1
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Jiang X, Wang W, Wang Z, Wang Z, Shi H, Meng L, Pang S, Fan M, Lin R. Gamma-glutamyl transferase secreted by Helicobacter pylori promotes the development of gastric cancer by affecting the energy metabolism and histone methylation status of gastric epithelial cells. Cell Commun Signal 2024; 22:402. [PMID: 39148040 PMCID: PMC11328474 DOI: 10.1186/s12964-024-01780-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: 01/21/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Helicobacter pylori (H. pylori) infection is critical in the development and occurrence of gastric cancer. H. pylori secretes gamma-glutamyl transferase (GGT), which affects energy metabolism and histone methylation in mesenchymal stem cells. However, its effect on human gastric epithelial cells remains unclear. This study aimed to investigate the effects of GGT on energy metabolism and histone methylation in gastric epithelial cells and determine its role in the development and progression of H. pylori-induced gastric cancer. METHODS A GGT knockout H. pylori strain and mouse gastric cancer model were constructed, and alpha-ketoglutarate (α-KG) was added. The underlying mechanism was investigated using proteomics, immunohistochemistry, Western blotting, and other experimental assays. RESULTS H. pylori can colonize the host's stomach and destroy the gastric epithelium. GGT secreted by H. pylori decreased the concentration of glutamine in the stomach and increased H3K9me3 and H3K27me3 expression, which promoted the proliferation and migration of gastric epithelial cells. Additionally, α-KG reversed this effect. GGT increased the tumorigenic ability of nude mice. GGT, secreted by H. pylori, promoted the expression of ribosomal protein L15 (RPL15), while GGT knockout and supplementation with α-KG and trimethylation inhibitors reduced RPL15 expression and Wnt signaling pathway expression. CONCLUSIONS H. pylori secreted GGT decreased the expression of glutamine and α-KG in gastric epithelial cells, increased the expression of histones H3K9me3 and H3K27me3, and activated the Wnt signaling pathway through RPL15 expression, ultimately changing the biological characteristics of the gastric epithelium and promoting the occurrence of gastric cancer. Altered energy metabolism and histone hypermethylation are important factors involved in this process.
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Affiliation(s)
- Xin Jiang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Weijun Wang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zeyu Wang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhe Wang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Huiying Shi
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lingjun Meng
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Suya Pang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Mengke Fan
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Rong Lin
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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2
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Chen F, Zhang Y, Shen L, Creighton CJ. The DNA methylome of pediatric brain tumors appears shaped by structural variation and predicts survival. Nat Commun 2024; 15:6775. [PMID: 39117669 PMCID: PMC11310301 DOI: 10.1038/s41467-024-51276-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
Structural variation heavily influences the molecular landscape of cancer, in part by impacting DNA methylation-mediated transcriptional regulation. Here, using multi-omic datasets involving >2400 pediatric brain and central nervous system tumors of diverse histologies from the Children's Brain Tumor Network, we report hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of somatic structural variant (SV) breakpoints is recurrently associated with altered expression or DNA methylation, respectively, including tumor suppressor genes ATRX and CDKN2A. Altered DNA methylation near enhancers associates with nearby somatic SV breakpoints, including MYC and MYCN. A subset of genes with SV-CGI methylation associations also have expression associations with patient survival, including BCOR, TERT, RCOR2, and PDLIM4. DNA methylation changes in recurrent or progressive tumors compared to the initial tumor within the same patient can predict survival in pediatric and adult cancers. Our comprehensive and pan-histology genomic analyses reveal mechanisms of noncoding alterations impacting cancer genes.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Lanlan Shen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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3
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Castro JP, Shindyapina AV, Barbieri A, Ying K, Strelkova OS, Paulo JA, Tyshkovskiy A, Meinl R, Kerepesi C, Petrashen AP, Mariotti M, Meer MV, Hu Y, Karamyshev A, Losyev G, Galhardo M, Logarinho E, Indzhykulian AA, Gygi SP, Sedivy JM, Manis JP, Gladyshev VN. Age-associated clonal B cells drive B cell lymphoma in mice. NATURE AGING 2024:10.1038/s43587-024-00671-7. [PMID: 39117982 DOI: 10.1038/s43587-024-00671-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 06/19/2024] [Indexed: 08/10/2024]
Abstract
Although cancer is an age-related disease, how the processes of aging contribute to cancer progression is not well understood. In this study, we uncovered how mouse B cell lymphoma develops as a consequence of a naturally aged system. We show here that this malignancy is associated with an age-associated clonal B cell (ACBC) population that likely originates from age-associated B cells. Driven by c-Myc activation, promoter hypermethylation and somatic mutations, IgM+ ACBCs clonally expand independently of germinal centers and show increased biological age. ACBCs become self-sufficient and support malignancy when transferred into young recipients. Inhibition of mTOR or c-Myc in old mice attenuates pre-malignant changes in B cells during aging. Although the etiology of mouse and human B cell lymphomas is considered distinct, epigenetic changes in transformed mouse B cells are enriched for changes observed in human B cell lymphomas. Together, our findings characterize the spontaneous progression of cancer during aging through both cell-intrinsic and microenvironmental changes and suggest interventions for its prevention.
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Affiliation(s)
- José P Castro
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Aging and Aneuploidy Laboratory, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | | | | | - Kejun Ying
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Olga S Strelkova
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - João A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | - Rico Meinl
- Retro Biosciences, Redwood City, CA, USA
| | - Csaba Kerepesi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Institute for Computer Science and Control (SZTAKI), Loránd Eötvös Research Network, Budapest, Hungary
| | - Anna P Petrashen
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Marco Mariotti
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Margarita V Meer
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- San Diego Institute of Sciences, Altos Labs, San Diego, CA, USA
| | - Yan Hu
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Grigoriy Losyev
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mafalda Galhardo
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Elsa Logarinho
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Artur A Indzhykulian
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - John P Manis
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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4
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Dong Q, Gong C, Jiang Q, Liu Y, Hu Y, Wang D, Liu H, Zheng T, Song C, Wang T, Ju R, Wang C, Song D, Liu Z, Liu Y, Lu Y, Fan J, Liu M, Gao T, An Z, Zhang J, Li P, Cao C, Liu X. Identification of differentially expressed tumour-related genes regulated by UHRF1-driven DNA methylation. Sci Rep 2024; 14:18371. [PMID: 39112494 PMCID: PMC11306747 DOI: 10.1038/s41598-024-69110-2] [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: 11/14/2023] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is an epigenetic regulator that plays critical roles in tumours. However, the DNA methylation alteration patterns driven by UHRF1 and the related differentially expressed tumour-related genes remain unclear. In this study, a UHRF1-shRNA MCF-7 cell line was constructed, and whole-genome bisulfite sequencing and RNA sequencing were performed. The DNA methylation alteration landscape was elucidated, and DNA methylation-altered regions (DMRs) were found to be distributed in both gene bodies and adjacent regions. The DMRs were annotated and categorized into 488 hypermethylated/1696 hypomethylated promoters and 1149 hypermethylated/5501 hypomethylated gene bodies. Through an integrated analysis with the RNA sequencing data, 217 methylation-regulated upregulated genes and 288 downregulated genes were identified, and these genes were primarily enriched in nervous system development and cancer signalling pathways. Further analysis revealed 21 downregulated oncogenes and 15 upregulated TSGs. We also showed that UHRF1 silencing inhibited cell proliferation and migration and suppressed tumour growth in vivo. Our study suggested that UHRF1 and the oncogenes or TSGs it regulates might serve as biomarkers and targets for breast cancer treatment.
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Affiliation(s)
- Qincai Dong
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Chunxue Gong
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Qian Jiang
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Yue Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Yong Hu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Di Wang
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Hainan Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Tong Zheng
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Caiwei Song
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Tingting Wang
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Ruixia Ju
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Chen Wang
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Dengcen Song
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Zijing Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Yuting Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Yuwei Lu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Jinlian Fan
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Mengzi Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Ting Gao
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Ziqian An
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Jiaxin Zhang
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Cheng Cao
- Beijing Institute of Biotechnology, Beijing, 100850, China.
| | - Xuan Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China.
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5
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Xu H, Long S, Xu C, Li Z, Chen J, Yang B, He Y, Xu Z, Li Z, Wei W, Li X. TNC upregulation promotes glioma tumourigenesis through TDG-mediated active DNA demethylation. Cell Death Discov 2024; 10:347. [PMID: 39090080 PMCID: PMC11294444 DOI: 10.1038/s41420-024-02098-w] [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: 03/30/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024] Open
Abstract
Gliomas represent the most predominant primary malignant tumor in central nervous system. Thymine DNA glycosylase (TDG) is a central component in active DNA demethylation. However, the specific mechanisms of TDG-mediated active DNA demethylation in gliomas remain unclear. This research indicates TDG expression is overexpressed in gliomas and correlated with poor prognosis. TDG knockdown suppressed the malignant phenotype of gliomas both in vitro and vivo. Notably, RNA-seq analysis revealed a strong association between TDG and tenascin-C (TNC). ChIP-qPCR and MeDIP-qPCR assays were undertaken to confirm that TDG participates in TNC active DNA demethylation process, revealing decreased DNA methylation levels and elevated TNC expression as a result. Silencing TNC expression also suppressed the tumor malignant phenotype in both in vitro and in vivo experiments. Additionally, simultaneous silencing of TNC reduced or even reversed the glioma promotion caused by TDG overexpression. Based on our findings, we conclude that TDG exerts an indispensable role in TNC active DNA demethylation in gliomas. The DNA demethylation process leads to alternations in TNC methylation levels and promotes its expression, thereby contributing to the development of gliomas. These results suggest a novel epigenetic therapeutic strategy targeting active DNA demethylation in gliomas.
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Affiliation(s)
- Hongyu Xu
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shengrong Long
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chengshi Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengwei Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jincao Chen
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bin Yang
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongze He
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ziyue Xu
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Wei Wei
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Xiang Li
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China.
- Medical Research Institute, Wuhan University, Wuhan, China.
- Sino-Italian Ascula Brain Science Joint Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China.
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6
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Blanchett R, Lau KH, Pfeifer GP. Homeobox and Polycomb target gene methylation in human solid tumors. Sci Rep 2024; 14:13912. [PMID: 38886487 PMCID: PMC11183203 DOI: 10.1038/s41598-024-64569-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
DNA methylation is an epigenetic mark that plays an important role in defining cancer phenotypes, with global hypomethylation and focal hypermethylation at CpG islands observed in tumors. These methylation marks can also be used to define tumor types and provide an avenue for biomarker identification. The homeobox gene class is one that has potential for this use, as well as other genes that are Polycomb Repressive Complex 2 targets. To begin to unravel this relationship, we performed a pan-cancer DNA methylation analysis using sixteen Illumina HM450k array datasets from TCGA, delving into cancer-specific qualities and commonalities between tumor types with a focus on homeobox genes. Our comparisons of tumor to normal samples suggest that homeobox genes commonly harbor significant hypermethylated differentially methylated regions. We identified two homeobox genes, HOXA3 and HOXD10, that are hypermethylated in all 16 cancer types. Furthermore, we identified several potential homeobox gene biomarkers from our analysis that are uniquely methylated in only one tumor type and that could be used as screening tools in the future. Overall, our study demonstrates unique patterns of DNA methylation in multiple tumor types and expands on the interplay between the homeobox gene class and oncogenesis.
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Affiliation(s)
- Reid Blanchett
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA
| | - Kin H Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA.
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7
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Pan W, Yun T, Ouyang X, Ruan Z, Zhang T, An Y, Wang R, Zhu P. A blood-based multi-omic landscape for the molecular characterization of kidney stone disease. Mol Omics 2024; 20:322-332. [PMID: 38623715 DOI: 10.1039/d3mo00261f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Kidney stone disease (KSD, also named renal calculi, nephrolithiasis, or urolithiasis) is a common urological disease entailing the formation of minerals and salts that form inside the urinary tract, frequently caused by diabetes, high blood pressure, hypertension, and monogenetic components in most patients. 10% of adults worldwide are affected by KSD, which continues to be highly prevalent and with increasing incidence. For the identification of novel therapeutic targets in KSD, we adopted high-throughput sequencing and mass spectrometry (MS) techniques in this study and carried out an integrative analysis of exosome proteomic data and DNA methylation data from blood samples of normal and KSD individuals. Our research delineated the profiling of exosomal proteins and DNA methylation in both healthy individuals and those afflicted with KSD, finding that the overexpressed proteins and the demethylated genes in KSD samples are associated with immune responses. The consistency of the results in proteomics and epigenetics supports the feasibility of the comprehensive strategy. Our insights into the molecular landscape of KSD pave the way for a deeper understanding of its pathogenic mechanism, providing an opportunity for more precise diagnosis and targeted treatment strategies for KSD.
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Affiliation(s)
- Weibing Pan
- Department of Urology, Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, China
| | - Tianwei Yun
- Department of Urology, Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, China
| | - Xin Ouyang
- Department of Laboratory Medicine, Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, China.
| | - Zhijun Ruan
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518020, China.
| | - Tuanjie Zhang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518020, China.
| | - Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518020, China.
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518020, China.
| | - Peng Zhu
- Department of Laboratory Medicine, Shenzhen Pingshan People's Hospital, Shenzhen, Guangdong 518118, China.
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8
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Pekkarinen M, Nordfors K, Uusi-Mäkelä J, Kytölä V, Hartewig A, Huhtala L, Rauhala M, Urhonen H, Häyrynen S, Afyounian E, Yli-Harja O, Zhang W, Helen P, Lohi O, Haapasalo H, Haapasalo J, Nykter M, Kesseli J, Rautajoki KJ. Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors. Life Sci Alliance 2024; 7:e202302088. [PMID: 38499326 PMCID: PMC10948937 DOI: 10.26508/lsa.202302088] [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: 04/11/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness and aberrant but still unresolved epigenetic regulation. To better understand their malignancy, we investigated how AT/RT-specific DNA hypermethylation was associated with gene expression and altered transcription factor binding and how it is linked to upstream regulation. Medulloblastomas, choroid plexus tumors, pluripotent stem cells, and fetal brain were used as references. A part of the genomic regions, which were hypermethylated in AT/RTs similarly as in pluripotent stem cells and demethylated in the fetal brain, were targeted by neural transcriptional regulators. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 and linked to suppressed genes with a role in neural development and tumorigenesis. Activity of the several NEUROG/NEUROD pioneer factors, which are unable to bind to methylated DNA, was compromised via the suppressed expression or DNA hypermethylation of their target sites, which was also experimentally validated for NEUROD1 in medulloblastomas and AT/RT samples. These results highlight and characterize the role of DNA hypermethylation in AT/RT malignancy and halted neural cell differentiation.
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Affiliation(s)
- Meeri Pekkarinen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kristiina Nordfors
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Unit of Pediatric Hematology and Oncology, Tampere University Hospital, Tampere, Finland
| | - Joonas Uusi-Mäkelä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ville Kytölä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Laura Huhtala
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Minna Rauhala
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Henna Urhonen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Sergei Häyrynen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ebrahim Afyounian
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Olli Yli-Harja
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Pauli Helen
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Olli Lohi
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Hannu Haapasalo
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Joonas Haapasalo
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Juha Kesseli
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kirsi J Rautajoki
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
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9
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Huang F, Jin L, Zhang X, Wang M, Zhou C. Integrated pan-cancer analysis reveals the immunological and prognostic potential of RBFOX2 in human tumors. Front Pharmacol 2024; 15:1302134. [PMID: 38881877 PMCID: PMC11176534 DOI: 10.3389/fphar.2024.1302134] [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: 09/26/2023] [Accepted: 05/08/2024] [Indexed: 06/18/2024] Open
Abstract
Background The role of RNA-binding fox one homolog 2 (RBFOX2) in the progression of multiple tumors is increasingly supported by evidence. However, the unclearness pertaining to the expression of RBFOX2, its prognostic potential, and its correlation with the tumor microenvironment (TME) in pan-cancer persists. This study aims to comprehensively investigate the immunological prognostic value of RBFOX2. Methods The Cancer Genome Atlas Gene Expression Omnibus Genotype-Tissue Expression (GTEx), TIMER2.0, Kaplan-Meier (K-M) Plotter, University of Alabama at Birmingham Cancer data analysis Portal (UALCAN), cbioportal, and Gene Expression Profiling Interactive Analysis 2 (GEPIA2) were utilized for a systematic analysis of RBFOX2. This analysis included studying its expression, prognostic value, DNA methylation, enrichment analysis, immune infiltration cells, and immune-related genes. Additionally, qRT-PCR, CCK-8, colony formation, transwell assays, and immunohistochemistry were employed to analyze the expression and biological function of RBFOX2 in liver cancer. Results Variations in RBFOX2 expression have been observed across diverse tumors and have been identified as indicators of unfavorable prognosis. It is closely linked to immune infiltration cells, immune checkpoints, chemokines, and chemokine receptors in the TME. Higher levels of RBFOX2 have been significantly associated with low response and poor prognosis in patients with non-small cell lung cancer (NSCLC) and melanoma who receive immunotherapy. Furthermore, the DNA methylation of RBFOX2 varies across different types of cancer and has shown better prognosis in patients with BLCA, BRCA, CESC, COAD, DLBC, HNSC, LAML, LGG, LUAD, PAAD, SKCM and THYM. Interestingly, RBFOX2 expression was found to be lower in hepatocellular carcinoma (HCC) patients' tumor tissues compared to their paired adjacent tissues. In vitro studies have shown that knockdown of RBFOX2 significantly promotes the growth and metastasis of liver cancer cells. Conclusion This study investigates the correlation between DNA methylation, prognostic value, and immune cell infiltration with the expression of RBFOX2 in pan-cancer and indicates its potential role to inhibit metastasis of liver cancer.
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Affiliation(s)
- Fengxian Huang
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Long Jin
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Xinyue Zhang
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Min Wang
- Department of Science and Education, Xi'an Children's Hospital Affiliated of Xi'an Jiaotong University, Xi'an, China
| | - Congya Zhou
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
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10
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Liao X, Lin R, Zhang Z, Tian D, Liu Z, Chen S, Xu G, Su M. Genome-wide DNA methylation and transcriptomic patterns of precancerous gastric cardia lesions. J Natl Cancer Inst 2024; 116:681-693. [PMID: 38258659 DOI: 10.1093/jnci/djad244] [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: 06/27/2023] [Revised: 10/25/2023] [Accepted: 11/15/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Intestinal metaplasia (IM) and intraepithelial neoplasia (IEN) are considered precursors of gastric cardia cancer (GCC). Here, we investigated the histopathologic and molecular profiles of precancerous gastric cardia lesions (PGCLs) and biomarkers for risk stratification of gastric cardia IM. METHODS We conducted a hospital-based evaluation (n = 4578) for PGCL profiles in high-incidence and non-high-incidence regions for GCC in China. We next performed 850K methylation arrays (n = 42) and RNA-seq (n = 44) in tissues with PGCLs. We then examined the protein expression of candidate biomarker using immunohistochemistry. RESULTS Of the 4578 participants, 791 were diagnosed with PGCLs (600 IM, 62 IM with IEN, and 129 IEN). We found that individuals from high-incidence regions (26.7%) were more likely to develop PGCLs than those from non-high-incidence areas (13.5%). DNA methylation and gene expression alterations, indicated by differentially methylated probes (DMPs) and differentially expressed genes (DEGs), exhibited a progressive increase from type I IM (DMP = 210, DEG = 24), type II IM (DMP = 3402, DEG = 129), to type III IM (DMP = 3735, DEG = 328), peaking in IEN (DMP = 47 373, DEG = 2278). Three DEGs with aberrant promoter methylation were identified, shared exclusively by type III IM and IEN. Of these DEGs, we found that OLFM4 expression appears in IMs and increases remarkably in IENs (P < .001). CONCLUSIONS We highlight that type III IM and IEN share similar epigenetic and transcriptional features in gastric cardia and propose biomarkers with potential utility in risk prediction.
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Affiliation(s)
- Xiaoqi Liao
- Department of Pathology, Shantou University Medical College, Shantou, People's Republic of China
| | - Runhua Lin
- Department of Pathology, Shantou University Medical College, Shantou, People's Republic of China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, People's Republic of China
| | - Zhihua Zhang
- Department of Pathology, Shantou University Medical College, Shantou, People's Republic of China
| | - Dongping Tian
- Department of Pathology, Shantou University Medical College, Shantou, People's Republic of China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, People's Republic of China
| | - Zhaohui Liu
- Department of Gastroenterology, Shenzhen Second People's Hospital/The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, People's Republic of China
| | - Songqin Chen
- Department of Pathology, Jieyang People's Hospital, Jieyang, People's Republic of China
| | - Guohua Xu
- Department of Gastroenterology, Huiyang Sanhe Hospital, Huizhou, People's Republic of China
| | - Min Su
- Department of Pathology, Shantou University Medical College, Shantou, People's Republic of China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, People's Republic of China
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11
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Ding Y, Jiang Y, Zeng H, Zhou M, Zhou X, Yu Z, Pan J, Geng X, Zhu Y, Zheng H, Huang S, Gong Y, Huang H, Xiong C, Huang D. Identification of a robust biomarker LAPTM4A for glioma based on comprehensive computational biology and experimental verification. Aging (Albany NY) 2024; 16:6954-6989. [PMID: 38613802 PMCID: PMC11087115 DOI: 10.18632/aging.205736] [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: 11/14/2023] [Accepted: 03/03/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND Glioma, a highly invasive and deadly form of human neoplasm, presents a pressing need for the exploration of potential therapeutic targets. While the lysosomal protein transmembrane 4A (LATPM4A) has been identified as a risk factor in pancreatic cancer patients, its role in glioma remains unexplored. METHODS The analysis of differentially expressed genes (DEG) was conducted from The Cancer Genome Atlas (TCGA) glioma dataset and the Genotype Tissue Expression (GTEx) dataset. Through weighted gene co-expression network analysis (WGCNA), the key glioma-related genes were identified. Among these, by using Kaplan-Meier (KM) analysis and univariate/multivariate COX methods, LAPTM4A emerged as the most influential gene. Moreover, the bioinformatics methods and experimental verification were employed to analyze its relationships with diagnosis, clinical parameters, epithelial-mesenchymal transition (EMT), metastasis, immune cell infiltration, immunotherapy, drug sensitivity, and ceRNA network. RESULTS Our findings revealed that LAPTM4A was up-regulated in gliomas and was associated with clinicopathological features, leading to poor prognosis. Furthermore, functional enrichment analysis demonstrated that LATPM4A played a role in the immune system and cancer progression. In vitro experiments indicated that LAPTM4A may influence metastasis through the EMT pathway in glioma. Additionally, we found that LAPTM4A was associated with the tumor microenvironment (TME) and immunotherapy. Notably, drug sensitivity analysis revealed that patients with high LAPTM4A expression were sensitive to doxorubicin, which contributed to a reduction in LAPTM4A expression. Finally, we uncovered the FGD5-AS1-hsa-miR-103a-3p-LAPTM4A axis as a facilitator of glioma progression. CONCLUSIONS In conclusion, our study identifies LATPM4A as a promising biomarker for prognosis and immune characteristics in glioma.
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Affiliation(s)
- Yongqi Ding
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yike Jiang
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hong Zeng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Minqin Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xuanrui Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Zichuan Yu
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xitong Geng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yanting Zhu
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hao Zheng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Shuhan Huang
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yiyang Gong
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Huabin Huang
- Department of Radiology, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Chengfeng Xiong
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Da Huang
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
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Gao J, Shi W, Wang J, Guan C, Dong Q, Sheng J, Zou X, Xu Z, Ge Y, Yang C, Li J, Bao H, Zhong X, Cui Y. Research progress and applications of epigenetic biomarkers in cancer. Front Pharmacol 2024; 15:1308309. [PMID: 38681199 PMCID: PMC11048075 DOI: 10.3389/fphar.2024.1308309] [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: 10/06/2023] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
Epigenetic changes are heritable changes in gene expression without changes in the nucleotide sequence of genes. Epigenetic changes play an important role in the development of cancer and in the process of malignancy metastasis. Previous studies have shown that abnormal epigenetic changes can be used as biomarkers for disease status and disease prediction. The reversibility and controllability of epigenetic modification changes also provide new strategies for early disease prevention and treatment. In addition, corresponding drug development has also reached the clinical stage. In this paper, we will discuss the recent progress and application status of tumor epigenetic biomarkers from three perspectives: DNA methylation, non-coding RNA, and histone modification, in order to provide new opportunities for additional tumor research and applications.
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Affiliation(s)
- Jianjun Gao
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wujiang Shi
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiangang Wang
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Canghai Guan
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qingfu Dong
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jialin Sheng
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinlei Zou
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhaoqiang Xu
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yifei Ge
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chengru Yang
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiehan Li
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Haolin Bao
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiangyu Zhong
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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13
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He Q, Wei Y, Zhu H, Liang Q, Chen P, Li S, Song Y, Liu L, Wang B, Xu X, Dong Y. The combined effect of MTHFR C677T and A1298C polymorphisms on the risk of digestive system cancer among a hypertensive population. Discov Oncol 2024; 15:97. [PMID: 38565713 PMCID: PMC10987447 DOI: 10.1007/s12672-024-00960-y] [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: 06/27/2023] [Accepted: 03/29/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND AND PURPOSE The enzyme methylenetetrahydrofolate reductase (MTHFR) plays a crucial role in directing folate species towards nucleotide synthesis or DNA methylation. The MTHFR polymorphisms C677T and A1298C have been linked to cancer susceptibility, but the evidence supporting this association has been equivocal. To investigate the individual and joint associations between MTHFR C677T, A1298C, and digestive system cancer in a Chinese hypertensive population, we conducted a population-based case-control study involving 751 digestive system cancer cases and one-to-one matched controls from the China H-type Hypertension Registry Study (CHHRS). METHODS We utilized the conditional logistic regression model to evaluate multivariate odds ratios (ORs) and 95% confidence intervals (CIs) of digestive system cancer. RESULTS The analysis revealed a significantly lower risk of digestive system cancer in individuals with the CT genotype (adjusted OR: 0.71; 95% CI 0.52, 0.97; P = 0.034) and TT genotype (adjusted OR: 0.57; 95% CI 0.40, 0.82; P = 0.003; P for trend = 0.003) compared to those with the 677CC genotype. Although A1298C did not show a measurable association with digestive system cancer risk, further stratification of 677CT genotype carriers by A1298C homozygotes (AA) and heterozygotes (AC) revealed a distinct trend within these subgroups. CONCLUSION These findings indicate a potential protective effect against digestive system cancer associated with the T allele of MTHFR C677T. Moreover, we observed that the presence of different combinations of MTHFR polymorphisms may contribute to varying susceptibilities to digestive system cancer.
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Affiliation(s)
- Qiangqiang He
- Shenzhen International Graduate School, Tsinghua University, University Town of Shenzhen, No. 2279, Lishui Road. Nanshan District, Shenzhen, 518055, Guangdong, China
- Shenzhen Evergreen Medical Institute, Shenzhen, 518057, Guangdong, China
| | - Yaping Wei
- College of Public Health, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Hehao Zhu
- School of Science, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Qiongyue Liang
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Ping Chen
- College of Pharmacy, Jinan University, Guangzhou, 510632, Guangdong, China
- Inspection and Testing Center, Key Laboratory of Cancer FSMP for State Market Regulation, Shenzhen, 518057, China
| | - Shuqun Li
- Department of Gastrointestinal Surgery/Clinical Nutrition, Capital Medical University Affiliated Beijing Shijitan Hospital, Beijing, 100038, China
| | - Yun Song
- Shenzhen Evergreen Medical Institute, Shenzhen, 518057, Guangdong, China
| | - Lishun Liu
- Shenzhen International Graduate School, Tsinghua University, University Town of Shenzhen, No. 2279, Lishui Road. Nanshan District, Shenzhen, 518055, Guangdong, China
- Shenzhen Evergreen Medical Institute, Shenzhen, 518057, Guangdong, China
- Guangdong Key Laboratory of H-Type Hypertension and Stroke Precision Prevention Research and Development Enterprise, Shenzhen, 518057, China
| | - Binyan Wang
- Shenzhen Evergreen Medical Institute, Shenzhen, 518057, Guangdong, China
- Institute of Biomedicine, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Xiping Xu
- National Clinical Research Center for Kidney Disease, State Key Laboratory for Organ Failure Research, Guangdong Provincial Key Laboratory of Renal Failure Research, Guangzhou Regenerative Medicine and Health, Guangdong Laboratory, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yuhan Dong
- Shenzhen International Graduate School, Tsinghua University, University Town of Shenzhen, No. 2279, Lishui Road. Nanshan District, Shenzhen, 518055, Guangdong, China.
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14
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Zhang Z, Zhang Y. Transcriptional regulation of cancer stem cell: regulatory factors elucidation and cancer treatment strategies. J Exp Clin Cancer Res 2024; 43:99. [PMID: 38561775 PMCID: PMC10986082 DOI: 10.1186/s13046-024-03021-y] [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: 12/04/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
Cancer stem cells (CSCs) were first discovered in the 1990s, revealing the mysteries of cancer origin, migration, recurrence and drug-resistance from a new perspective. The expression of pluripotent genes and complex signal regulatory networks are significant features of CSC, also act as core factors to affect the characteristics of CSC. Transcription is a necessary link to regulate the phenotype and potential of CSC, involving chromatin environment, nucleosome occupancy, histone modification, transcription factor (TF) availability and cis-regulatory elements, which suffer from ambient pressure. Especially, the expression and activity of pluripotent TFs are deeply affected by both internal and external factors, which is the foundation of CSC transcriptional regulation in the current research framework. Growing evidence indicates that regulating epigenetic modifications to alter cancer stemness is effective, and some special promoters and enhancers can serve as targets to influence the properties of CSC. Clarifying the factors that regulate CSC transcription will assist us directly target key stem genes and TFs, or hinder CSC transcription through environmental and other related factors, in order to achieve the goal of inhibiting CSC and tumors. This paper comprehensively reviews the traditional aspects of transcriptional regulation, and explores the progress and insights of the impact on CSC transcription and status through tumor microenvironment (TME), hypoxia, metabolism and new meaningful regulatory factors in conjunction with the latest research. Finally, we present opinions on omnidirectional targeting CSCs transcription to eliminate CSCs and address tumor resistance.
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Affiliation(s)
- Zhengyue Zhang
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, People's Republic of China
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, People's Republic of China
| | - Yanjie Zhang
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, People's Republic of China.
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, People's Republic of China.
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15
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Li Y, Gong J, Sun Q, Vong EG, Cheng X, Wang B, Yuan Y, Jin L, Gamazon ER, Zhou D, Lai M, Zhang D. Alternative polyadenylation quantitative trait methylation mapping in human cancers provides clues into the molecular mechanisms of APA. Am J Hum Genet 2024; 111:562-583. [PMID: 38367620 PMCID: PMC10940021 DOI: 10.1016/j.ajhg.2024.01.010] [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: 09/12/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/19/2024] Open
Abstract
Genetic variants are involved in the orchestration of alternative polyadenylation (APA) events, while the role of DNA methylation in regulating APA remains unclear. We generated a comprehensive atlas of APA quantitative trait methylation sites (apaQTMs) across 21 different types of cancer (1,612 to 60,219 acting in cis and 4,448 to 142,349 in trans). Potential causal apaQTMs in non-cancer samples were also identified. Mechanistically, we observed a strong enrichment of cis-apaQTMs near polyadenylation sites (PASs) and both cis- and trans-apaQTMs in proximity to transcription factor (TF) binding regions. Through the integration of ChIP-signals and RNA-seq data from cell lines, we have identified several regulators of APA events, acting either directly or indirectly, implicating novel functions of some important genes, such as TCF7L2, which is known for its involvement in type 2 diabetes and cancers. Furthermore, we have identified a vast number of QTMs that share the same putative causal CpG sites with five different cancer types, underscoring the roles of QTMs, including apaQTMs, in the process of tumorigenesis. DNA methylation is extensively involved in the regulation of APA events in human cancers. In an attempt to elucidate the potential underlying molecular mechanisms of APA by DNA methylation, our study paves the way for subsequent experimental validations into the intricate biological functions of DNA methylation in APA regulation and the pathogenesis of human cancers. To present a comprehensive catalog of apaQTM patterns, we introduce the Pancan-apaQTM database, available at https://pancan-apaqtm-zju.shinyapps.io/pancanaQTM/.
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Affiliation(s)
- Yige Li
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jingwen Gong
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China
| | - Qingrong Sun
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, Zhejiang Province, China; College of Information Science and Technology, ZheJiang Shuren University, Hangzhou 310015, ZheJiang, China
| | - Eu Gene Vong
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Department of Biochemistry and Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Xiaoqing Cheng
- Department of Pathology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Binghong Wang
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Ying Yuan
- Department of Medical Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Chinese National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Data Science Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan Zhou
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Maode Lai
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.
| | - Dandan Zhang
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.
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16
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Xie J, Deng X, Xie Y, Zhu H, Liu P, Deng W, Ning L, Tang Y, Sun Y, Tang H, Cai M, Xie X, Zou Y. Multi-omics analysis of disulfidptosis regulators and therapeutic potential reveals glycogen synthase 1 as a disulfidptosis triggering target for triple-negative breast cancer. MedComm (Beijing) 2024; 5:e502. [PMID: 38420162 PMCID: PMC10901283 DOI: 10.1002/mco2.502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Disruption of disulfide homeostasis during biological processes can have fatal consequences. Excess disulfides induce cell death in a novel manner, termed as "disulfidptosis." However, the specific mechanism of disulfidptosis has not yet been elucidated. To determine the cancer types sensitive to disulfidptosis and outline the corresponding treatment strategies, we firstly investigated the crucial functions of disulfidptosis regulators pan-cancer at multi-omics levels. We found that different tumor types expressed dysregulated levels of disulfidptosis regulators, most of which had an impact on tumor prognosis. Moreover, we calculated the disulfidptosis activity score in tumors and validated it using multiple independent datasets. Additionally, we found that disulfidptosis activity was correlated with classic biological processes and pathways in various cancers. Disulfidptosis activity was also associated with tumor immune characteristics and could predict immunotherapy outcomes. Notably, the disulfidptosis regulator, glycogen synthase 1 (GYS1), was identified as a promising target for triple-negative breast cancer and validated via in vitro and in vivo experiments. In conclusion, our study elucidated the complex molecular phenotypes and clinicopathological correlations of disulfidptosis regulators in tumors, laying a solid foundation for the development of disulfidptosis-targeting strategies for cancer treatment.
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Affiliation(s)
- Jindong Xie
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Xinpei Deng
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Yi Xie
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Hongbo Zhu
- The First Affiliated HospitalHengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
| | - Peng Liu
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Wei Deng
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Li Ning
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Yuhui Tang
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Yuying Sun
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Hailin Tang
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Manbo Cai
- The First Affiliated HospitalHengyang Medical SchoolUniversity of South ChinaHengyangHunanChina
| | - Xiaoming Xie
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
| | - Yutian Zou
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐Sen University Cancer CenterGuangzhouGuangdongChina
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Agudelo MC, Agudelo S, Lorincz A, Ramírez AT, Castañeda KM, Garcés-Palacio I, Zea AH, Piyathilake C, Sanchez GI. Folate deficiency modifies the risk of CIN3+ associated with DNA methylation levels: a nested case-control study from the ASCUS-COL trial. Eur J Nutr 2024; 63:563-572. [PMID: 38129362 PMCID: PMC10899296 DOI: 10.1007/s00394-023-03289-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
PURPOSE To our knowledge, there are very few studies evaluating if the levels of folate modify the risk of cervical intraepithelial neoplasia grade 2 and higher (CIN2+ and CIN3+) associated with the levels of HPV genome methylation, two cofactors related to single carbon metabolism and independently associated with cervical cancer in previous studies. We conducted a case-control study nested in a three-arm randomized clinical pragmatic trial (ASCUS-COL trial) to evaluate the risk of CIN3+ associated with methylation levels according to serum folate concentrations. METHODS Cases (n = 155) were women with histologically confirmed CIN2+ (113 CIN2, 38 CIN3, and 4 SCC) and controls were age and follow-up time at diagnosis-matched women with histologically confirmed ≤ CIN1 (n = 155), selected from the 1122 hrHPV + women of this trial. The concentrations of serum folate were determined by the radioimmunoassay SimulTRAC-SNB-VitaminB12/Folate-RIAKit and the methylation levels by the S5 classifier. Stepwise logistic regression models were used to estimate the association between folate or methylation levels and CIN2+ or CIN3+. The joint effect of folate levels and methylation on the risk of CIN3+ was estimated using combinations of categorical stratifications. RESULTS Folate levels were significantly lower in women with CIN3+ than in other diagnostic groups (p = 0.019). The risk of CIN3+ was eight times higher (OR 8.9, 95% CI 3.4-24.9) in women with folate deficiency and high methylation levels than in women with normal folate and high methylation levels (OR 1.4, 95% CI 0.4-4.6). CONCLUSION High methylation and deficient folate independently increased the risk of CIN3+ while deficient folate combined with high methylation was associated with a substantially elevated risk of CIN3+.
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Affiliation(s)
- María C Agudelo
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
| | - Samuel Agudelo
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
| | - Attila Lorincz
- Centre for Cancer Prevention, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Arianis Tatiana Ramírez
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
- Postdoctoral Fellow at the Prevention and Implementation Group, International Agency for Research On Cancer/World Health Organization, Lyon, France
| | - Kelly Melisa Castañeda
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia
| | - Isabel Garcés-Palacio
- Epidemiology Group, School of Public Health, Universidad de Antioquia, Medellín, Colombia
| | - Arnold H Zea
- Stanley S. Scott Cancer Center, Microbiology, Immunology and Parasitology, LSU Health Sciences Center, New Orleans, USA
| | - Chandrika Piyathilake
- Department of Nutrition Sciences, The University of Alabama at Birmingham, Birmingham, USA
| | - Gloria Ines Sanchez
- Infection and Cancer Group, School of Medicine, Universidad de Antioquia, Carrera 51D No 62-29, 050010, Medellín, Colombia.
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Xue X, Feng Q, Hong X, Lin Z, Luo Y, Li Y, Yao G, Wang N, Chen L. Comprehensive analysis of ALG3 in pan-cancer and validation of ALG3 as an onco-immunological biomarker in breast cancer. Aging (Albany NY) 2024; 16:2320-2339. [PMID: 38329424 PMCID: PMC10911369 DOI: 10.18632/aging.205483] [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: 09/18/2023] [Accepted: 12/14/2023] [Indexed: 02/09/2024]
Abstract
ALG3 has significant modulatory function in the process of tumor development. Yet how ALG3 involves in the advancement of different malignancies isn't fully understood. We performed a pan-cancer assessment on ALG3 utilizing datasets from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) to examine its tumor-related roles across malignancies and its link to particular molecules and cells in the tumor microenvironment (TME). Furthermore, we focused on breast cancer to examine the influence of ALG3-mediated signaling pathways and intercellular interactions in the advancement of tumors. The biological effects of ALG3 were verified by breast cancer cells. Enhanced ALG3 expression was discovered to be substantially linked to patients' grim prognoses in a number of malignancies. Furthermore, the expression of ALG3 in the TME was linked to the infiltration of stromal and immune cells, and ALG3-related immune checkpoints, TMB, and MSI were also discovered. We also discovered that cancer patients having a high level of ALG3 exhibited a lower probability of benefiting from immunotherapy. Furthermore, our research found that KEGG enrichment, single-cell RNA and spatial sequencing analyses were effective in identifying key signaling pathways in ALG3-associated tumor growth. In vitro, knockdown of ALG3 could decrease the proliferation of breast cancer cells. In summary, our research offers a comprehensive insight into the advancement of tumors under the mediation of ALG3. ALG3 appears to be intimately associated with tumor development in the TME. ALG3 might be a viable treatment target for cancer therapy, particularly in the case of breast cancer.
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Affiliation(s)
- Xiaolei Xue
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Qiaoli Feng
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Xi Hong
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Zhousheng Lin
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yingrui Luo
- Basic Medical Academy, Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yingshi Li
- Basic Medical Academy, Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Guangyu Yao
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Nisha Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Lujia Chen
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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Geissler F, Nesic K, Kondrashova O, Dobrovic A, Swisher EM, Scott CL, J. Wakefield M. The role of aberrant DNA methylation in cancer initiation and clinical impacts. Ther Adv Med Oncol 2024; 16:17588359231220511. [PMID: 38293277 PMCID: PMC10826407 DOI: 10.1177/17588359231220511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/21/2023] [Indexed: 02/01/2024] Open
Abstract
Epigenetic alterations, including aberrant DNA methylation, are now recognized as bone fide hallmarks of cancer, which can contribute to cancer initiation, progression, therapy responses and therapy resistance. Methylation of gene promoters can have a range of impacts on cancer risk, clinical stratification and therapeutic outcomes. We provide several important examples of genes, which can be silenced or activated by promoter methylation and highlight their clinical implications. These include the mismatch DNA repair genes MLH1 and MSH2, homologous recombination DNA repair genes BRCA1 and RAD51C, the TERT oncogene and genes within the P15/P16/RB1/E2F tumour suppressor axis. We also discuss how these methylation changes might occur in the first place - whether in the context of the CpG island methylator phenotype or constitutional DNA methylation. The choice of assay used to measure methylation can have a significant impact on interpretation of methylation states, and some examples where this can influence clinical decision-making are presented. Aberrant DNA methylation patterns in circulating tumour DNA (ctDNA) are also showing great promise in the context of non-invasive cancer detection and monitoring using liquid biopsies; however, caution must be taken in interpreting these results in cases where constitutional methylation may be present. Thus, this review aims to provide researchers and clinicians with a comprehensive summary of this broad, but important subject, illustrating the potentials and pitfalls of assessing aberrant DNA methylation in cancer.
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Affiliation(s)
- Franziska Geissler
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ksenija Nesic
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alexander Dobrovic
- University of Melbourne Department of Surgery, Austin Health, Heidelberg, VIC, Australia
| | | | - Clare L. Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Royal Women’s Hospital, Parkville, VIC, Australia
- Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Matthew J. Wakefield
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
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Waseem M, Wang BD. Organoids: An Emerging Precision Medicine Model for Prostate Cancer Research. Int J Mol Sci 2024; 25:1093. [PMID: 38256166 PMCID: PMC10816550 DOI: 10.3390/ijms25021093] [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: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Prostate cancer (PCa) has been known as the most prevalent cancer disease and the second leading cause of cancer mortality in men almost all over the globe. There is an urgent need for establishment of PCa models that can recapitulate the progress of genomic landscapes and molecular alterations during development and progression of this disease. Notably, several organoid models have been developed for assessing the complex interaction between PCa and its surrounding microenvironment. In recent years, PCa organoids have been emerged as powerful in vitro 3D model systems that recapitulate the molecular features (such as genomic/epigenomic changes and tumor microenvironment) of PCa metastatic tumors. In addition, application of organoid technology in mechanistic studies (i.e., for understanding cellular/subcellular and molecular alterations) and translational medicine has been recognized as a promising approach for facilitating the development of potential biomarkers and novel therapeutic strategies. In this review, we summarize the application of PCa organoids in the high-throughput screening and establishment of relevant xenografts for developing novel therapeutics for metastatic, castration resistant, and neuroendocrine PCa. These organoid-based studies are expected to expand our knowledge from basic research to clinical applications for PCa diseases. Furthermore, we also highlight the optimization of PCa cultures and establishment of promising 3D organoid models for in vitro and in vivo investigations, ultimately facilitating mechanistic studies and development of novel clinical diagnosis/prognosis and therapies for PCa.
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Affiliation(s)
- Mohammad Waseem
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA;
| | - Bi-Dar Wang
- Department of Pharmaceutical Sciences, School of Pharmacy and Health Professions, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA;
- Hormone Related Cancers Program, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
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Wu W, Li H, Wang Z, Dai Z, Liang X, Luo P, Liu K, Zhang H, Zhang N, Li S, Zhang C. The tertiary lymphoid structure-related signature identified PTGDS in regulating PD-L1 and promoting the proliferation and migration of glioblastoma. Heliyon 2024; 10:e23915. [PMID: 38205335 PMCID: PMC10777022 DOI: 10.1016/j.heliyon.2023.e23915] [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: 06/20/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Background Tertiary lymphoid structure (TLS) is a unique organ that carries out tumor cell elimination at tumor sites. It is continuously stimulated by inflammatory tumor signals and has been found to augment immunotherapy response. However, the detailed mechanisms behind it still need to be defined. Methods To explore and grasp the whole picture of TLS from a pan-cancer view, we collected nine TLS-related genes from previous studies. We performed a comprehensive analysis of 9637 samples across 33 tumor types accessed from The Cancer Genome Atlas (TCGA) database. EdU, Transwell, and flow cytometry were performed on the feature gene PTGDS in U251 cells. The regulatory role of PTGDS on PD-L1 expression and macrophage polarization was verified. Results Alteration analysis showed that mutations of TLS-related genes were widespread and relatively high. Clustering analysis based on the expression of these nine genes obtained two distinct clusters, with high EIF1AY and PTGDS in cluster 2 and better overall survival in cluster 1. To distinguish the two clusters, we utilized six machine learning algorithms and filtrated EIF1AY, PTGDS, SKAP1, and RBP5 as the characteristic genes, among which the former two genes were proved to be hazardous. PTGDS was found to regulate PD-L1 expression and also promoted the proliferation and migration of U251 cells. The knockdown of PTGDS could reduce the migration of macrophages and inhibit the polarization of macrophages into M2-phenotype. In addition, we established a TLS score to demonstrate patients' TLS activity. The low TLS-score group overlapped with cluster 1 and displayed a better prognosis. Besides, the low TLS-score group was related to better immunotherapy responses. The HE staining of histopathological sections confirmed that the low TLS-score group exhibited higher infiltration of immune cells. Conclusion This study reveals broad molecular, tumorigenic, and immunogenic signatures for further functional and therapeutic studies of tertiary lymphoid structure. The TLS score we established effectively predicted immunotherapy response and patients' survival. Its future application and combination await more research.
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Affiliation(s)
- Wantao Wu
- The Animal Laboratory Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - He Li
- The Animal Laboratory Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Changsha Medical University, Changsha, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xisong Liang
- Department of Neurosurgery, Xiangya Hospital, Central South University Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Kun Liu
- Department of Neurosugery, The Second People's Hospital of Hunan Province, The Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Nan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- College of Bioinformatics Science and Technology, Harbin Medical University Harbin, China
| | - Shuyu Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Chi Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Zhang WJ, Yue KL, Wang JZ, Zhang Y. Association between heat shock factor protein 4 methylation and colorectal cancer risk and potential molecular mechanisms: A bioinformatics study. World J Gastrointest Oncol 2023; 15:2150-2168. [PMID: 38173437 PMCID: PMC10758642 DOI: 10.4251/wjgo.v15.i12.2150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 12/14/2023] Open
Abstract
BACKGROUND We previously demonstrated that heat shock factor protein 4 (HSF4) facilitates colorectal cancer (CRC) progression. DNA methylation, a major modifier of gene expression and stability, is involved in CRC development and outcome. AIM To investigate the correlation between HSF4 methylation and CRC risk, and to uncover the underlying molecular mechanisms. METHODS Differences in β values of HSF4 methylation loci in multiple malignancies and their correlation with HSF4 mRNA expression were analyzed based on Shiny Methylation Analysis Resource Tool. HSF4 methylation-related genes were identified by LinkedOmics in CRC, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed. Protein-protein interaction network of HSF4 methylation-related genes was constructed by String database and MCODE algorithm. RESULTS A total of 19 CpG methylation loci were identified in HSF4, and their β values were significantly increased in CRC tissues and exhibited a positive correlation with HSF4 mRNA expression. Unfortunately, the prognostic and diagnostic performance of these CpG loci in CRC patients was mediocre. In CRC, there were 1694 HSF4 methylation-related genes; 1468 of which displayed positive and 226 negative associations, and they were involved in regulating phenotypes such as immune, inflammatory, and metabolic reprogramming. EGFR, RELA, STAT3, FCGR3A, POLR2K, and AXIN1 are hub genes among the HSF4 methylation-related genes. CONCLUSION HSF4 is highly methylated in CRC, but there is no significant correlation between it and the prognosis and diagnosis of CRC. HSF4 methylation may serve as one of the ways in which HSF4 mediates the CRC process.
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Affiliation(s)
- Wen-Jing Zhang
- Department of Medical Oncology, The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan Province, China
| | - Ke-Lin Yue
- Department of Gastroenterology, The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan Province, China
| | - Jing-Zhai Wang
- Department of Gastroenterology, The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan Province, China
| | - Yu Zhang
- Department of Gastroenterology, The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan Province, China
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Liu Y, Yin Z, Wang Y, Chen H. Exploration and validation of key genes associated with early lymph node metastasis in thyroid carcinoma using weighted gene co-expression network analysis and machine learning. Front Endocrinol (Lausanne) 2023; 14:1247709. [PMID: 38144565 PMCID: PMC10739373 DOI: 10.3389/fendo.2023.1247709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023] Open
Abstract
Background Thyroid carcinoma (THCA), the most common endocrine neoplasm, typically exhibits an indolent behavior. However, in some instances, lymph node metastasis (LNM) may occur in the early stages, with the underlying mechanisms not yet fully understood. Materials and methods LNM potential was defined as the tumor's capability to metastasize to lymph nodes at an early stage, even when the tumor volume is small. We performed differential expression analysis using the 'Limma' R package and conducted enrichment analyses using the Metascape tool. Co-expression networks were established using the 'WGCNA' R package, with the soft threshold power determined by the 'pickSoftThreshold' algorithm. For unsupervised clustering, we utilized the 'ConsensusCluster Plus' R package. To determine the topological features and degree centralities of each node (protein) within the Protein-Protein Interaction (PPI) network, we used the CytoNCA plugin integrated with the Cytoscape tool. Immune cell infiltration was assessed using the Immune Cell Abundance Identifier (ImmuCellAI) database. We applied the Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine (SVM), and Random Forest (RF) algorithms individually, with the 'glmnet,' 'e1071,' and 'randomForest' R packages, respectively. Ridge regression was performed using the 'oncoPredict' algorithm, and all the predictions were based on data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. To ascertain the protein expression levels and subcellular localization of genes, we consulted the Human Protein Atlas (HPA) database. Molecular docking was carried out using the mcule 1-click Docking server online. Experimental validation of gene and protein expression levels was conducted through Real-Time Quantitative PCR (RT-qPCR) and immunohistochemistry (IHC) assays. Results Through WGCNA and PPI network analysis, we identified twelve hub genes as the most relevant to LNM potential from these two modules. These 12 hub genes displayed differential expression in THCA and exhibited significant correlations with the downregulation of neutrophil infiltration, as well as the upregulation of dendritic cell and macrophage infiltration, along with activation of the EMT pathway in THCA. We propose a novel molecular classification approach and provide an online web-based nomogram for evaluating the LNM potential of THCA (http://www.empowerstats.net/pmodel/?m=17617_LNM). Machine learning algorithms have identified ERBB3 as the most critical gene associated with LNM potential in THCA. ERBB3 exhibits high expression in patients with THCA who have experienced LNM or have advanced-stage disease. The differential methylation levels partially explain this differential expression of ERBB3. ROC analysis has identified ERBB3 as a diagnostic marker for THCA (AUC=0.89), THCA with high LNM potential (AUC=0.75), and lymph nodes with tumor metastasis (AUC=0.86). We have presented a comprehensive review of endocrine disruptor chemical (EDC) exposures, environmental toxins, and pharmacological agents that may potentially impact LNM potential. Molecular docking revealed a docking score of -10.1 kcal/mol for Lapatinib and ERBB3, indicating a strong binding affinity. Conclusion In conclusion, our study, utilizing bioinformatics analysis techniques, identified gene modules and hub genes influencing LNM potential in THCA patients. ERBB3 was identified as a key gene with therapeutic implications. We have also developed a novel molecular classification approach and a user-friendly web-based nomogram tool for assessing LNM potential. These findings pave the way for investigations into the mechanisms underlying differences in LNM potential and provide guidance for personalized clinical treatment plans.
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Affiliation(s)
- Yanyan Liu
- Department of General Surgery, The Third Affiliated Hospital of Anhui Medical University (The First People’s Hospital of Hefei), Hefei, Anhui, China
| | - Zhenglang Yin
- Department of General Surgery, The Third Affiliated Hospital of Anhui Medical University (The First People’s Hospital of Hefei), Hefei, Anhui, China
| | - Yao Wang
- Digestive Endoscopy Department, Jiangsu Province Hospital, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Haohao Chen
- Department of General Surgery, The Third Affiliated Hospital of Anhui Medical University (The First People’s Hospital of Hefei), Hefei, Anhui, China
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Yang Y, Tang X, Lin Z, Zheng T, Zhang S, Liu T, Yang X. An integrative evaluation of circadian gene TIMELESS as a pan-cancer immunological and predictive biomarker. Eur J Med Res 2023; 28:563. [PMID: 38053143 DOI: 10.1186/s40001-023-01519-3] [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: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND The gene TIMELESS, which is involved in the circadian clock and the cell cycle, has recently been linked to various human cancers. Nevertheless, the association between TIMELESS expression and the prognosis of individuals afflicted with pan-cancer remains largely unknown. OBJECTIVES The present study aims to exhaustively scrutinize the expression patterns, functional attributes, prognostic implications, and immunological contributions of TIMELESS across diverse types of human cancer. METHODS The expression of TIMELESS in normal and malignant tissues was examined, as well as their clinicopathologic and survival data. The characteristics of genetic alteration and molecular subtypes of cancers were also investigated. In addition, the relationship of TIMELESS with immune infiltration, tumor mutation burden (TMB), microsatellite instability (MSI), and drug sensitivity was illustrated. Immunohistochemistry (IHC) was used to validate the expression of TIMELESS in clinical patients with several types of cancer. RESULTS In contrast to the matching normal controls, most tumor types were found to often overexpress TIMELESS. Abnormal expression of TIMELESS was significantly related to more advanced tumor stage and poorer prognosis of breast cancer, as well as infiltrating immune cells such as cancer-associated fibroblast infiltration in various tumors. Multiple cancer types exhibited abnormal expression of TIMELESS, which was also highly correlated with MSI and TMB. More crucially, TIMELESS showed promise in predicting the effectiveness of immunotherapy and medication sensitivity in cancer therapy. Moreover, cell cycle, DNA replication, circadian rhythm, and mismatch repair were involved in the functional mechanisms of TIMELESS on carcinogenesis. Furthermore, immunohistochemical results manifested that the TIMELESS expression was abnormal in some cancers. CONCLUSIONS This study provides new insights into the link between the circadian gene TIMELESS and the development of various malignant tumors. The findings suggest that TIMELESS could be a prospective prognostic and immunological biomarker for pan-cancer.
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Affiliation(s)
- Yaocheng Yang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Xianzhe Tang
- Department of Orthopedics, Chenzhou First People's Hospital, Chenzhou, Hunan, China
| | - Zhengjun Lin
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Tao Zheng
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Sheng Zhang
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Xiaolun Yang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China.
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Li J, Yin Y, Huang H, Li M, Li H, Zhang M, Jiang C, Yang R. RUNX1 methylation as a cancer biomarker in differentiating papillary thyroid cancer from benign thyroid nodules. Epigenomics 2023; 15:1257-1272. [PMID: 38126720 DOI: 10.2217/epi-2023-0338] [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] [Indexed: 12/23/2023] Open
Abstract
Aim: It remains a challenge to accurately identify malignancy of thyroid nodules when biopsy is indeterminate. The authors aimed to investigate the abnormal DNA methylation signatures in papillary thyroid cancer (PTC) compared with benign thyroid nodules (BTNs). Methods: The authors performed genome profiling by 850K array and RNA sequencing in early-stage PTC and BTN tissue samples. The identified gene was validated in two independent case-control studies using mass spectrometry. Results: Hypomethylation of RUNX1 in PTC was identified and verified (all odds ratios: ≥1.50). RUNX1 methylation achieved good accuracy in differentiating early-stage PTC from BTNs, especially for younger women. Conclusion: The authors disclosed a significant association between RUNX1 hypomethylation and PTC, suggesting RUNX1 methylation as a potential biomarker for companion diagnosis of malignant thyroid nodules.
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Affiliation(s)
- Junjie Li
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, China
| | - Yifei Yin
- Department of Thyroid & Breast Surgery, Affiliated Huai'an Hospital of Xuzhou Medical University & Second People's Hospital of Huai'an, Huai'an, 223000, China
| | - Haixia Huang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, China
| | - Mengxia Li
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, China
| | - Hong Li
- Department of Pathology, Affiliated Huai'an Hospital of Xuzhou Medical University & Second People's Hospital of Huai'an, Huai'an, 223000, China
| | - Minmin Zhang
- Department of Thyroid & Breast Surgery, Affiliated Huai'an Hospital of Xuzhou Medical University & Second People's Hospital of Huai'an, Huai'an, 223000, China
| | - Chenxia Jiang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, China
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Dewenter I, Kumbrink J, Poxleitner P, Smolka W, Liokatis P, Fliefel R, Otto S, Obermeier KT. New insights into redox-related risk factors and therapeutic targets in oral squamous cell carcinoma. Oral Oncol 2023; 147:106573. [PMID: 37951115 DOI: 10.1016/j.oraloncology.2023.106573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 11/13/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is the most common cancer in the oral cavity accounting for 90 % of oral cancer with a global incidence of 350.000 new cases per year. Curative resection along with adjuvant radiation therapy or a combination of radiotherapy with chemotherapy remain as gold standard in treating OSCC. Still, local recurrence, lymph nodal recurrence, and complications of radiation remain the main cause of tumor-related mortality. Reactive oxygen species are not only correlated to the etiology of OSCC due to oxidative DNA damage, lipid peroxidation or effecting signal transduction cascades that effect cell proliferation and tumorigenesis, but are also of great interest in the therapy of OSCC patients. As induced oxidative stress can be used therapeutically for the induction of tumor cell death, redox targets might be a therapeutic addition to the conventional treatment options. In this review, we discuss markers of impaired redox homeostasis as well as potential redox-related treatment targets in OSCC.
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Affiliation(s)
- Ina Dewenter
- Department of Oral and Maxillofacial Surgery and Facial Plastic Surgery, University Hospital, Ludwig Maximilians University, 80337 Munich, Germany.
| | - Joerg Kumbrink
- Institute of Pathology, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | - Philipp Poxleitner
- Department of Oral and Maxillofacial Surgery and Facial Plastic Surgery, University Hospital, Ludwig Maximilians University, 80337 Munich, Germany
| | - Wenko Smolka
- Department of Oral and Maxillofacial Surgery and Facial Plastic Surgery, University Hospital, Ludwig Maximilians University, 80337 Munich, Germany
| | - Paris Liokatis
- Department of Oral and Maxillofacial Surgery and Facial Plastic Surgery, University Hospital, Ludwig Maximilians University, 80337 Munich, Germany
| | - Riham Fliefel
- Department of Oral and Maxillofacial Surgery and Facial Plastic Surgery, University Hospital, Ludwig Maximilians University, 80337 Munich, Germany
| | - Sven Otto
- Department of Oral and Maxillofacial Surgery and Facial Plastic Surgery, University Hospital, Ludwig Maximilians University, 80337 Munich, Germany
| | - Katharina Theresa Obermeier
- Department of Oral and Maxillofacial Surgery and Facial Plastic Surgery, University Hospital, Ludwig Maximilians University, 80337 Munich, Germany
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Liu Q, Qi J, Li W, Tian X, Zhang J, Liu F, Lu X, Zang H, Liu C, Ma C, Yu Y, Jiang S. Therapeutic effect and transcriptome-methylome characteristics of METTL3 inhibition in liver hepatocellular carcinoma. Cancer Cell Int 2023; 23:298. [PMID: 38012755 PMCID: PMC10683134 DOI: 10.1186/s12935-023-03096-1] [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: 07/12/2023] [Accepted: 10/11/2023] [Indexed: 11/29/2023] Open
Abstract
Methyltransferase-like 3 (METTL3) is the key subunit of methyltransferase complex responsible for catalyzing N6-methyladenosine (m6A) modification on mRNA, which is the most prevalent post-transcriptional modification in eukaryotes. In this study, we utilized online databases to analyze the association between METTL3 expression and various aspects of tumorigenesis, including gene methylation, immunity, and prognosis. Our investigation revealed that METTL3 serves as a prognostic marker and therapeutic target for liver hepatocellular carcinoma (LIHC). Through experimental studies, we observed frequent upregulation of METTL3 in LIHC tumor tissue and cells. Subsequent inhibition of METTL3 using a novel small molecule inhibitor, STM2457, significantly impeded tumor growth in LIHC cell lines, spheroids, and xenograft tumor model. Further, transcriptome and m6A sequencing of xenograft bodies unveiled that inhibition of METTL3-m6A altered genes enriched in SMAD and MAPK signaling pathways that are critical for tumorigenesis. These findings suggest that targeting METTL3 represents a promising therapeutic strategy for LIHC.
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Affiliation(s)
- Qingbin Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Shandong First Medical University, Jining, 272000, People's Republic of China
- Cisen Pharmaceutical Co. Ltd, Jining, 272000, China
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250100, Shandong, China
| | - Jingjing Qi
- Johannes Kepler University Linz, Altenberger Strasse 69, 4040, Linz, Austria
| | - Weiyang Li
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People's Hospital, Shandong First Medical University, Jining, 272000, People's Republic of China
| | - Jiaqi Zhang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Shandong First Medical University, Jining, 272000, People's Republic of China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Shandong First Medical University, Jining, 272000, People's Republic of China
| | - Xiulian Lu
- Cisen Pharmaceutical Co. Ltd, Jining, 272000, China
| | - Hengchang Zang
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250100, Shandong, China
| | - Chenqiao Liu
- Hepatobiliary Surgery Department, Jining First People's Hospital, Shandong First Medical University, Jining, 272000, China
| | - Changlin Ma
- Hepatobiliary Surgery Department, Jining First People's Hospital, Shandong First Medical University, Jining, 272000, China.
| | - Yong Yu
- Johannes Kepler University Linz, Altenberger Strasse 69, 4040, Linz, Austria.
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Shandong First Medical University, Jining, 272000, People's Republic of China.
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28
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Cheng MW, Mitra M, Coller HA. Pan-cancer landscape of epigenetic factor expression predicts tumor outcome. Commun Biol 2023; 6:1138. [PMID: 37973839 PMCID: PMC10654613 DOI: 10.1038/s42003-023-05459-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 10/13/2023] [Indexed: 11/19/2023] Open
Abstract
Oncogenic pathways that drive cancer progression reflect both genetic changes and epigenetic regulation. Here we stratified primary tumors from each of 24 TCGA adult cancer types based on the gene expression patterns of epigenetic factors (epifactors). The tumors for five cancer types (ACC, KIRC, LGG, LIHC, and LUAD) separated into two robust clusters that were better than grade or epithelial-to-mesenchymal transition in predicting clinical outcomes. The majority of epifactors that drove the clustering were also individually prognostic. A pan-cancer machine learning model deploying epifactor expression data for these five cancer types successfully separated the patients into poor and better outcome groups. Single-cell analysis of adult and pediatric tumors revealed that expression patterns associated with poor or worse outcomes were present in individual cells within tumors. Our study provides an epigenetic map of cancer types and lays a foundation for discovering pan-cancer targetable epifactors.
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Affiliation(s)
- Michael W Cheng
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Mithun Mitra
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hilary A Coller
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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29
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Yamada Y, Venkadakrishnan VB, Mizuno K, Bakht M, Ku SY, Garcia MM, Beltran H. Targeting DNA methylation and B7-H3 in RB1-deficient and neuroendocrine prostate cancer. Sci Transl Med 2023; 15:eadf6732. [PMID: 37967200 PMCID: PMC10954288 DOI: 10.1126/scitranslmed.adf6732] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 10/25/2023] [Indexed: 11/17/2023]
Abstract
Aberrant DNA methylation has been implicated as a key driver of prostate cancer lineage plasticity and histologic transformation to neuroendocrine prostate cancer (NEPC). DNA methyltransferases (DNMTs) are highly expressed, and global DNA methylation is dysregulated in NEPC. We identified that deletion of DNMT genes decreases expression of neuroendocrine lineage markers and substantially reduced NEPC tumor development and metastasis in vivo. Decitabine, a pan-DNMT inhibitor, attenuated tumor growth in NEPC patient-derived xenograft models, as well as retinoblastoma gene (RB1)-deficient castration-resistant prostate adenocarcinoma (CRPC) models compared with RB1-proficient CRPC. We further found that DNMT inhibition increased expression of B7 homolog 3 (B7-H3), an emerging druggable target, via demethylation of B7-H3. We tested DS-7300a (i-DXd), an antibody-drug conjugate targeting B7-H3, alone and in combination with decitabine in models of advanced prostate cancer. There was potent single-agent antitumor activity of DS-7300a in both CRPC and NEPC bearing high expression of B7-H3. In B7-H3-low models, combination therapy of decitabine plus DS-7300a resulted in enhanced response. DNMT inhibition may therefore be a promising therapeutic target for NEPC and RB1-deficient CRPC and may sensitize B7-H3-low prostate cancer to DS-7300a through increasing target expression. NEPC and RB1-deficient CRPC represent prostate cancer subgroups with poor prognosis, and the development of biomarker-driven therapeutic strategies for these populations may ultimately help improve patient outcomes.
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Affiliation(s)
- Yasutaka Yamada
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Varadha Balaji Venkadakrishnan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Kei Mizuno
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Martin Bakht
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Sheng-Yu Ku
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Maria Mica Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
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30
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Yan K, Niu L, Wu B, He C, Deng L, Chen C, Lan Z, Lin C, Kuang W, Lin H, Zou J, Zhang W, Luo Z. Copy number variants landscape of multiple cancers and clinical applications based on NGS gene panel. Ann Med 2023; 55:2280708. [PMID: 37967237 PMCID: PMC10653745 DOI: 10.1080/07853890.2023.2280708] [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: 06/21/2023] [Accepted: 10/30/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND The rapid adoption of next-generation sequencing in clinical oncology has enabled detection of molecular biomarkers which are shared between multiple tumour types. Intra-tumour heterogeneity is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the tumour-related copy number variants (CNVs), as key regulators of cancer origination, development, and progression, across various types of cancers are poorly understood. METHODS We performed pan-cancer CNV analysis of cancer-related genes in 15 types of cancers including 1438 cancerous patients by next-generation sequencing using a commercially available pan-cancer panel (Onco PanScan™). Downstream bioinformatics analysis was performed in order to detect CNVs, cluster analysis of the found CNVs, and comparison of the frequency of gained CNVs between different types of cancers. LASSO analysis was used for identification of the most important CNVs. RESULTS We also identified 523 CNVs among which 16 CNVs were common while 22 CNVs were caner-specific CNVs. Meanwhile, FAM58A was most commonly found in all studied cancers in this study and significant differences were found in FAM58A between female and male patients (p = .001). Common CNVs, such as FOXA1, NFKBIA, HEY1, MECOM, CHD7, AGO2, were mutated in 6.79%, 8.45%, 7.51%, 6.43%, 7.59%, 8.16% of tumours, while most of these mutations have proven roles in positive regulation of transcription from RNA polymerase II promoter. 11 features including sex, DIS3, EPHB1, ERBB2, FLT1, HCK, KEAP1, MYD88, PARP3, TBX3, and TOP2A were found as the key features for classification of cancers using CNVs. CONCLUSION The 16 common CNVs between cancers can be used to identify the target of pan-cancer drug design and targeted therapies. Additionally, 22 caner-specific CNVs can be used as unique diagnostic markers for each cancer type.
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Affiliation(s)
- Kangpeng Yan
- Department of Abdominal Oncology Surgery, Jiangxi Cancer Hospital, Nanchang, China
| | - Li Niu
- CheerLand Clinical Laboratory Co., Ltd., Peking University Medical Industrial Park, Zhongguancun Life Science Park, Beijing, China
| | - Boyu Wu
- Department of General Surgery, Shangrao Municipal Hospital, Shangrao, China
| | - Chongwu He
- Department of Breast Surgery, Jiangxi Cancer Hospital, Nanchang, China
| | - Lei Deng
- Department of Medical Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Chuan Chen
- Shenzhen Cheerland Biotechnology Co., Ltd., Shenzhen, China
| | - Zhangzhang Lan
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Chao Lin
- Department of Abdominal Oncology Surgery, Jiangxi Cancer Hospital, Nanchang, China
| | - Weihua Kuang
- Department of Abdominal Oncology Surgery, Jiangxi Cancer Hospital, Nanchang, China
| | - Huihong Lin
- Operating Room, Jiangxi Cancer Hospital, Nanchang, China
| | - Jun Zou
- Department of Abdominal Oncology Surgery, Jiangxi Cancer Hospital, Nanchang, China
| | - Wenyong Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Zhiqiang Luo
- Chest Radiotherapy Department 1, Jiangxi Cancer Hospital, Nanchang, China
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Barnell EK, Wurtzler EM, La Rocca J, Fitzgerald T, Petrone J, Hao Y, Kang Y, Holmes FL, Lieberman DA. Multitarget Stool RNA Test for Colorectal Cancer Screening. JAMA 2023; 330:1760-1768. [PMID: 37870871 PMCID: PMC10594178 DOI: 10.1001/jama.2023.22231] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023]
Abstract
Importance Noninvasive tests for colorectal cancer screening must include sensitive detection of colorectal cancer and precancerous lesions. These tests must be validated for the intended-use population, which includes average-risk individuals 45 years or older. Objective To evaluate the sensitivity and specificity of a noninvasive, multitarget stool RNA (mt-sRNA) test (ColoSense) test compared with results from a colonoscopy. Design, Setting, and Participants This phase 3 clinical trial (CRC-PREVENT) was a blinded, prospective, cross-sectional study to support a premarket approval application for a class III medical device. A total of 8920 participants were identified online using social media platforms and enrolled from June 2021 to June 2022 using a decentralized nurse call center. All participants completed the mt-sRNA test, which incorporated a commercially available fecal immunochemical test (FIT), concentration of 8 RNA transcripts, and participant-reported smoking status. Stool samples were collected prior to participants completing a colonoscopy at their local endoscopy center. The mt-sRNA test results (positive or negative) were compared with index lesions observed on colonoscopy. Over the course of 12 months, individuals 45 years and older were enrolled in the clinical trial using the decentralized recruitment strategy. Participants were enrolled from 49 US states and obtained colonoscopies at more than 3800 different endoscopy centers. Main Outcomes and Measures The primary outcomes included the sensitivity of the mt-sRNA test for detecting colorectal cancer and advanced adenomas and the specificity for no lesions on colonoscopy. Results The mean (range) age of participants was 55 (45-90) years, with 4% self-identified as Asian, 11% as Black, and 7% as Hispanic. Of the 8920 eligible participants, 36 (0.40%) had colorectal cancer and 606 (6.8%) had advanced adenomas. The mt-sRNA test sensitivity for detecting colorectal cancer was 94%, sensitivity for detecting advanced adenomas was 46%, and specificity for no lesions on colonoscopy was 88%. The mt-sRNA test showed significant improvement in sensitivity for colorectal cancer (94% vs 78%; McNemar P = .01) and advanced adenomas (46% vs 29%; McNemar P < .001) compared with results of the FIT. Conclusions and Relevance In individuals 45 years and older, the mt-sRNA test showed high sensitivity for colorectal neoplasia (colorectal cancer and advanced adenoma) with significant improvement in sensitivity relative to the FIT. Specificity for no lesions on colonoscopy was comparable to existing molecular diagnostic tests. Trial Registration ClinicalTrials.gov Identifier: NCT04739722.
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Affiliation(s)
- Erica K. Barnell
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri
- Geneoscopy Inc, St Louis, Missouri
| | | | | | | | | | - Yansheng Hao
- University of Rochester Medical Center, Rochester, New York
| | | | | | - David A. Lieberman
- Division of Gastroenterology, Department of Medicine, Oregon Health and Science University, Portland
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32
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Fan YC, Wu W, Leng XF, Zhang HW. Utility of G protein-coupled oestrogen receptor 1 as a biomarker for pan-cancer diagnosis, prognosis and immune infiltration: a comprehensive bioinformatics analysis. Aging (Albany NY) 2023; 15:12021-12067. [PMID: 37921845 PMCID: PMC10683611 DOI: 10.18632/aging.205162] [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: 01/15/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND The G protein-coupled oestrogen receptor (GPER) 1 mediates non-genomic oestrogen-related signalling and plays an important role in the regulation of cell growth and programmed cell death through multiple downstream pathways. Despite the increasing interest in the role of GPER1 in cancer development, no pan-cancer analysis has been available for GPER1. METHODS In this study we performed a comprehensive analysis of the role of GPER1 in pan-cancer via Human Protein Atlas (HPA), The Cancer Genome Atlas (TCGA), University of California, Santa Cruz Xena (UCSC XENA), Genotype-Tissue Expression (GTEx), MethSurv, The University of Alabama at Birmingham CANcer data analysis Portal (UALCAN), cBioPortal, STRING and TISIDB detabases, followed by enrichment analysis using R software. RESULTS GPER1 was widely expressed in tissues and organs and differed in expression from normal tissue in a variety of cancers. In diagnostic assessment, it's Area Under the Curve (AUC) surpassed 0.9 in nine cancer types. Survival analysis showed that GPER1 was correlated with the prognosis of 11 cancer types. Moreover, GPER1 expression was associated with immune infiltration in multiple cancers. CONCLUSIONS In summary, GPER1 has good diagnostic or prognostic value across various malignancies. Together with its extensive correlation with immune components, the aforementioned results suggests that GPER1 shows promise in tumour diagnosis and prognosis, providing new ideas for precise and personalised anti-tumour strategies.
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Affiliation(s)
- Yu-Chao Fan
- Department of Anesthesiology, Sichuan Cancer Center, Sichuan Cancer Hospital and Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Wen Wu
- Department of Anesthesiology, Xichang People’s Hospital, Xichang, Sichuan, China
| | - Xue-Feng Leng
- Division of Thoracic Surgery, Sichuan Cancer Center, Sichuan Cancer Hospital and Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Hong-Wei Zhang
- Department of Anesthesiology, Sichuan Cancer Center, Sichuan Cancer Hospital and Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
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Huang C, Zhang K, Guo Y, Shen C, Liu X, Huang H, Dou X, Yu B. The crucial roles of m 6A RNA modifications in cutaneous cancers: Implications in pathogenesis, metastasis, drug resistance, and targeted therapies. Genes Dis 2023; 10:2320-2330. [PMID: 37554186 PMCID: PMC10404882 DOI: 10.1016/j.gendis.2022.03.006] [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: 12/20/2021] [Revised: 02/11/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification on RNA. It is a dynamical and reversible process, which is regulated by m6A methyltransferase and m6A demethylase. The m6A modified RNA can be specifically recognized by the m6A reader, leading to RNA splicing, maturation, degradation or translation. The abnormality of m6A RNA modification is closely related to a variety of biological processes, especially the occurrence and development of tumors. Recent studies have shown that m6A RNA modification is involved in the pathogenesis of skin cancers. However, the precise molecular mechanisms of m6A-mediated cutaneous tumorigenesis have not been fully elucidated. Therefore, this review will summarize the biological characteristics of m6A modification, its regulatory role and mechanism in skin cancers, and the recent research progress of m6A-related molecular drugs, aiming to provide new ideas for clinical diagnosis and targeted therapy of cutaneous cancers.
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Affiliation(s)
- Cong Huang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, China
| | - Kaoyuan Zhang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China
| | - Yang Guo
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, China
| | - Changbing Shen
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China
| | - Xiaoming Liu
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China
| | - Haiyan Huang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China
| | - Xia Dou
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China
| | - Bo Yu
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, China
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Desaulniers D, Zhou G, Stalker A, Cummings-Lorbetskie C. Effects of Copper or Zinc Organometallics on Cytotoxicity, DNA Damage and Epigenetic Changes in the HC-04 Human Liver Cell Line. Int J Mol Sci 2023; 24:15580. [PMID: 37958568 PMCID: PMC10650525 DOI: 10.3390/ijms242115580] [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: 09/12/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
Copper and zinc organometallics have multiple applications and many are considered "data-poor" because the available toxicological information is insufficient for comprehensive health risk assessments. To gain insight into the chemical prioritization and potential structure activity relationship, the current work compares the in vitro toxicity of nine "data-poor" chemicals to five structurally related chemicals and to positive DNA damage inducers (4-nitroquinoline-oxide, aflatoxin-B1). The HC-04 non-cancer human liver cell line was used to investigate the concentration-response effects (24 h and 72 h exposure) on cell proliferation, DNA damage (γH2AX and DNA unwinding assays), and epigenetic effects (global genome changes in DNA methylation and histone modifications using flow cytometry). The 24 h exposure screening data (DNA abundance and damage) suggest a toxicity hierarchy, starting with copper dimethyldithiocarbamate (CDMDC, CAS#137-29-1) > zinc diethyldithiocarbamate (ZDEDC, CAS#14324-55-1) > benzenediazonium, 4-chloro-2-nitro-, and tetrachlorozincate(2-) (2:1) (BDCN4CZ, CAS#14263-89-9); the other chemicals were less toxic and had alternate ranking positions depending on assays. The potency of CDMDC for inducing DNA damage was close to that of the human hepatocarcinogen aflatoxin-B1. Further investigation using sodium-DMDC (SDMDC, CAS#128-04-1), CDMDC and copper demonstrated the role of the interactions between copper and the DMDC organic moiety in generating a high level of CDMDC toxicity. In contrast, additive interactions were not observed with respect to the DNA methylation flow cytometry data in 72 h exposure experiments. They revealed chemical-specific effects, with hypo and hypermethylation induced by copper chloride (CuCl2, CAS#10125-13-0) and zinc-DMDC (ZDMDC, CAS#137-30-4), respectively, but did not show any significant effect of CDMDC or SDMDC. Histone-3 hypoacetylation was a sensitive flow cytometry marker of 24 h exposure to CDMDC. This study can provide insights regarding the prioritization of chemicals for future study, with the aim being to mitigate chemical hazards.
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Affiliation(s)
- Daniel Desaulniers
- Health Canada, Environmental Health Science and Research Bureau, Ottawa, ON K1A 0K9, Canada; (D.D.)
| | - Gu Zhou
- Health Canada, Environmental Health Science and Research Bureau, Ottawa, ON K1A 0K9, Canada; (D.D.)
| | - Andrew Stalker
- Health Canada, Regulatory Research Division, Biologics and Radiopharmaceutical Drugs Directorate, Ottawa, ON K1A 0K9, Canada
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Zhao J, Dong Y, Bai H, Bai F, Yan X, Duan J, Wan R, Xu J, Fei K, Wang J, Wang Z. Multi-omics indicators of long-term survival benefits after immune checkpoint inhibitor therapy. CELL REPORTS METHODS 2023; 3:100596. [PMID: 37738982 PMCID: PMC10626191 DOI: 10.1016/j.crmeth.2023.100596] [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: 02/18/2023] [Revised: 05/08/2023] [Accepted: 08/30/2023] [Indexed: 09/24/2023]
Abstract
Molecular indicators of long-term survival (LTS) in response to immune-checkpoint inhibitor (ICI) treatment have the potential to provide both mechanistic and therapeutic insights. In this study, we construct predictive models of LTS following ICI therapy based on data from 158 clinical trials involving 21,023 patients of 25 cancer types with available 1-year overall survival (OS) rates. We present evidence for the use of 1-year OS rate as a surrogate for LTS. Based on these and corresponding TCGA multi-omics data, total neoantigen, metabolism score, CD8+ T cell, and MHC_score were identified as predictive biomarkers. These were integrated into a Gaussian process regression model that estimates "long-term survival predictive score of immunotherapy" (iLSPS). We found that iLSPS outperformed the predictive capabilities of individual biomarkers and successfully predicted LTS of patient groups with melanoma and lung cancer. Our study explores the feasibility of modeling LTS based on multi-omics indicators and machine-learning methods.
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Affiliation(s)
- Jie Zhao
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Yiting Dong
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Hua Bai
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100021, China
| | - Xiaoyan Yan
- Clinical Research Institute, Peking University, Beijing 100021, China
| | - Jianchun Duan
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Rui Wan
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Jiachen Xu
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Kailun Fei
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Jie Wang
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China.
| | - Zhijie Wang
- CAMS Key Laboratory of Translational Research on Lung Cancer, State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China.
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Loo CE, Hix MA, Wang T, Cisneros GA, Kohli RM. Revealing Drivers for Carboxy- S-adenosyl-l-methionine Use by Neomorphic Variants of a DNA Methyltransferase. ACS Chem Biol 2023; 18:2224-2232. [PMID: 37379458 PMCID: PMC10592258 DOI: 10.1021/acschembio.3c00184] [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] [Indexed: 06/30/2023]
Abstract
Methylation of DNA plays a key role in diverse biological processes spanning from bacteria to mammals. DNA methyltransferases (MTases) typically employ S-adenosyl-l-methionine (SAM) as a critical cosubstrate and the relevant methyl donor for modification of the C5 position of cytosine. Recently, work on the CpG-specific bacterial MTase, M.MpeI, has shown that a single N374K point mutation can confer the enzyme with the neomorphic ability to use the sparse, naturally occurring metabolite carboxy-S-adenosyl-l-methionine (CxSAM) in order to generate the unnatural DNA modification, 5-carboxymethylcytosine (5cxmC). Here, we aimed to investigate the mechanistic basis for this DNA carboxymethyltransferase (CxMTase) activity by employing a combination of computational modeling and in vitro characterization. Modeling of substrate interactions with the enzyme variant allowed us to identify a favorable salt bridge between CxSAM and N374K that helps to rationalize selectivity of the CxMTase. Unexpectedly, we also discovered a potential role for a key active site E45 residue that makes a bidentate interaction with the ribosyl sugar of CxSAM, located on the opposite face of the CxMTase active site. Prompted by these modeling results, we further explored the space-opening E45D mutation and found that the E45D/N374K double mutant in fact inverts selectivity, preferring CxSAM over SAM in biochemical assays. These findings provide new insight into CxMTase active site architecture and may offer broader utility given the numerous opportunities offered by using SAM analogs for selective molecular labeling in concert with nucleic acid or even protein-modifying MTases.
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Affiliation(s)
- Christian E. Loo
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Mark A. Hix
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Tong Wang
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - G. Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75801, United States; Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75801, United States
| | - Rahul M. Kohli
- Department of Medicine and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Alzahrani AS. Clinical use of Molecular Data in Thyroid Nodules and Cancer. J Clin Endocrinol Metab 2023; 108:2759-2771. [PMID: 37200449 DOI: 10.1210/clinem/dgad282] [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: 04/12/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/20/2023]
Abstract
Over the past 3 decades, advances in the molecular genetics of thyroid cancer (TC) have been translated into diagnostic tests, prognostic markers, and therapeutic agents. The main drivers in differentiated TC pathogenesis are single-point mutations and gene fusions in components of the Mitogen-activated protein kinase (MAPK) and phosphoinositide-3-kinase-protein kinase B/Akt (PI3K/Akt) pathways. Other important genetic alterations in the more advanced types of TC include TERT promoter, TP53, EIF1AX, and epigenetic alterations. Using this knowledge, several molecular tests have been developed for cytologically indeterminate thyroid nodules. Currently, 3 commercially available tests are in use including a DNA/RNA-based test (ThyroSeq v.3), an RNA-based test (Afirma Gene Sequencing Classifier), and a hybrid DNA/miRNA test, ThyGeNEXT/ThyraMIR. These tests are mostly used to rule out malignancy in Bethesda III and IV thyroid nodules because they all have high sensitivities and negative predictive values. Their common use, predominantly in the United States, has resulted in a significant reduction in unnecessary thyroid surgeries for benign nodules. Some of these tests also provide information on the underlying molecular drivers of TC; this may support decision making in initial TC management planning, although this practice has not yet been widely adopted. More importantly, molecular testing is essential in patients with advanced disease before using specific mono-kinase inhibitors (eg, selpercatinib for RET-altered TC) because these drugs are ineffective in the absence of a specific molecular target. This mini-review discusses the utilization of molecular data in the clinical management of patients with thyroid nodules and TC in these different clinical situations.
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Affiliation(s)
- Ali S Alzahrani
- Department of Medicine and Department of Molecular Oncology, King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia
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Liu C, Tang H, Hu N, Li T. Methylomics and cancer: the current state of methylation profiling and marker development for clinical care. Cancer Cell Int 2023; 23:242. [PMID: 37840147 PMCID: PMC10577916 DOI: 10.1186/s12935-023-03074-7] [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: 07/14/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
Epigenetic modifications have long been recognized as an essential level in transcriptional regulation linking behavior and environmental conditions or stimuli with biological processes and disease development. Among them, methylation is the most abundant of these reversible epigenetic marks, predominantly occurring on DNA, RNA, and histones. Methylation modification is intimately involved in regulating gene transcription and cell differentiation, while aberrant methylation status has been linked with cancer development in several malignancies. Early detection and precise restoration of dysregulated methylation form the basis for several epigenetics-based therapeutic strategies. In this review, we summarize the current basic understanding of the regulation and mechanisms responsible for methylation modification and cover several cutting-edge research techniques for detecting methylation across the genome and transcriptome. We then explore recent advances in clinical diagnostic applications of methylation markers of various cancers and address the current state and future prospects of methylation modifications in therapies for different diseases, especially comparing pharmacological methylase/demethylase inhibitors with the CRISPRoff/on methylation editing systems. This review thus provides a resource for understanding the emerging role of epigenetic methylation in cancer, the use of methylation-based biomarkers in cancer detection, and novel methylation-targeted drugs.
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Affiliation(s)
- Chengyin Liu
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Georgetown University, Washington, DC, USA
| | - Han Tang
- BioChain (Beijing) Science & Technology Inc., Beijing, People's Republic of China
| | - Nana Hu
- BioChain (Beijing) Science & Technology Inc., Beijing, People's Republic of China
| | - Tianbao Li
- Department of Molecular Medicine, The University of Texas Health, San Antonio, USA.
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Camilo V, Pacheco MB, Moreira-Silva F, Outeiro-Pinho G, Gaspar VM, Mano JF, Marques CJ, Henrique R, Jerónimo C. Novel Insights on the Role of Epigenetics in Androgen Receptor's Expression in Prostate Cancer. Biomolecules 2023; 13:1526. [PMID: 37892208 PMCID: PMC10605369 DOI: 10.3390/biom13101526] [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: 08/28/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The androgens/androgen receptor (AR) axis is the main therapeutic target in prostate cancer (PCa). However, while initially responsive, a subset of tumors loses AR expression through mechanisms putatively associated with epigenetic modifications. In this study, we assessed the link between the presence of CpG methylation in the 5'UTR and promoter regions of AR and loss of AR expression. Hence, we characterized and compared the methylation signature at CpG resolution of these regulatory regions in vitro, both at basal levels and following treatment with 5-aza-2-deoxycytidine (DAC) alone, or in combination with Trichostatin A (TSA). Our results showed heterogeneity in the methylation signature of AR negative cell lines and pinpointed the proximal promoter region as the most consistently methylated site in DU-145. Furthermore, this region was extremely resistant to the demethylating effects of DAC and was only significantly demethylated upon concomitant treatment with TSA. Nevertheless, no AR re-expression was detected at the mRNA or protein level. Importantly, after treatment, there was a significant increase in repressive histone marks at AR region 1 in DU-145 cells. Altogether, our data indicate that AR region 1 genomic availability is crucial for AR expression and that the inhibition of histone methyltransferases might hold promise for AR re-expression.
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Affiliation(s)
- Vânia Camilo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
| | - Mariana Brütt Pacheco
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
| | - Filipa Moreira-Silva
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
| | - Gonçalo Outeiro-Pinho
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
| | - Vítor M. Gaspar
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (V.M.G.)
| | - João F. Mano
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (V.M.G.)
| | - C. Joana Marques
- Genetics Unit, Department of Pathology, Faculty of Medicine, University of Porto (FMUP), Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal;
- i3S-Institute for Research and Innovation in Health, University of Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
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Zhu J, Chen Q, Zeng L, Gao H, Wu T, He Y, Xu J, Pang J, Peng J, Deng Y, Han Y, Yi W. Multi-omics analysis reveals the involvement of origin recognition complex subunit 6 in tumor immune regulation and malignant progression. Front Immunol 2023; 14:1236806. [PMID: 37901236 PMCID: PMC10602784 DOI: 10.3389/fimmu.2023.1236806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Background Origin recognition complex 6 (ORC6) is one of the six highly conserved subunit proteins required for DNA replication and is essential for maintaining genome stability during cell division. Recent research shows that ORC6 regulates the advancement of multiple cancers; however, it remains unclear what regulatory impact it has on the tumor immune microenvironment. Methods Unpaired Wilcoxon rank sum and signed rank tests were used to analyze the differences in the expression of ORC6 in normal tissues and corresponding tumor tissues. Multiple online databases have evaluated the genetic alterations, protein expression and localization, and clinical relevance of ORC6. To evaluate the potential prognostic impact and diagnostic significance of ORC6 expression, we carried out log-rank, univariate Cox regression, and receiver operating characteristic curve analysis. The ICGC-LIRI-JP cohort, CGGA-301 cohort, CGGA-325 cohort, CGGA-693 cohort, and GSE13041 cohort were used for external validation of the study findings. The associations between ORC6 expression and immune cell infiltration, immune checkpoint expression, and immunotherapy cohorts was further analyzed. To explore the functional and signaling pathways related to ORC6 expression, gene set enrichment analysis was performed. To clarify the expression and function of ORC6 in hepatocellular carcinoma (LIHC) and glioma, we conducted in vitro experiments. Results Expression of ORC6 is upregulated in the majority of cancer types and is associated with poor patient prognosis, notably in cases of LIHC and gliomas. In addition, ORC6 may be involved in multiple signaling pathways related to cancer progression and immune regulation. High expression of ORC6 correlates with an immunosuppressive state in the tumor microenvironment. The results of further immunotherapy cohort analysis suggested that patients in the ORC6 high-expression group benefited from immunotherapy. Inhibiting ORC6 expression suppressed the proliferative and migratory abilities of LIHC and glioma cells. Conclusion High expression of ORC6 may be used as a biomarker to predict the poor prognosis of most tumor patients. The high expression of ORC6 may be involved in the regulation of the tumor immunosuppressive environment, and it is expected to become a molecular target for inhibiting tumor progression.
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Affiliation(s)
- Jinfeng Zhu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Qitong Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Liyun Zeng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Hongyu Gao
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Tong Wu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Yeqing He
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Jiachi Xu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Jian Pang
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Jing Peng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Yueqiong Deng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Yi Han
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
| | - Wenjun Yi
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, Hunan, China
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Xie J, Gan L, Xue B, Wang X, Pei X. Emerging roles of interactions between ncRNAs and other epigenetic modifications in breast cancer. Front Oncol 2023; 13:1264090. [PMID: 37901333 PMCID: PMC10602744 DOI: 10.3389/fonc.2023.1264090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023] Open
Abstract
Up till the present moment, breast cancer is still the leading cause of cancer-related death in women worldwide. Although the treatment methods and protocols for breast cancer are constantly improving, the long-term prognosis of patients is still not optimistic due to the complex heterogeneity of the disease, multi-organ metastasis, chemotherapy and radiotherapy resistance. As a newly discovered class of non-coding RNAs, ncRNAs play an important role in various cancers. Especially in breast cancer, lncRNAs have received extensive attention and have been confirmed to regulate cancer progression through a variety of pathways. Meanwhile, the study of epigenetic modification, including DNA methylation, RNA methylation and histone modification, has developed rapidly in recent years, which has greatly promoted the attention to the important role of non-coding RNAs in breast cancer. In this review, we carefully and comprehensively describe the interactions between several major classes of epigenetic modifications and ncRNAs, as well as their different subsequent biological effects, and discuss their potential for practical clinical applications.
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Affiliation(s)
| | | | | | | | - Xinhong Pei
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Xu P, Zhang B. Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types. Genome Res 2023; 33:1806-1817. [PMID: 37907329 PMCID: PMC10691533 DOI: 10.1101/gr.278063.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/22/2023] [Indexed: 11/02/2023]
Abstract
Cancer is a complex disease with diverse molecular mechanisms that affect patient prognosis. Network-based approaches are effective in revealing a holistic picture of cancer prognosis and gene interactions. However, a comprehensive landscape of coexpression networks and prognostic gene modules across multiple cancer types remains elusive. In this study, we performed a systematic analysis of coexpression networks in 32 cancer types. Our analysis identified 4749 prognostic modules that play a vital role in regulating cancer progression. Integrative epigenomic analyses revealed that these modules were regulated by interactions between gene expression and methylation. Coregulated genes of network modules were enriched in chromosome cytobands and preferentially localized in open chromatin regions. The preserved network modules formed 330 module clusters that resided in chromosome hot spots. The cancer-type-specific prognostic modules participated in unique essential biological processes in different cancer types. Overall, our study provides rich resources of prevalent gene networks and underlying multiscale regulatory mechanisms driving cancer prognosis, which lay a foundation for biomarker discovery and therapeutic target development.
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Affiliation(s)
- Peng Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA;
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA;
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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Kang Z, Jiang L, Chen D, Yan G, Zhang G, Lai Y, Zeng Q, Wang X. Whole genome methylation sequencing reveals epigenetic landscape and abnormal expression of FABP5 in extramammary Paget's disease. Skin Res Technol 2023; 29:e13497. [PMID: 37881057 PMCID: PMC10579628 DOI: 10.1111/srt.13497] [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: 08/31/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Extramammary Paget's disease (EMPD) is a rare cutaneous malignant tumor with a high recurrence rate after surgery. However, the genetic and epigenetic alterations underlying its pathogenesis remain unknown. DNA methylation is an important epigenetic modification involved in many biological processes. METHODS In this study, enzymatic methyl-sequencing (EM-seq) technique was used to investigate the landscape of genome-wide DNA methylation from three pairs of tumor tissues and adjacent tissues of patients with EMPD. Additionally, we conducted histopathological examinations to assess the expression of fatty acid-binding protein 5 (FABP5) in another three paired samples from EMPD patients. RESULTS The cluster analysis showed the good quality of the samples. A differential methylation region (DMR) heat map was used to quantitatively characterize genome-wide methylation differences between tumors and controls. Global DNA methylation level is lower in EMPD tissue compared to matched controls, indicating that DNA methylation discriminates between tumor and normal skin. And the top hypomethylation gene on the promoter region in tumor tissues was FABP5 on chromosome 8 with 38.44% decreased median methylation. We next identified the expression of FABP5 in paired tumors and adjacent tissues in three additional patients with EMPD. Immunofluorescence results showed FABP5 highly expressed in tumor tissues and co-located with CK7, CK20 and EMA. GO and KEGG enrichment analysis showed DMR genes on promoter are mainly enriched in the calcium ion transport, GTPase mediated signal transduction, Rap1 signaling pathway and GnRH signaling pathway. CONCLUSION Taken together, our findings provide the first description of the whole genome methylation map of EMPD and identify FABP5 as a pathogenic target of EMPD.
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Affiliation(s)
- Ziwei Kang
- Institute of PhotomedicineShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
- Skin Cancer CenterShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Long Jiang
- Skin Cancer CenterShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Diyan Chen
- Institute of PhotomedicineShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
- Skin Cancer CenterShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Guorong Yan
- Institute of PhotomedicineShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
- Skin Cancer CenterShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Guolong Zhang
- Institute of PhotomedicineShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
- Skin Cancer CenterShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Yongxian Lai
- Skin Cancer CenterShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Qingyu Zeng
- Institute of PhotomedicineShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
- Skin Cancer CenterShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
| | - Xiuli Wang
- Institute of PhotomedicineShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
- Skin Cancer CenterShanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghaiChina
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Liang WW, Lu RJH, Jayasinghe RG, Foltz SM, Porta-Pardo E, Geffen Y, Wendl MC, Lazcano R, Kolodziejczak I, Song Y, Govindan A, Demicco EG, Li X, Li Y, Sethuraman S, Payne SH, Fenyö D, Rodriguez H, Wiznerowicz M, Shen H, Mani DR, Rodland KD, Lazar AJ, Robles AI, Ding L. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin. Cancer Cell 2023; 41:1567-1585.e7. [PMID: 37582362 DOI: 10.1016/j.ccell.2023.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/30/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
DNA methylation plays a critical role in establishing and maintaining cellular identity. However, it is frequently dysregulated during tumor development and is closely intertwined with other genetic alterations. Here, we leveraged multi-omic profiling of 687 tumors and matched non-involved adjacent tissues from the kidney, brain, pancreas, lung, head and neck, and endometrium to identify aberrant methylation associated with RNA and protein abundance changes and build a Pan-Cancer catalog. We uncovered lineage-specific epigenetic drivers including hypomethylated FGFR2 in endometrial cancer. We showed that hypermethylated STAT5A is associated with pervasive regulon downregulation and immune cell depletion, suggesting that epigenetic regulation of STAT5A expression constitutes a molecular switch for immunosuppression in squamous tumors. We further demonstrated that methylation subtype-enrichment information can explain cell-of-origin, intra-tumor heterogeneity, and tumor phenotypes. Overall, we identified cis-acting DNA methylation events that drive transcriptional and translational changes, shedding light on the tumor's epigenetic landscape and the role of its cell-of-origin.
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Affiliation(s)
- Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rita Jui-Hsien Lu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Reyka G Jayasinghe
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Steven M Foltz
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Eduard Porta-Pardo
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rossana Lazcano
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Iga Kolodziejczak
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Yizhe Song
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Akshay Govindan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Elizabeth G Demicco
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Xiang Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Sunantha Sethuraman
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Heliodor Swiecicki Clinical Hospital in Poznań, Ul. Przybyszewskiego 49, 60-355 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA.
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Nguyen TT, Rajakannu P, Pham MDT, Weman L, Jucht A, Buri MC, Van Dommelen K, Hegi ME. Epigenetic silencing of HTATIP2 in glioblastoma contributes to treatment resistance by enhancing nuclear translocation of the DNA repair protein MPG. Mol Oncol 2023; 17:1744-1762. [PMID: 37491696 PMCID: PMC10483604 DOI: 10.1002/1878-0261.13494] [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: 03/26/2023] [Revised: 05/02/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023] Open
Abstract
Glioblastoma, the most malignant brain tumor in adults, exhibits characteristic patterns of epigenetic alterations that await elucidation. The DNA methylome of glioblastoma revealed recurrent epigenetic silencing of HTATIP2, which encodes a negative regulator of importin β-mediated cytoplasmic-nuclear protein translocation. Its deregulation may thus alter the functionality of cancer-relevant nuclear proteins, such as the base excision repair (BER) enzyme N-methylpurine DNA glycosylase (MPG), which has been associated with treatment resistance in GBM. We found that induction of HTATIP2 expression in GBM cells leads to a significant shift of predominantly nuclear to cytoplasmic MPG, whereas depletion of endogenous HTATIP2 results in enhanced nuclear MPG localization. Reduced nuclear MPG localization, prompted by HTATIP2 expression or by depletion of MPG, yielded less phosphorylated-H2AX-positive cells upon treatment with an alkylating agent. This suggested reduced MPG-mediated formation of apurinic/apyrimidinic sites, leaving behind unrepaired DNA lesions, reflecting a reduced capacity of BER in response to the alkylating agent. Epigenetic silencing of HTATIP2 may thus increase nuclear localization of MPG, thereby enhancing the capacity of the glioblastoma cells to repair treatment-related lesions and contributing to treatment resistance.
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Affiliation(s)
- Thi Tham Nguyen
- Neuroscience Research Center and Service of NeurosurgeryLausanne University Hospital (CHUV) and University of LausanneEpalingesSwitzerland
| | - Premnath Rajakannu
- Neuroscience Research Center and Service of NeurosurgeryLausanne University Hospital (CHUV) and University of LausanneEpalingesSwitzerland
| | - Minh Diêu Thanh Pham
- Neuroscience Research Center and Service of NeurosurgeryLausanne University Hospital (CHUV) and University of LausanneEpalingesSwitzerland
| | - Leo Weman
- Neuroscience Research Center and Service of NeurosurgeryLausanne University Hospital (CHUV) and University of LausanneEpalingesSwitzerland
| | - Alexander Jucht
- Neuroscience Research Center and Service of NeurosurgeryLausanne University Hospital (CHUV) and University of LausanneEpalingesSwitzerland
| | - Michelle C. Buri
- Neuroscience Research Center and Service of NeurosurgeryLausanne University Hospital (CHUV) and University of LausanneEpalingesSwitzerland
| | - Kristof Van Dommelen
- Neuroscience Research Center and Service of NeurosurgeryLausanne University Hospital (CHUV) and University of LausanneEpalingesSwitzerland
| | - Monika E. Hegi
- Neuroscience Research Center and Service of NeurosurgeryLausanne University Hospital (CHUV) and University of LausanneEpalingesSwitzerland
- Lundin Family Brain Tumor CenterLausanne University Hospital (CHUV) and University of LausanneSwitzerland
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Li Y, Porta-Pardo E, Tokheim C, Bailey MH, Yaron TM, Stathias V, Geffen Y, Imbach KJ, Cao S, Anand S, Akiyama Y, Liu W, Wyczalkowski MA, Song Y, Storrs EP, Wendl MC, Zhang W, Sibai M, Ruiz-Serra V, Liang WW, Terekhanova NV, Rodrigues FM, Clauser KR, Heiman DI, Zhang Q, Aguet F, Calinawan AP, Dhanasekaran SM, Birger C, Satpathy S, Zhou DC, Wang LB, Baral J, Johnson JL, Huntsman EM, Pugliese P, Colaprico A, Iavarone A, Chheda MG, Ricketts CJ, Fenyö D, Payne SH, Rodriguez H, Robles AI, Gillette MA, Kumar-Sinha C, Lazar AJ, Cantley LC, Getz G, Ding L. Pan-cancer proteogenomics connects oncogenic drivers to functional states. Cell 2023; 186:3921-3944.e25. [PMID: 37582357 DOI: 10.1016/j.cell.2023.07.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/30/2022] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
Cancer driver events refer to key genetic aberrations that drive oncogenesis; however, their exact molecular mechanisms remain insufficiently understood. Here, our multi-omics pan-cancer analysis uncovers insights into the impacts of cancer drivers by identifying their significant cis-effects and distal trans-effects quantified at the RNA, protein, and phosphoprotein levels. Salient observations include the association of point mutations and copy-number alterations with the rewiring of protein interaction networks, and notably, most cancer genes converge toward similar molecular states denoted by sequence-based kinase activity profiles. A correlation between predicted neoantigen burden and measured T cell infiltration suggests potential vulnerabilities for immunotherapies. Patterns of cancer hallmarks vary by polygenic protein abundance ranging from uniform to heterogeneous. Overall, our work demonstrates the value of comprehensive proteogenomics in understanding the functional states of oncogenic drivers and their links to cancer development, surpassing the limitations of studying individual cancer types.
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Affiliation(s)
- Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Eduard Porta-Pardo
- Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Matthew H Bailey
- Department of Biology and Simmons Center for Cancer Research, Brigham Young University, Provo, UT 84602, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Vasileios Stathias
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Kathleen J Imbach
- Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yo Akiyama
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yizhe Song
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Erik P Storrs
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wubing Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mustafa Sibai
- Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Victoria Ruiz-Serra
- Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Nadezhda V Terekhanova
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Fernanda Martins Rodrigues
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Qing Zhang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Francois Aguet
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anna P Calinawan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chet Birger
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Jessika Baral
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Pietro Pugliese
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Antonio Iavarone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Neurological Surgery, Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Milan G Chheda
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Neurology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA.
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Steers GJ, O’Leary BR, Du J, Wagner BA, Carroll RS, Domann FE, Goswami PC, Buettner GR, Cullen JJ. Pharmacologic Ascorbate and DNMT Inhibitors Increase DUOX Expression and Peroxide-Mediated Toxicity in Pancreatic Cancer. Antioxidants (Basel) 2023; 12:1683. [PMID: 37759986 PMCID: PMC10525653 DOI: 10.3390/antiox12091683] [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: 07/13/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Recent studies have demonstrated an important role for vitamin C in the epigenetic regulation of cancer-related genes via DNA demethylation by the ten-eleven translocation (TET) methylcytosine dioxygenase enzymes. DNA methyltransferase (DNMT) reverses this, increasing DNA methylation and decreasing gene expression. Dual oxidase (DUOX) enzymes produce hydrogen peroxide (H2O2) in normal pancreatic tissue but are silenced in pancreatic cancer (PDAC). Treatment of PDAC with pharmacologic ascorbate (P-AscH-, intravenous, high dose vitamin C) increases DUOX expression. We hypothesized that inhibiting DNMT may act synergistically with P-AscH- to further increase DUOX expression and cytotoxicity of PDAC. PDAC cells demonstrated dose-dependent increases in DUOX mRNA and protein expression when treated with DNMT inhibitors. PDAC cells treated with P-AscH- + DNMT inhibitors demonstrated increased DUOX expression, increased intracellular oxidation, and increased cytotoxicity in vitro and in vivo compared to either treatment alone. These findings suggest a potential therapeutic, epigenetic mechanism to treat PDAC.
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Affiliation(s)
- Garett J. Steers
- Free Radical and Radiation Biology Division, Department of Radiation Oncology, Iowa City, IA 52242, USA; (G.J.S.); (B.R.O.); (J.D.); (B.A.W.); (R.S.C.); (F.E.D.); (P.C.G.); (G.R.B.)
- The Department of Surgery, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Brianne R. O’Leary
- Free Radical and Radiation Biology Division, Department of Radiation Oncology, Iowa City, IA 52242, USA; (G.J.S.); (B.R.O.); (J.D.); (B.A.W.); (R.S.C.); (F.E.D.); (P.C.G.); (G.R.B.)
- The Department of Surgery, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Juan Du
- Free Radical and Radiation Biology Division, Department of Radiation Oncology, Iowa City, IA 52242, USA; (G.J.S.); (B.R.O.); (J.D.); (B.A.W.); (R.S.C.); (F.E.D.); (P.C.G.); (G.R.B.)
- The Department of Surgery, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Brett A. Wagner
- Free Radical and Radiation Biology Division, Department of Radiation Oncology, Iowa City, IA 52242, USA; (G.J.S.); (B.R.O.); (J.D.); (B.A.W.); (R.S.C.); (F.E.D.); (P.C.G.); (G.R.B.)
| | - Rory S. Carroll
- Free Radical and Radiation Biology Division, Department of Radiation Oncology, Iowa City, IA 52242, USA; (G.J.S.); (B.R.O.); (J.D.); (B.A.W.); (R.S.C.); (F.E.D.); (P.C.G.); (G.R.B.)
- The Department of Surgery, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Frederick E. Domann
- Free Radical and Radiation Biology Division, Department of Radiation Oncology, Iowa City, IA 52242, USA; (G.J.S.); (B.R.O.); (J.D.); (B.A.W.); (R.S.C.); (F.E.D.); (P.C.G.); (G.R.B.)
| | - Prabhat C. Goswami
- Free Radical and Radiation Biology Division, Department of Radiation Oncology, Iowa City, IA 52242, USA; (G.J.S.); (B.R.O.); (J.D.); (B.A.W.); (R.S.C.); (F.E.D.); (P.C.G.); (G.R.B.)
| | - Garry R. Buettner
- Free Radical and Radiation Biology Division, Department of Radiation Oncology, Iowa City, IA 52242, USA; (G.J.S.); (B.R.O.); (J.D.); (B.A.W.); (R.S.C.); (F.E.D.); (P.C.G.); (G.R.B.)
| | - Joseph J. Cullen
- Free Radical and Radiation Biology Division, Department of Radiation Oncology, Iowa City, IA 52242, USA; (G.J.S.); (B.R.O.); (J.D.); (B.A.W.); (R.S.C.); (F.E.D.); (P.C.G.); (G.R.B.)
- The Department of Surgery, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
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Yue K, Sheng D, Xue X, Zhao L, Zhao G, Jin C, Zhang L. Bidirectional Mediation Effects between Intratumoral Microbiome and Host DNA Methylation Changes Contribute to Stomach Adenocarcinoma. Microbiol Spectr 2023; 11:e0090423. [PMID: 37260411 PMCID: PMC10434028 DOI: 10.1128/spectrum.00904-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/06/2023] [Indexed: 06/02/2023] Open
Abstract
The induction of aberrant DNA methylation is the major pathway by which Helicobacter pylori infection induces stomach adenocarcinoma (STAD). The involvement of the non-H. pylori gastric microbiota in this mechanism remains to be examined. RNA sequencing data, clinical information, and DNA methylation data were obtained from The Cancer Genome Atlas (TCGA) STAD project. The Kraken 2 pipeline was employed to explore the microbiome profiles. The microbiome was associated with occurrence, distal metastasis, and prognosis, and differential methylation changes related to distal metastasis and prognosis were analyzed. Bi-directional mediation effects of the intratumoral microbiome and host DNA methylation changes on the metastasis and prognosis of STAD were identified by mediation analysis. The expression of the ZNF215 gene was verified by real-time quantitative PCR (RT-qPCR). A cell counting kit 8 (CCK8) cell proliferation experiment and a cell clone formation experiment were used to evaluate the proliferation and invasion abilities of gastric cells. Our analysis revealed that H. pylori and other cancer-related microorganisms were related to the occurrence, progression, or prognosis of STAD. The related methylated genes were particularly enriched in related cancer pathways. Kytococcus sedentarius and Actinomyces oris, which interacted strongly with methylation changes in immune genes, were associated with prognosis. Cell experiments verified that Staphylococcus saccharolyticus could promote the proliferation and cloning of gastric cells by regulating the gene expression level of the ZNF215 gene. Our study suggested that the bi-directional mediation effect between intratumoral microorganisms and host epigenetics was key to the distal metastasis of cancer cells and survival deterioration in the tumor microenvironment of stomach tissues of patients with STAD. IMPORTANCE The burgeoning field of oncobiome research declared that members of the intratumoral microbiome besides Helicobacter pylori existed in tumor tissues and participated in the occurrence and development of gastric cancer, and the methylation of host DNA may be a potential target of microbes and their metabolites. Current research focuses mostly on species composition, but the functional genes of the members of the microbiota are also key to their interaction with the host. Therefore, we focused on characterizing the species composition and functional gene composition of microbes in gastric cancer, and we suggest that microbes may further participate in the occurrence and development of cancer by influencing abnormal epigenetic changes in the host. Some key bioinformatics analysis results were verified by in vitro experiments. Thus, we consider that the tumor microbiota-host epigenetic axis of gastric cancer microorganisms and the host explains the mechanism of the microbiota participating in cancer occurrence and development, and we make some verifiable experimental predictions.
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Affiliation(s)
- Kaile Yue
- Microbiome-X, National Institute of Health Data Science of China, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Dashuang Sheng
- Microbiome-X, National Institute of Health Data Science of China, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xinxin Xue
- Microbiome-X, National Institute of Health Data Science of China, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lanlan Zhao
- Microbiome-X, National Institute of Health Data Science of China, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guoping Zhao
- Microbiome-X, National Institute of Health Data Science of China, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chuandi Jin
- Microbiome-X, National Institute of Health Data Science of China, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lei Zhang
- Microbiome-X, National Institute of Health Data Science of China, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Wei X, Ruan H, Zhang Y, Qin T, Zhang Y, Qin Y, Li W. Pan-cancer analysis of IFN-γ with possible immunotherapeutic significance: a verification of single-cell sequencing and bulk omics research. Front Immunol 2023; 14:1202150. [PMID: 37646041 PMCID: PMC10461559 DOI: 10.3389/fimmu.2023.1202150] [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: 04/07/2023] [Accepted: 07/17/2023] [Indexed: 09/01/2023] Open
Abstract
Background Interferon-gamma (IFN-γ), commonly referred to as type II interferon, is a crucial cytokine that coordinates the tumor immune process and has received considerable attention in tumor immunotherapy research. Previous studies have discussed the role and mechanisms associated with IFN-γ in specific tumors or diseases, but the relevant role of IFN-γ in pan-cancer remains uncertain. Methods TCGA and GTEx RNA expression data and clinical data were downloaded. Additionally, we analyzed the role of IFN-γ on tumors by using a bioinformatic approach, which included the analysis of the correlation between IFN-γ in different tumors and expression, prognosis, functional status, TMB, MSI, immune cell infiltration, and TIDE. We also developed a PPI network for topological analysis of the network, identifying hub genes as those having a degree greater than IFN-γ levels. Result IFN-γ was differentially expressed and predicted different survival statuses in a majority of tumor types in TCGA. Additionally, IFN-γ expression was strongly linked to factors like infiltration of T cells, immune checkpoints, immune-activating genes, immunosuppressive genes, chemokines, and chemokine receptors, as well as tumor purity, functional statuses, and prognostic value. Also, prognosis, CNV, and treatment response were all substantially correlated with IFN-γ-related gene expression. Particularly, the IFN-γ-related gene STAT1 exhibited the greatest percentage of SNVs and the largest percentage of SNPs in UCEC. Elevated expression levels of IFN-γ-related genes were found in a wide variety of tumor types, and this was shown to be positively linked to drug sensitivity for 20 different types of drugs. Conclusion IFN-γ is a good indicator of response to tumor immunotherapy and is likely to limit tumor progression, offering a novel approach for immunotherapy's future development.
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Affiliation(s)
- Xiaoying Wei
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region and Research Center of Health Management, Guangxi Academy of Medical Sciences, Nanning, China
| | - Hanyi Ruan
- Department of Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yan Zhang
- Department of Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Tianyu Qin
- Department of Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yujie Zhang
- Department of Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yan Qin
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region and Research Center of Health Management, Guangxi Academy of Medical Sciences, Nanning, China
| | - Wei Li
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region and Research Center of Health Management, Guangxi Academy of Medical Sciences, Nanning, China
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Sarwar MS, Ramirez CN, Dina Kuo HC, Chou P, Wu R, Sargsyan D, Yang Y, Shannar A, Mary Peter R, Yin R, Wang Y, Su X, Kong AN. The environmental carcinogen benzo[a]pyrene regulates epigenetic reprogramming and metabolic rewiring in a two-stage mouse skin carcinogenesis model. Carcinogenesis 2023; 44:436-449. [PMID: 37100755 PMCID: PMC10414144 DOI: 10.1093/carcin/bgad024] [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: 11/10/2022] [Revised: 03/30/2023] [Accepted: 04/25/2023] [Indexed: 04/28/2023] Open
Abstract
Non-melanoma skin cancer (NMSC) is the most common cancer in the world. Environmental exposure to carcinogens is one of the major causes of NMSC initiation and progression. In the current study, we utilized a two-stage skin carcinogenesis mouse model generated by sequential exposure to cancer-initiating agent benzo[a]pyrene (BaP) and promoting agent 12-O-tetradecanoylphorbol-13-acetate (TPA), to study epigenetic, transcriptomic and metabolic changes at different stages during the development of NMSC. BaP/TPA caused significant alterations in DNA methylation and gene expression profiles in skin carcinogenesis, as evidenced by DNA-seq and RNA-seq analysis. Correlation analysis between differentially expressed genes and differentially methylated regions found that the mRNA expression of oncogenes leucine rich repeat LGI family member 2 (Lgi2), kallikrein-related peptidase 13 (Klk13) and SRY-Box transcription factor (Sox5) are correlated with the promoter CpG methylation status, indicating BaP/TPA regulates these oncogenes through regulating their promoter methylation at different stages of NMSC. Pathway analysis identified that the modulation of macrophage-stimulating protein-recepteur d'origine nantais and high-mobility group box 1 signaling pathways, superpathway of melatonin degradation, melatonin degradation 1, sirtuin signaling and actin cytoskeleton signaling pathways are associated with the development of NMSC. The metabolomic study showed BaP/TPA regulated cancer-associated metabolisms like pyrimidine and amino acid metabolisms/metabolites and epigenetic-associated metabolites, such as S-adenosylmethionine, methionine and 5-methylcytosine, indicating a critical role in carcinogen-mediated metabolic reprogramming and its consequences on cancer development. Altogether, this study provides novel insights integrating methylomic, transcriptomic and metabolic-signaling pathways that could benefit future skin cancer treatment and interception studies.
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Affiliation(s)
- Md. Shahid Sarwar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christina N Ramirez
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Hsiao-Chen Dina Kuo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Pochung Chou
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yuqing Yang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ahmad Shannar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rebecca Mary Peter
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ran Yin
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yujue Wang
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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