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Agrawal P, Jain N, Gopalan V, Timon A, Singh A, Rajagopal PS, Hannenhalli S. Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer. iScience 2024; 27:109752. [PMID: 38699227 PMCID: PMC11063905 DOI: 10.1016/j.isci.2024.109752] [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: 09/18/2023] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 05/05/2024] Open
Abstract
Breast cancers (BRCA) exhibit substantial transcriptional heterogeneity, posing a significant clinical challenge. The global transcriptional changes in a disease context, however, are likely mediated by few key genes which reflect disease etiology better than the differentially expressed genes (DEGs). We apply our network-based tool PathExt to 1,059 BRCA tumors across 4 subtypes to identify key mediator genes in each subtype. Compared to conventional differential expression analysis, PathExt-identified genes exhibit greater concordance across tumors, revealing shared and subtype-specific biological processes; better recapitulate BRCA-associated genes in multiple benchmarks, and are more essential in BRCA subtype-specific cell lines. Single-cell transcriptomic analysis reveals a subtype-specific distribution of PathExt-identified genes in multiple cell types from the tumor microenvironment. Application of PathExt to a TNBC chemotherapy response dataset identified subtype-specific key genes and biological processes associated with resistance. We described putative drugs that target key genes potentially mediating drug resistance.
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Affiliation(s)
- Piyush Agrawal
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Vishaka Gopalan
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Annan Timon
- University of Pennsylvania, Philadelphia, PA, USA
| | - Arashdeep Singh
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Padma S. Rajagopal
- Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, MD, USA
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2
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Xu F, Xu K, Fan L, Li X, Liu Y, Yang F, Zhu C, Guan X. Estrogen receptor beta suppresses the androgen receptor oncogenic effects in triple-negative breast cancer. Chin Med J (Engl) 2024; 137:338-349. [PMID: 38105538 PMCID: PMC10836903 DOI: 10.1097/cm9.0000000000002930] [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: 05/31/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is an aggressive type of breast cancer associated with poor prognosis and limited treatment options. The androgen receptor (AR) has emerged as a potential therapeutic target for luminal androgen receptor (LAR) TNBC. However, multiple studies have claimed that anti-androgen therapy for AR-positive TNBC only has limited clinical benefits. This study aimed to investigate the role of AR in TNBC and its detailed mechanism. METHODS Immunohistochemistry and TNBC tissue sections were applied to investigate AR and nectin cell adhesion molecule 4 (NECTIN4) expression in TNBC tissues. Then, in vitro and in vivo assays were used to explore the function of AR and estrogen receptor beta (ERβ) in TNBC. Chromatin immunoprecipitation sequencing (ChIP-seq), co-immunoprecipitation (co-IP), molecular docking method, and luciferase reporter assay were performed to identify key molecules that affect the function of AR. RESULTS Based on the TNBC tissue array analysis, we revealed that ERβ and AR were positive in 21.92% (32/146) and 24.66% (36/146) of 146 TNBC samples, respectively, and about 13.70% (20/146) of TNBC patients were ERβ positive and AR positive. We further demonstrated the pro-tumoral effects of AR on TNBC cells, however, the oncogenic biology was significantly suppressed when ERβ transfection in LAR TNBC cell lines but not in AR-negative TNBC. Mechanistically, we identified that NECTIN4 promoter -42 bp to -28 bp was an AR response element, and that ERβ interacted with AR thus impeding the AR-mediated NECTIN4 transcription which promoted epithelial-mesenchymal transition in tumor progression. CONCLUSIONS This study suggests that ERβ functions as a suppressor mediating the effect of AR in TNBC prognosis and cell proliferation. Therefore, our current research facilitates a better understanding of the role and mechanisms of AR in TNBC carcinogenesis.
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Affiliation(s)
- Feng Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Kun Xu
- Department of Oncology, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210009, China
| | - Lingling Fan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xintong Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yiqiu Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Fang Yang
- The Comprehensive Cancer Center of Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu 210008, China
| | - Chengjun Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xiaoxiang Guan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
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3
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Vural-Ozdeniz M, Calisir K, Acar R, Yavuz A, Ozgur MM, Dalgıc E, Konu O. CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters. Brief Bioinform 2024; 25:bbad536. [PMID: 38279653 PMCID: PMC10818169 DOI: 10.1093/bib/bbad536] [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: 10/02/2023] [Revised: 12/04/2023] [Accepted: 12/21/2024] [Indexed: 01/28/2024] Open
Abstract
Cluster analysis is one of the most widely used exploratory methods for visualization and grouping of gene expression patterns across multiple samples or treatment groups. Although several existing online tools can annotate clusters with functional terms, there is no all-in-one webserver to effectively prioritize genes/clusters using gene essentiality as well as congruency of mRNA-protein expression. Hence, we developed CAP-RNAseq that makes possible (1) upload and clustering of bulk RNA-seq data followed by identification, annotation and network visualization of all or selected clusters; and (2) prioritization using DepMap gene essentiality and/or dependency scores as well as the degree of correlation between mRNA and protein levels of genes within an expression cluster. In addition, CAP-RNAseq has an integrated primer design tool for the prioritized genes. Herein, we showed using comparisons with the existing tools and multiple case studies that CAP-RNAseq can uniquely aid in the discovery of co-expression clusters enriched with essential genes and prioritization of novel biomarker genes that exhibit high correlations between their mRNA and protein expression levels. CAP-RNAseq is applicable to RNA-seq data from different contexts including cancer and available at http://konulabapps.bilkent.edu.tr:3838/CAPRNAseq/ and the docker image is downloadable from https://hub.docker.com/r/konulab/caprnaseq.
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Affiliation(s)
| | - Kubra Calisir
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Türkiye
| | - Rana Acar
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Türkiye
| | - Aysenur Yavuz
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Türkiye
| | - Mustafa M Ozgur
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Türkiye
| | - Ertugrul Dalgıc
- Department of Medical Biology, School of Medicine, Zonguldak Bülent Ecevit University, Zonguldak, Türkiye
| | - Ozlen Konu
- Department of Neuroscience, Bilkent University, Ankara, Türkiye
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Türkiye
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4
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Sun M, Lv F, Qin C, Du D, Li W, Liu S. The Potential Mechanism of Liujunzi Decoction in the Treatment of Breast Cancer based on Network Pharmacology and Molecular Docking Technology. Curr Pharm Des 2024; 30:702-726. [PMID: 38415453 DOI: 10.2174/0113816128289900240219104854] [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: 10/28/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Liujunzi Decoction (LJZD) is a potential clinical treatment for Breast Cancer (BC), but the active ingredients and mechanisms underlying its effectiveness remain unclear. OBJECTIVE The study aimed to investigate the target gene of LJZD compatibility and the possible mechanism of action in the treatment of breast cancer by using network pharmacology and molecular docking. METHODS Based on TCMSP, ETCM, and BATMAN database searching and screening to obtain the ingredients of LJZD, the related targets were obtained. Breast cancer-related targets were collected through GEO, Geencards, OMIM, and other databases, and drug-disease Venn diagrams were drawn by R. The PPI network map was constructed by using Cytoscape. The intersecting targets were imported into the STRING database, and the core targets were analyzed and screened. The intersected targets were analyzed by the DAVID database for GO and KEGG enrichment. AutoDock Vina and Gromacs were used for molecular docking and simulation of the core targets and active ingredients. RESULTS 126 active ingredients of LJZD were obtained; 241 targets related to breast cancer were sought after screening, and 180 intersection targets were identified through Venn diagram analysis. The core targets were FOS and ESR1. KEGG enrichment analysis mainly involved PI3K/Akt, MAPK, and other signaling pathways. CONCLUSION This study has explored the possible targets and signaling pathways of LJZD in treating breast cancer through network pharmacology and bioinformatics analysis. Molecular docking and simulation have further validated the potential mechanism of action of LJZD in breast cancer treatment, providing essential experimental data for future studies.
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Affiliation(s)
- Mei Sun
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Feng Lv
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Chunmeng Qin
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Dan Du
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Wenjun Li
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Songqing Liu
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
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5
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Elmasry H, Khadrawy SM, Kamel MM, Ibrahim MH, Abuelsaad ASA, Zanaty MI. Evaluation of MMP-13 and Micro RNA-138 as prognostic biomarkers for breast cancer in Egyptian women patients. Pathol Res Pract 2024; 253:155045. [PMID: 38176307 DOI: 10.1016/j.prp.2023.155045] [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: 10/08/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Elevated serum levels of MMP-13 are linked to tumor growth and metastasis, while miR-138 dysregulation is observed in breast cancer cases. The aim of this study is to investigate the expression of miR-138 and MMP-13 levels as potential biomarkers for the prognosis of breast cancer. PATIENTS AND METHOD In this retrospective case-control study, 119 female subjects were recruited and divided into three groups. MMP-13 level was measured using Enzyme Linked Immunosorbent Assay (ELISA), while real-time PCR technique was employed to quantify miR-138 expression. RESULTS Both non-metastatic and metastatic groups showed significantly higher levels of serum MMP-13 compared to other groups. MMP-13 levels are significantly increased among patients with advanced tumor size, lymph node metastasis, and triple-negative breast cancer cases. An inverse significant association between MMP-13 levels and response to treatment was observed. Expression of miR-138 underwent a significant down-regulation in breast cancer patients, and a statistically significant association was established between miR-138 expression and triple-negative breast cancer cases. A positive association was detected between the increase in miR-138 expression and the good response to treatment. The expression of miR-138 was inversely correlated with the MMP-13 levels. CONCLUSION MMP-13 levels were significantly higher in breast cancer, especially in advanced cases, suggesting its role in promoting tumor invasion and metastasis. MiR-138 was down-regulated in breast cancer, especially in triple-negative breast cancer patients, rendering it a promising biomarker for triple-negative breast cancer. Modulation of miR-138 expression and MMP-13 levels may represent therapeutic targets for breast cancer.
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Affiliation(s)
- Hossam Elmasry
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef, Egypt; Baheya Centre of Early Detection and Treatment of Breast Cancer, Giza, Egypt
| | - Sally M Khadrawy
- Genetics and Molecular Biology, Zoology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62521, Egypt
| | - Mahmoud M Kamel
- Clinical and Chemical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt.
| | - Mona H Ibrahim
- Clinical and Chemical Pathology Department, Medical Division, National Research Centre, Cairo, Egypt
| | - Abdelaziz S A Abuelsaad
- Immunology Division, Zoology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62521, Egypt
| | - Mohamed I Zanaty
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef, Egypt
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Angarola BL, Sharma S, Katiyar N, Gu Kang H, Nehar-Belaid D, Park S, Gott R, Eryilmaz GN, LaBarge MA, Palucka K, Chuang JH, Korstanje R, Ucar D, Anczukow O. Comprehensive single cell aging atlas of mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563147. [PMID: 37961129 PMCID: PMC10634680 DOI: 10.1101/2023.10.20.563147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Aging is the greatest risk factor for breast cancer; however, how age-related cellular and molecular events impact cancer initiation is unknown. We investigate how aging rewires transcriptomic and epigenomic programs of mouse mammary glands at single cell resolution, yielding a comprehensive resource for aging and cancer biology. Aged epithelial cells exhibit epigenetic and transcriptional changes in metabolic, pro-inflammatory, or cancer-associated genes. Aged stromal cells downregulate fibroblast marker genes and upregulate markers of senescence and cancer-associated fibroblasts. Among immune cells, distinct T cell subsets (Gzmk+, memory CD4+, γδ) and M2-like macrophages expand with age. Spatial transcriptomics reveal co-localization of aged immune and epithelial cells in situ. Lastly, transcriptional signatures of aging mammary cells are found in human breast tumors, suggesting mechanistic links between aging and cancer. Together, these data uncover that epithelial, immune, and stromal cells shift in proportions and cell identity, potentially impacting cell plasticity, aged microenvironment, and neoplasia risk.
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Affiliation(s)
| | | | - Neerja Katiyar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hyeon Gu Kang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Giray N Eryilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mark A LaBarge
- Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
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7
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Chen J, Zhong K, Qin S, Jing Y, Liu S, Li D, Peng C. Astragalin: a food-origin flavonoid with therapeutic effect for multiple diseases. Front Pharmacol 2023; 14:1265960. [PMID: 37920216 PMCID: PMC10619670 DOI: 10.3389/fphar.2023.1265960] [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: 07/26/2023] [Accepted: 09/27/2023] [Indexed: 11/04/2023] Open
Abstract
Naturally occurring flavonoids have long been utilized as essential templates for the development of novel drugs and as critical ingredients for functional foods. Astragalin (AG) is a natural flavonoid that can be isolated from a variety of familiar edible plants, such as the seeds of green tea, Morus alba L., and Cuscuta chinensis. It is noteworthy that AG has a wide range of pharmacological activities and possesses therapeutic effects against a variety of diseases, covering cancers, osteoarthritis, osteoporosis, ulcerative colitis, mastitis, obesity, diabetes mellitus, diabetic complications, ischemia/reperfusion injury, neuropathy, respiratory diseases, and reproductive system diseases. This article reviewed the natural source and pharmacokinetics of AG and systematically summarized the pharmacological activities and potential mechanisms of AG in treating diverse diseases in order to promote the development of AG as a functional food, in doing so providing references for its clinical application in disease therapy.
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Affiliation(s)
| | | | | | | | | | - Dan Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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8
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Zhu W, Wu L, Xie W, Zhang G, Gu Y, Hou Y, He Y. Screening of renal clear cell carcinoma prognostic marker genes based on TCGA and GTEx chip data and construction of transcription factor-related regulatory networks. Heliyon 2023; 9:e18870. [PMID: 37636479 PMCID: PMC10458329 DOI: 10.1016/j.heliyon.2023.e18870] [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: 05/08/2023] [Revised: 07/17/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
This study aimed to identify prognostic marker genes for renal clear cell carcinoma (RCCC) and construct a regulatory network of transcription factors and prognostic marker genes. Three hundred eighty-six genes were significantly differentially expressed in RCCC, with functional enrichment analysis suggesting a relationship between these genes and kidney function and development. Cox and Lasso regression analyses revealed 10 prognostic marker genes (RNASET2, MSC, DPEP1, FGF1, ATP1A1, CLDN10, PLG, SLC44A1, PCSK1N, and LGI4) that accurately predicted RCCC patient prognosis. Upstream transcription factors of these genes were also identified, and in vitro experiments suggested that ATP1A1 may play a key role in RCCC patient prognosis. The findings of this study provide important insights into the molecular mechanisms of RCCC and may have implications for personalized treatment strategies.
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Affiliation(s)
- Wei Zhu
- Department of Urology, The First Hospital of Jiaxing & The Affiliated Hospital of Jiaxing University, Jiaxing 314000, PR China
| | - Lingfeng Wu
- Department of Urology, The First Hospital of Jiaxing & The Affiliated Hospital of Jiaxing University, Jiaxing 314000, PR China
| | - Wenhua Xie
- Department of Urology, The First Hospital of Jiaxing & The Affiliated Hospital of Jiaxing University, Jiaxing 314000, PR China
| | - Gaoyue Zhang
- Department of Urology, The First Hospital of Jiaxing & The Affiliated Hospital of Jiaxing University, Jiaxing 314000, PR China
| | - Yanqin Gu
- Department of Urology, The First Hospital of Jiaxing & The Affiliated Hospital of Jiaxing University, Jiaxing 314000, PR China
| | - Yansong Hou
- Department of Urology, The First Hospital of Jiaxing & The Affiliated Hospital of Jiaxing University, Jiaxing 314000, PR China
| | - Yi He
- Department of Urology, The First Hospital of Jiaxing & The Affiliated Hospital of Jiaxing University, Jiaxing 314000, PR China
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9
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Lee KH, Hwang HJ, Im YJ, Nam AR, Lee JW, Cho JY. New oncogenic functions of LINE1 retroelement as a ceRNA for tumor suppressive microRNA miR-126 on ENPP5. PLoS One 2023; 18:e0286814. [PMID: 37352273 PMCID: PMC10289412 DOI: 10.1371/journal.pone.0286814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/23/2023] [Indexed: 06/25/2023] Open
Abstract
Retroelements (REs) had been considered 'Junk' until the encyclopedia of DNA elements (ENCODE) project demonstrated that most genome is functional. Although the function of retroelements has been reported in diverse cancers including human breast cancer (HBC) and subtypes, only a few studies have suggested the putative functions of REs via their random genome integration. A canine mammary tumor (CMT) has been highlighted due to the similarities in molecular and pathophysiology with HBC. This study investigated the putative roles of REs common in both HBC and CMT. The human LINE and HERV-K sequences harbor many miRNAs responsive elements (MREs) for tumor-suppressive miRNA such as let-7. We also observed that various MREs are exist in the ERV and LINE highly expressed in the transcriptome data of CMT as well as HBC sets. MREs against miR-126 were highly expressed in both HBC and CMT while the levels of miR-126 were down-regulated. Oppositely, the expression of miR-126 target genes was significantly up-regulated in the cancers. Moreover, cancer patients with an increased level of miR-126 showed better overall survival. The expression of ENPP5, a putative miR-126 target gene, was downregulated by miR-126 mimic. Importantly, overexpression of LINE fragment significantly suppressed miR-126 function on the target gene expression. We propose the functional role of REs expression in tumorigenesis as competing endogenous RNAs (ceRNA) against tumor-suppressive miRNAs. This study provided pieces of evidence that LINE expression, even partial and fragmented, have a regulatory function in ENPP5 gene expression via the competition with miR-126.
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Affiliation(s)
- Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Hyeon-Ji Hwang
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Yeo-Jin Im
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - A-Reum Nam
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Jeong-Woon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
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Chen C, Yang Y, Guo Y, He J, Chen Z, Qiu S, Zhang Y, Ding H, Pan J, Pan Y. CYP1B1 inhibits ferroptosis and induces anti-PD-1 resistance by degrading ACSL4 in colorectal cancer. Cell Death Dis 2023; 14:271. [PMID: 37059712 PMCID: PMC10104818 DOI: 10.1038/s41419-023-05803-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Immune checkpoint blockade (ICB) is a promising treatment strategy for colorectal cancer (CRC) patients. However, most CRC patients do not response well to ICB therapy. Increasing evidence indicates that ferroptosis plays a critical role in immunotherapy. ICB efficacy may be enhanced by inducing tumor ferroptosis. Cytochrome P450 1B1 (CYP1B1) is a metabolic enzyme that participates in arachidonic acid metabolism. However, the role of CYP1B1 in ferroptosis remains unclear. In this study, we demonstrated that CYP1B1 derived 20-HETE activated the protein kinase C pathway to increase FBXO10 expression, which in turn promoted the ubiquitination and degradation of acyl-CoA synthetase long-chain family member 4 (ACSL4), ultimately inducing tumor cells resistance to ferroptosis. Furthermore, inhibiting CYP1B1 sensitized tumor cells to anti-PD-1 antibody in a mouce model. In addition, CYP1B1 expression was negatively correlated with ACSL4 expression, and high expression indicates poor prognosis in CRC. Taken together, our work identified CYP1B1 as a potential biomarker for enhancing anti-PD-1 therapy in CRC.
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Affiliation(s)
- Congcong Chen
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yabing Yang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yanguan Guo
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jiashuai He
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zuyang Chen
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Shenghui Qiu
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yiran Zhang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Hui Ding
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Jinghua Pan
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Yunlong Pan
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China.
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes. Institute of Life and Health Engineering, Jinan University, Guangzhou, China.
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11
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Seraphin G, Rieger S, Hewison M, Capobianco E, Lisse TS. The impact of vitamin D on cancer: A Mini Review. J Steroid Biochem Mol Biol 2023; 231:106308. [PMID: 37054849 DOI: 10.1016/j.jsbmb.2023.106308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
In this review, we summarize the most recent advances in vitamin D cancer research to provide molecular clarity, as well as its translational trajectory across the cancer landscape. Vitamin D is well known for its role in regulating mineral homeostasis; however, vitamin D deficiency has also been linked to the development and progression of a number of cancer types. Recent epigenomic, transcriptomic, and proteomic studies have revealed novel vitamin D-mediated biological mechanisms that regulate cancer cell self-renewal, differentiation, proliferation, transformation, and death. Tumor microenvironmental studies have also revealed dynamic relationships between the immune system and vitamin D's anti-neoplastic properties. These findings help to explain the large number of population-based studies that show clinicopathological correlations between circulating vitamin D levels and risk of cancer development and death. The majority of evidence suggests that low circulating vitamin D levels are associated with an increased risk of cancers, whereas supplementation alone or in combination with other chemo/immunotherapeutic drugs may improve clinical outcomes even further. These promising results still necessitate further research and development into novel approaches that target vitamin D signaling and metabolic systems to improve cancer outcomes.
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Affiliation(s)
- Gerbenn Seraphin
- University of Miami, Department of Biology, Coral Gables, Florida USA
| | - Sandra Rieger
- University of Miami, Department of Biology, Coral Gables, Florida USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida USA
| | - Martin Hewison
- University of Birmingham, Institute of Metabolism and Systems Research, Birmingham UK
| | | | - Thomas S Lisse
- University of Miami, Department of Biology, Coral Gables, Florida USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida USA; iCURA LLC, Malvern, Pennsylvania USA.
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Zhou M, Li J, Xu J, Zheng L, Xu S. Exploring human CYP4 enzymes: physiological roles, function in diseases and focus on inhibitors. Drug Discov Today 2023; 28:103560. [PMID: 36958639 DOI: 10.1016/j.drudis.2023.103560] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/06/2023] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
The cytochrome P450 (CYP)4 family of enzymes are monooxygenases responsible for the ω-oxidation of endogenous fatty acids and eicosanoids and play a crucial part in regulating numerous eicosanoid signaling pathways. Recently, CYP4 gained attention as a potential therapeutic target for several human diseases, including cancer, cardiovascular diseases and inflammation. Small-molecule inhibitors of CYP4 could provide promising treatments for these diseases. The aim of the present review is to highlight the advances in the field of CYP4, discussing the physiology and pathology of the CYP4 family and compiling CYP4 inhibitors into groups based on their chemical classes to provide clues for the future discovery of drug candidates targeting CYP4. Teaser: This review provides an updated view of the physiology and pathology of CYP4 enzymes. CYP4 inhibitors are compiled based on their skeletons to provide clues for the future discovery of drug candidates targeting CYP4.
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Affiliation(s)
- Manzhen Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Junda Li
- Department of Medicinal Chemistry, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Jinyi Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Lufeng Zheng
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Shengtao Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China; Department of Hepatobiliary Surgery, The First People's Hospital of Kunshan, Suzhou, 215300, China.
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13
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Saeki S, Kumegawa K, Takahashi Y, Yang L, Osako T, Yasen M, Otsuji K, Miyata K, Yamakawa K, Suzuka J, Sakimoto Y, Ozaki Y, Takano T, Sano T, Noda T, Ohno S, Yao R, Ueno T, Maruyama R. Transcriptomic intratumor heterogeneity of breast cancer patient-derived organoids may reflect the unique biological features of the tumor of origin. Breast Cancer Res 2023; 25:21. [PMID: 36810117 PMCID: PMC9942352 DOI: 10.1186/s13058-023-01617-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/10/2023] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND The intratumor heterogeneity (ITH) of cancer cells plays an important role in breast cancer resistance and recurrence. To develop better therapeutic strategies, it is necessary to understand the molecular mechanisms underlying ITH and their functional significance. Patient-derived organoids (PDOs) have recently been utilized in cancer research. They can also be used to study ITH as cancer cell diversity is thought to be maintained within the organoid line. However, no reports investigated intratumor transcriptomic heterogeneity in organoids derived from patients with breast cancer. This study aimed to investigate transcriptomic ITH in breast cancer PDOs. METHODS We established PDO lines from ten patients with breast cancer and performed single-cell transcriptomic analysis. First, we clustered cancer cells for each PDO using the Seurat package. Then, we defined and compared the cluster-specific gene signature (ClustGS) corresponding to each cell cluster in each PDO. RESULTS Cancer cells were clustered into 3-6 cell populations with distinct cellular states in each PDO line. We identified 38 clusters with ClustGS in 10 PDO lines and used Jaccard similarity index to compare the similarity of these signatures. We found that 29 signatures could be categorized into 7 shared meta-ClustGSs, such as those related to the cell cycle or epithelial-mesenchymal transition, and 9 signatures were unique to single PDO lines. These unique cell populations appeared to represent the characteristics of the original tumors derived from patients. CONCLUSIONS We confirmed the existence of transcriptomic ITH in breast cancer PDOs. Some cellular states were commonly observed in multiple PDOs, whereas others were specific to single PDO lines. The combination of these shared and unique cellular states formed the ITH of each PDO.
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Affiliation(s)
- Sumito Saeki
- grid.410807.a0000 0001 0037 4131Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550 Japan ,grid.410807.a0000 0001 0037 4131Breast Surgical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kohei Kumegawa
- grid.410807.a0000 0001 0037 4131Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yoko Takahashi
- grid.410807.a0000 0001 0037 4131Breast Surgical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Liying Yang
- grid.410807.a0000 0001 0037 4131Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550 Japan
| | - Tomo Osako
- grid.410807.a0000 0001 0037 4131Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mahmut Yasen
- grid.410807.a0000 0001 0037 4131Cancer Informatics and Biobanking Platform Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kazutaka Otsuji
- grid.410807.a0000 0001 0037 4131Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kenichi Miyata
- grid.410807.a0000 0001 0037 4131Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550 Japan
| | - Kaoru Yamakawa
- grid.410807.a0000 0001 0037 4131Cancer Informatics and Biobanking Platform Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Jun Suzuka
- grid.410807.a0000 0001 0037 4131Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuri Sakimoto
- grid.410807.a0000 0001 0037 4131Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550 Japan
| | - Yukinori Ozaki
- grid.410807.a0000 0001 0037 4131Breast Medical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Toshimi Takano
- grid.410807.a0000 0001 0037 4131Breast Medical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takeshi Sano
- grid.410807.a0000 0001 0037 4131Department of Gastroenterological Surgery, Gastroenterological Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tetsuo Noda
- grid.410807.a0000 0001 0037 4131Director’s Room, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Shinji Ohno
- grid.410807.a0000 0001 0037 4131Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryoji Yao
- grid.410807.a0000 0001 0037 4131Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takayuki Ueno
- grid.410807.a0000 0001 0037 4131Breast Surgical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550, Japan. .,Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan.
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Liu B, Dong C, Chen Q, Fan Z, Zhang Y, Wu Y, Cui T, Liu F. Circ_0007534 as new emerging target in cancer: Biological functions and molecular interactions. Front Oncol 2022; 12:1031802. [PMID: 36505874 PMCID: PMC9730518 DOI: 10.3389/fonc.2022.1031802] [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: 08/30/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022] Open
Abstract
Circular RNA (circRNAs), an important member of the non-coding RNA (ncRNA) family, are widely expressed in a variety of biological cells. Owing to their stable structures, sequence conservations, and cell- or tissue-specific expressions, these RNA have become a popular subject of scientific research. With the development of sequencing methods, it has been revealed that circRNAs exert their biological function by sponging microRNAs (miRNAs), regulating transcription, or binding to proteins. Humans have historically been significantly impacted by various types of cancer. Studies have shown that circRNAs are abnormally expressed in various cancers and are involved in the occurrence and development of malignant tumors, such as tumor cell proliferation, migration, and invasion. As one of its star molecules, circ_0007534 is upregulated in colorectal, cervical, and pancreatic cancers; is closely related to the occurrence, development, and prognosis of tumors; and is expected to become a novel tumor marker and therapeutic target. This article briefly reviews the expression and mechanism of circ_0007534 in malignant tumors based on the domestic and foreign literature.
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Tao L, Ding X, Yan L, Xu G, Zhang P, Ji A, Zhang L. CD36 accelerates the progression of hepatocellular carcinoma by promoting FAs absorption. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:202. [PMID: 36175596 DOI: 10.1007/s12032-022-01808-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022]
Abstract
CD36 is emerging as a potential strategy for cancer treatment because of its function of regulating fatty acid intake. The purpose of this study was to clarify the molecular mechanism of CD36 in the progression of HCC. TCGA database was used to analyze the relationship of CD36 with HCC. The expression of CD36 in HCC clinical samples and cell lines was detected by qRT-PCR and western blot. Huh7 cells and HCCLM3 cells were transfected and treated into different group. CCK-8 and clone formation assay were used to detect the cell proliferation ability. Wound healing and transwell experiment were used to detect the metastatic ability. HCC xenografts were constructed in nude mice by subcutaneous injection of stably transfected Huh7 cells. The expression of CD36 in HCC was detected by immunohistochemistry (IHC). The contents of phospholipids and triglycerides in HCC cells were detected by ELISA. And the content of neutral lipids in HCC cells was detected by staining with BODIPY 493/503 and DAPI dye. Then transcriptional sequencing was used to determine the downstream mechanism of CD36 in HCC, and the differentially expressed genes (DEGs) were analyzed. CD36 was upregulated in HCC. Knockdown of CD36 could suppress the proliferation and metastasis of HCC in vitro and in vivo by regulating FAs intake in HCC. In addition, the expression of AKR1C2 was suppressed by sh-CD36, and which was also involved in the regulation of FAs intake. The molecular mechanism by which CD36 accelerated the progression of HCC was to promote the expression of AKR1C2 and thus enhance fatty acids (FAs) intake.
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Affiliation(s)
- Lide Tao
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, No. 368, Hanjiang Middle Road, Yangzhou, 225012, China
| | - Xiangmin Ding
- Department of Hepatobiliary Pancreatic Surgery, Subei People's Hospital of Jiangsu Province, Yangzhou, China
| | - Lele Yan
- Department of Hepatobiliary Pancreatic Surgery, Subei People's Hospital of Jiangsu Province, Yangzhou, China
| | - Guangcai Xu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, No. 368, Hanjiang Middle Road, Yangzhou, 225012, China
| | - Peijian Zhang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, No. 368, Hanjiang Middle Road, Yangzhou, 225012, China
| | - Anlai Ji
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, No. 368, Hanjiang Middle Road, Yangzhou, 225012, China
| | - Lihong Zhang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, No. 368, Hanjiang Middle Road, Yangzhou, 225012, China.
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Zheng J, Huang J, Liang Z. Acetyltransferase P300 Inhibits the Proliferation, Invasion, and Migration of Esophageal Cancer via Survivin Acetylation. Chin Med 2022. [DOI: 10.4236/cm.2022.134005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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