by Intact Transition Epitope Mapping-Thermodynamic Weak-Force Order Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:171-181. [PMID: 36656134 DOI: 10.1021/jasms.2c00244] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
With Intact Transition Epitope Mapping-Thermodynamic Weak-force Order (ITEM-TWO) analysis in combination with molecular modeling, the phosphorylation-dependent molecular recognition motif of the anti-HpTGEKP antibody has been investigated with binary and ternary component mixtures consisting of antibody and (phospho-) peptides. Amino acid sequences have been selected to match either the antibody's recognition motif or the cancer-related zinc finger protein mutations and phosphorylations of the respective amino acid residues. Upon electrospraying of all the components of the mixtures, that is, hexapeptides, antibody, and intact immune complexes, the produced ions were subjected to mass spectrometric mass filtering. The antibody ions as well as the immune complex ions traversed into the mass spectrometer's collision chamber, whereas paths of unbound peptide ions were blocked prior to entering the collision cell. After dissociation of the multiply charged immune complexes in the gas phase, the complex-released peptide ions were recorded after having traversed the second mass filter. Complex-released peptides were unambiguously identified by their masses using mass analysis with isotope resolution. From the results of our studies with seven (phospho-) peptides with distinct amino acid sequences, which resembled either the antibody's binding motif or mutations, we conclude the following: (i) A negatively charged phospho group, located near the peptide's N-terminus is mandatory for antibody binding when placed on the peptide surface at a precise distance to the C-terminally located positively charged ε-amino group of a lysinyl residue. (ii) A bulky amino acid residue, such as the tyrosinyl residue at the N-terminal position of the (phospho-) threoninyl residue, abolishes antibody binding. (iii) Two closely spaced phospho groups negatively interfere with the surface polarity pattern and abolish antibody binding as well. (iv) Non-phosphorylated peptides are not binding partners of the anti-HpTGEKP antibody.
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Affiliation(s)
- Maximilian Scherf
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
| | - Claudia Röwer
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
| | - Andrei Neamtu
- TRANSCEND Centre, Regional Institute of Oncology (IRO) Iasi, Str. General Henri Mathias Berthelot Nr. 2-4, 700483 Iasi, Romania
- Department of Physiology, Grigore T. Popa University of Medicine and Pharmacy of Iasi, Str. Universitatii Nr. 16, 700115 Iasi, Romania
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
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Xu Y, Chen R, Zeng Q. Ferroptosis As a Mechanism for Health Effects of Essential Trace Elements and Potentially Toxic Trace Elements. Biol Trace Elem Res 2022:10.1007/s12011-022-03523-w. [PMID: 36575272 DOI: 10.1007/s12011-022-03523-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/08/2022] [Indexed: 12/29/2022]
Abstract
Ferroptosis is a unique form of programmed cell death driven by iron-dependent phospholipid peroxidation that was proposed in recent years. It plays an important role in processes of various trace element-related diseases and is regulated by redox homeostasis and various cellular metabolic pathways (iron, amino acids, lipids, sugars), as well as disease-related signaling pathways. Some limited pioneering studies have demonstrated ferroptosis as a mechanism for the health effects of essential trace elements and potentially toxic trace elements, with crosstalk among them. The aim of this review is to bring together research articles and identify key direct and indirect evidence regarding essential trace elements (iron, selenium, zinc, copper, chromium, manganese) and potentially toxic trace elements (arsenic, aluminum, mercury) and their possible roles in ferroptosis. Our review may help determine future research priorities and opportunities.
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Affiliation(s)
- Yuyan Xu
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education & School of Public Helath, Guizhou Medical University, Guiyang, 550025, China.
| | - Ruobi Chen
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education & School of Public Helath, Guizhou Medical University, Guiyang, 550025, China
| | - Qibing Zeng
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education & School of Public Helath, Guizhou Medical University, Guiyang, 550025, China.
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Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses. BIOTECHNOLOGIA 2022; 103:355-384. [PMID: 36685700 PMCID: PMC9837557 DOI: 10.5114/bta.2022.120706] [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: 08/22/2021] [Revised: 07/25/2022] [Accepted: 09/16/2022] [Indexed: 01/06/2023] Open
Abstract
Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.
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Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells. Genes (Basel) 2022; 13:genes13122342. [PMID: 36553609 PMCID: PMC9778113 DOI: 10.3390/genes13122342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria involved in the pathogenic processes leading to mastitis and metritis in animals such as dairy cattle. LPS causes cell proliferation associated with endometrium inflammation. Former in vitro studies have demonstrated that LPS induces an intense stimulation of the proliferation of a pure population of bovine endometrial epithelial cells. In a follow-up transcriptomic study based on RNA-sequencing data obtained after 24 h exposure of primary bovine endometrial epithelial cells to 0, 2, and 8 μg/mL LPS, 752 and 727 differentially expressed genes (DEGs) were detected between the controls and LPS-treated samples that encode proteins known to be associated with either proliferation or apoptosis, respectively. The present bioinformatic analysis was performed to decipher the gene networks involved to obtain a deeper understanding of the mechanisms underlying the proliferative and apoptosis processes. Our findings have revealed 116 putative transcription factors (TFs) and the most significant number of interactions between these TFs and DEGs belong to NFKβ1, TP53, STAT1, and HIF1A. Moreover, our results provide novel insights into the early signaling and metabolic pathways in bovine endometrial epithelial cells associated with the innate immune response and cell proliferation to Escherichia coli-LPS infection. The results further indicated that LPS challenge elicited a strong transcriptomic response, leading to potent activation of pro-inflammatory pathways that are associated with a marked endometrial cancer, Toll-like receptor, NFKβ, AKT, apoptosis, and MAPK signaling pathways. This effect may provide a mechanistic explanation for the relationship between LPS and cell proliferation.
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Scherf M, Danquah BD, Koy C, Lorenz P, Steinbeck F, Neamtu A, Thiesen H, Glocker MO. Epitope Fine Mapping by Mass Spectrometry: Investigations of Immune Complexes Consisting of Monoclonal Anti-HpTGEKP Antibody and Zinc Finger Protein Linker Phospho-Hexapeptides. Chembiochem 2022; 23:e202200390. [PMID: 35950614 PMCID: PMC9826235 DOI: 10.1002/cbic.202200390] [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: 07/12/2022] [Revised: 08/03/2022] [Indexed: 01/11/2023]
Abstract
Accurate formation of antibody-antigen complexes has been relied on in both, multitudes of scientific projects and ample therapeutic and diagnostic applications. Mass spectrometrically determined dissociation behavior of immune complexes with the anti-HpTGEKP antibody revealed that the ten most frequently occurring phospho-hexapeptide linker sequences from C2H2 zinc finger proteins could be divided into two classes: orthodox binders, where strong noncovalent interactions developed as anticipated, and unorthodox binders with deviating structures and weaker binding. Phosphorylation of threonine was compulsory for antibody binding in an orthodox manner. Gas phase dissociation energy determinations of seven C2H2 zinc finger protein linker phospho-hexapeptides with orthodox binding properties revealed a bipolar binding motif of the antibody paratope. Epitope peptides, which in addition to the negatively charged phospho-threonine residue were C-terminally flanked by positively charged residues provided stronger binding, i. e. dissociation was endothermic, than peptides with acidic amino acid residues at these positions, for which dissociation was exothermic.
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Affiliation(s)
- Maximilian Scherf
- Proteome Center RostockUniversity Medicine Rostock and University of RostockSchillingallee 6918059RostockGermany
| | - Bright D. Danquah
- Proteome Center RostockUniversity Medicine Rostock and University of RostockSchillingallee 6918059RostockGermany
| | - Cornelia Koy
- Proteome Center RostockUniversity Medicine Rostock and University of RostockSchillingallee 6918059RostockGermany
| | - Peter Lorenz
- Institute of ImmunologyUniversity Medicine RostockSchillingallee 7018059RostockGermany
| | - Felix Steinbeck
- Institute of ImmunologyUniversity Medicine RostockSchillingallee 7018059RostockGermany,Gesellschaft für Individualisierte Medizin mbH (IndyMed)Industriestrasse 1518069RostockGermany
| | - Andrei Neamtu
- Department of PhysiologyGr. T. Popa University of Medicine and Pharmacy of IasiStr. Universitatii nr. 16Iasi Jud.Romania
| | - Hans‐Jürgen Thiesen
- Institute of ImmunologyUniversity Medicine RostockSchillingallee 7018059RostockGermany,Gesellschaft für Individualisierte Medizin mbH (IndyMed)Industriestrasse 1518069RostockGermany
| | - Michael O. Glocker
- Proteome Center RostockUniversity Medicine Rostock and University of RostockSchillingallee 6918059RostockGermany
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