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Shu M, Huang L, Chen Y, Wang Y, Xie Z, Li S, Zhou J, Wei L, Fu T, Liu B, Chen H, Tang K, Ke Z. Identification of a DNA-methylome-based signature for prognosis prediction in driver gene-negative lung adenocarcinoma. Cancer Lett 2024; 593:216835. [PMID: 38548216 DOI: 10.1016/j.canlet.2024.216835] [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: 11/30/2023] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 06/01/2024]
Abstract
"Driver gene-negative" lung adenocarcinoma (LUAD) was of rare treatment options and a poor prognosis. Presently, for them, few biomarkers are available for stratification analysis to make appropriate treatment strategy. This study aimed to develop a DNA-methylome-based signature to realize the precise risk-stratifying. Here, an Illumina MethylationEPIC Beadchip was applied to obtain differentially methylated CpG sites (DMCs). A four-CpG-based signature, named as TLA, was successfully established, whose prognosis-predicting power was well verified in one internal (n = 78) and other external (n = 110) validation cohorts. Patients with high-risk scores had shorter overall survival (OS) in all cohorts [hazard ratio (HR): 11.79, 5.16 and 2.99, respectively]. Additionally, it can effectively divide patients into low-risk and high-risk groups, with significantly different OS in the diverse subgroups stratified by the standard clinical parameters. As an independent prognostic factor, TLA may assist in improving the nomogram's 5-year OS-predicting ability (AUC 0.756, 95% CI:0.695-0.816), superior to TNM alone (AUC 0.644, 95% CI: 0.590-0.698). Additionally, the relationship of TLA-related genes, TAC1, LHX9, and ALX1, with prognosis and tumour invasion made them serve as potential therapy targets for driver gene-negative LUAD.
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Affiliation(s)
- Man Shu
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Leilei Huang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Yu Chen
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China; Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, PR China
| | - Yanxia Wang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Zhongpeng Xie
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Shuhua Li
- Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Jianwen Zhou
- Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Lihong Wei
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Tongze Fu
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Bixia Liu
- Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China
| | - Honglei Chen
- Department of Pathology, School of Basic Medical Science, Wuhan University, Wuhan, Hubei, PR China.
| | - Kejing Tang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, PR China.
| | - Zunfu Ke
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China; Molecular Diagnosis and Gene Test Centre, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China.
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2
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Yu PC, Hou D, Chang B, Liu N, Xu CH, Chen X, Hu CL, Liu T, Wang X, Zhang Q, Liu P, Jiang Y, Fei MY, Zong LJ, Zhang JY, Liu H, Chen BY, Chen SB, Wang Y, Li ZJ, Li X, Deng CH, Ren YY, Zhao M, Jiang S, Wang R, Jin J, Yang S, Xue K, Shi J, Chang CK, Shen S, Wang Z, He PC, Chen Z, Chen SJ, Sun XJ, Wang L. SMARCA5 reprograms AKR1B1-mediated fructose metabolism to control leukemogenesis. Dev Cell 2024:S1534-5807(24)00296-X. [PMID: 38776924 DOI: 10.1016/j.devcel.2024.04.023] [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: 11/14/2023] [Revised: 03/13/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
A significant variation in chromatin accessibility is an epigenetic feature of leukemia. The cause of this variation in leukemia, however, remains elusive. Here, we identify SMARCA5, a core ATPase of the imitation switch (ISWI) chromatin remodeling complex, as being responsible for aberrant chromatin accessibility in leukemia cells. We find that SMARCA5 is required to maintain aberrant chromatin accessibility for leukemogenesis and then promotes transcriptional activation of AKR1B1, an aldo/keto reductase, by recruiting transcription co-activator DDX5 and transcription factor SP1. Higher levels of AKR1B1 are associated with a poor prognosis in leukemia patients and promote leukemogenesis by reprogramming fructose metabolism. Moreover, pharmacological inhibition of AKR1B1 has been shown to have significant therapeutic effects in leukemia mice and leukemia patient cells. Thus, our findings link the aberrant chromatin state mediated by SMARCA5 to AKR1B1-mediated endogenous fructose metabolism reprogramming and shed light on the essential role of AKR1B1 in leukemogenesis, which may provide therapeutic strategies for leukemia.
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Affiliation(s)
- Peng-Cheng Yu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Dan Hou
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Binhe Chang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Na Liu
- Department of Hematology, Institute of Hematology, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Chun-Hui Xu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinchi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng-Long Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ting Liu
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiaoning Wang
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Qunling Zhang
- Department of Medical Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ping Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yilun Jiang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming-Yue Fei
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li-Juan Zong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Ying Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Liu
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Bing-Yi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shu-Bei Chen
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zi-Juan Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiya Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chu-Han Deng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi-Yi Ren
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Muying Zhao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shiyu Jiang
- Department of Medical Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Roujia Wang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Jiacheng Jin
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Shaoxin Yang
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Kai Xue
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jun Shi
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Chun-Kang Chang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhikai Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei 230027, China
| | - Peng-Cheng He
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao-Jian Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lan Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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3
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Horie S, Saito Y, Kogure Y, Mizuno K, Ito Y, Tabata M, Kanai T, Murakami K, Koya J, Kataoka K. Pan-Cancer Comparative and Integrative Analyses of Driver Alterations Using Japanese and International Genomic Databases. Cancer Discov 2024; 14:786-803. [PMID: 38276885 DOI: 10.1158/2159-8290.cd-23-0902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/02/2023] [Accepted: 01/23/2024] [Indexed: 01/27/2024]
Abstract
Using 48,627 samples from the Center for Cancer Genomics and Advanced Therapeutics (C-CAT), we present a pan-cancer landscape of driver alterations and their clinical actionability in Japanese patients. Comparison with White patients in Genomics Evidence Neoplasia Information Exchange (GENIE) demonstrates high TP53 mutation frequencies in Asian patients across multiple cancer types. Integration of C-CAT, GENIE, and The Cancer Genome Atlas data reveals many cooccurring and mutually exclusive relationships between driver mutations. At pathway level, mutations in epigenetic regulators frequently cooccur with PI3K pathway molecules. Furthermore, we found significant cooccurring mutations within the epigenetic pathway. Accumulation of mutations in epigenetic regulators causes increased proliferation-related transcriptomic signatures. Loss-of-function of many epigenetic drivers inhibits cell proliferation in their wild-type cell lines, but this effect is attenuated in those harboring mutations of not only the same but also different epigenetic drivers. Our analyses dissect various genetic properties and provide valuable resources for precision medicine in cancer. SIGNIFICANCE We present a genetic landscape of 26 principal cancer types/subtypes, including Asian-prevalent ones, in Japanese patients. Multicohort data integration unveils numerous cooccurring and exclusive relationships between driver mutations, identifying cooccurrence of multiple mutations in epigenetic regulators, which coordinately cause transcriptional and phenotypic changes. These findings provide insights into epigenetic regulator-driven oncogenesis. This article is featured in Selected Articles from This Issue, p. 695.
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Affiliation(s)
- Sara Horie
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kota Mizuno
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yuta Ito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Clinical Oncology and Hematology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Mariko Tabata
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takanori Kanai
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Murakami
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
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4
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Parreno V, Loubiere V, Schuettengruber B, Fritsch L, Rawal CC, Erokhin M, Győrffy B, Normanno D, Di Stefano M, Moreaux J, Butova NL, Chiolo I, Chetverina D, Martinez AM, Cavalli G. Transient loss of Polycomb components induces an epigenetic cancer fate. Nature 2024; 629:688-696. [PMID: 38658752 PMCID: PMC11096130 DOI: 10.1038/s41586-024-07328-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Although cancer initiation and progression are generally associated with the accumulation of somatic mutations1,2, substantial epigenomic alterations underlie many aspects of tumorigenesis and cancer susceptibility3-6, suggesting that genetic mechanisms might not be the only drivers of malignant transformation7. However, whether purely non-genetic mechanisms are sufficient to initiate tumorigenesis irrespective of mutations has been unknown. Here, we show that a transient perturbation of transcriptional silencing mediated by Polycomb group proteins is sufficient to induce an irreversible switch to a cancer cell fate in Drosophila. This is linked to the irreversible derepression of genes that can drive tumorigenesis, including members of the JAK-STAT signalling pathway and zfh1, the fly homologue of the ZEB1 oncogene, whose aberrant activation is required for Polycomb perturbation-induced tumorigenesis. These data show that a reversible depletion of Polycomb proteins can induce cancer in the absence of driver mutations, suggesting that tumours can emerge through epigenetic dysregulation leading to inheritance of altered cell fates.
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Affiliation(s)
- V Parreno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - V Loubiere
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - B Schuettengruber
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - L Fritsch
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - C C Rawal
- University of Southern California, Los Angeles, CA, USA
| | - M Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - B Győrffy
- Semmelweis University Department of Bioinformatics, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - D Normanno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - M Di Stefano
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - J Moreaux
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- UFR Medicine, University of Montpellier, Montpellier, France
| | - N L Butova
- University of Southern California, Los Angeles, CA, USA
| | - I Chiolo
- University of Southern California, Los Angeles, CA, USA
| | - D Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - A-M Martinez
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
| | - G Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
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Khan R, Pari B, Puszynski K. Comprehensive Bioinformatic Investigation of TP53 Dysregulation in Diverse Cancer Landscapes. Genes (Basel) 2024; 15:577. [PMID: 38790205 PMCID: PMC11121236 DOI: 10.3390/genes15050577] [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: 03/03/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
P53 overexpression plays a critical role in cancer pathogenesis by disrupting the intricate regulation of cellular proliferation. Despite its firmly established function as a tumor suppressor, elevated p53 levels can paradoxically contribute to tumorigenesis, influenced by factors such as exposure to carcinogens, genetic mutations, and viral infections. This phenomenon is observed across a spectrum of cancer types, including bladder (BLCA), ovarian (OV), cervical (CESC), cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), diffuse large B-cell lymphoma (DLBC), esophageal carcinoma (ESCA), head and neck squamous cell carcinoma (HNSC), kidney chromophobe (KICH), kidney renal clear cell carcinoma (KIRC), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), and uterine corpus endometrial carcinoma (UCEC). This broad spectrum of cancers is often associated with increased aggressiveness and recurrence risk. Effective therapeutic strategies targeting tumors with p53 overexpression require a comprehensive approach, integrating targeted interventions aimed at the p53 gene with conventional modalities such as chemotherapy, radiation therapy, and targeted drugs. In this extensive study, we present a detailed analysis shedding light on the multifaceted role of TP53 across various cancers, with a specific emphasis on its impact on disease-free survival (DFS). Leveraging data from the TCGA database and the GTEx dataset, along with GEPIA, UALCAN, and STRING, we identify TP53 overexpression as a significant prognostic indicator, notably pronounced in prostate adenocarcinoma (PRAD). Supported by compelling statistical significance (p < 0.05), our analysis reveals the distinct influence of TP53 overexpression on DFS outcomes in PRAD. Additionally, graphical representations of overall survival (OS) underscore the notable disparity in OS duration between tumors exhibiting elevated TP53 expression (depicted by the red line) and those with lower TP53 levels (indicated by the blue line). The hazard ratio (HR) further emphasizes the profound impact of TP53 on overall survival. Moreover, our investigation delves into the intricate TP53 protein network, unveiling genes exhibiting robust positive correlations with TP53 expression across 13 out of 27 cancers. Remarkably, negative correlations emerge with pivotal tumor suppressor genes. This network analysis elucidates critical proteins, including SIRT1, CBP, p300, ATM, DAXX, HSP 90-alpha, Mdm2, RPA70, 14-3-3 protein sigma, p53, and ASPP2, pivotal in regulating cell cycle dynamics, DNA damage response, and transcriptional regulation. Our study underscores the paramount importance of deciphering TP53 dynamics in cancer, providing invaluable insights into tumor behavior, disease-free survival, and potential therapeutic avenues.
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Affiliation(s)
- Ruby Khan
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
| | - Bakht Pari
- Principal, Nursing School, Lady Reading Hospital Peshawar, Peshawar 25000, Pakistan;
| | - Krzysztof Puszynski
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
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Huang J, Jin S, Guo R, Wu W, Yang C, Qin Y, Chen Q, He X, Qu J, Yang Z. Histone lysine demethylase KDM5B facilitates proliferation and suppresses apoptosis in human acute myeloid leukemia cells through the miR-140-3p/BCL2 axis. RNA (NEW YORK, N.Y.) 2024; 30:435-447. [PMID: 38296629 PMCID: PMC10946434 DOI: 10.1261/rna.079865.123] [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: 10/04/2023] [Accepted: 01/21/2024] [Indexed: 02/02/2024]
Abstract
The histone lysine demethylase KDM5B is frequently up-regulated in various human cancer cells. However, its expression and functional role in human acute myeloid leukemia (AML) cells remain unclear. Here, we found that the expression level of KDM5B is high in primary human AML cells. We have demonstrated that knocking down KDM5B leads to apoptosis and impairs proliferation in primary human AML and some human AML cell lines. We further identified miR-140-3p as a downstream target gene of KDM5B. KDM5B expression was inversely correlated with the miR-140-3p level in primary human AML cells. Molecular studies showed that silencing KDM5B enhanced H3K4 trimethylation (H3K4me3) at the promoter of miR-140-3p, leading to high expression of miR-140-3p, which in turn inhibited B-cell CLL/lymphoma 2 (BCL2) expression. Finally, we demonstrate that the defective proliferation induced by KDM5B knockdown (KD) can be rescued with the miR-140-3p inhibitor or enhanced by combining KDM5B KD with a BCL2 inhibitor. Altogether, our data support the conclusion that KDM5B promotes tumorigenesis in human AML cells through the miR-140-3p/BCL2 axis. Targeting the KDM5B/miR-140-3p/BCL2 pathway may hold therapeutic promise for treating human AML.
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Affiliation(s)
- Jiaojuan Huang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuiling Jin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Rongqun Guo
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Wei Wu
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Chengxuan Yang
- Department of Galactophore, Xinxiang First People's Hospital, Xinxiang 453000, China
| | - Yali Qin
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qingchuan Chen
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ximiao He
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jing Qu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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7
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Zhao JW, Zhao WY, Cui XH, Xing L, Shi JC, Yu L. The role of the mitochondrial ribosomal protein family in detecting hepatocellular carcinoma and predicting prognosis, immune features, and drug sensitivity. Clin Transl Oncol 2024; 26:496-514. [PMID: 37407805 DOI: 10.1007/s12094-023-03269-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 06/25/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common types of malignant tumors, with a slow onset, rapid progression, and frequent recurrence. Previous research has implicated mitochondrial ribosomal genes in the development, metastasis, and prognosis of various cancers. However, further research is necessary to establish a link between mitochondrial ribosomal protein (MRP) family expression and HCC diagnosis, prognosis, ferroptosis-related gene (FRG) expression, m6A modification-related gene expression, tumor immunity, and drug sensitivity. METHODS Bioinformatics resources were used to analyze data from patients with HCC retrieved from the TCGA, ICGC, and GTEx databases (GEPIA, UALCAN, Xiantao tool, cBioPortal, STRING, Cytoscape, TISIDB, and GSCALite). RESULTS Among the 82 MRP family members, 14 MRP genes (MRPS21, MRPS23, MRPL9, DAP3, MRPL13, MRPL17, MRPL24, MRPL55, MRPL16, MRPL14, MRPS17, MRPL47, MRPL21, and MRPL15) were significantly upregulated differentially expressed genes (DEGs) in HCC tumor samples in comparison to normal samples. Receiver-operating characteristic curve analysis indicated that all 14 DEGs show good diagnostic performance. Furthermore, TCGA analysis revealed that the mRNA expression of 39 MRPs was associated with overall survival (OS) in HCC. HCC was divided into two molecular subtypes (C1 and C2) with distinct prognoses using clustering analysis. The clusters showed different FRG expression and m6A methylation profiles and immune features, and prognostic models showed that the model integrating 5 MRP genes (MRPS15, MRPL3, MRPL9, MRPL36, and MRPL37) and 2 FRGs (SLC1A5 and SLC5A11) attained a greater clinical net benefit than three other prognostic models. Finally, analysis of the CTRP and GDSC databases revealed several potential drugs that could target prognostic MRP genes. CONCLUSION We identified 14 MRP genes as HCC diagnostic markers. We investigated FRG and m6A modification-related gene expression profiles and immune features in patients with HCC, and developed and validated a model incorporating MRP and FRG expression that accurately and reliably predicts HCC prognosis and may predict disease progression and treatment response.
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Affiliation(s)
- Jin-Wei Zhao
- Department of Hepatopancreatobiliary Surgery of Second Hospital of Jilin University, State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin Province, China
| | - Wei-Yi Zhao
- Medical College of YanBian University, YanBian, 133000, China
| | - Xin-Hua Cui
- Department of Hepatopancreatobiliary Surgery of Second Hospital of Jilin University, State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin Province, China
| | - Lin Xing
- Department of Hepatopancreatobiliary Surgery of Second Hospital of Jilin University, State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin Province, China
| | - Jia-Cheng Shi
- Department of Hepatopancreatobiliary Surgery of Second Hospital of Jilin University, State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin Province, China
| | - Lu Yu
- Department of Hepatopancreatobiliary Surgery of Second Hospital of Jilin University, State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin Province, China.
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8
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Yu X, Zhao H, Wang R, Chen Y, Ouyang X, Li W, Sun Y, Peng A. Cancer epigenetics: from laboratory studies and clinical trials to precision medicine. Cell Death Discov 2024; 10:28. [PMID: 38225241 PMCID: PMC10789753 DOI: 10.1038/s41420-024-01803-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/23/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Epigenetic dysregulation is a common feature of a myriad of human diseases, particularly cancer. Defining the epigenetic defects associated with malignant tumors has become a focus of cancer research resulting in the gradual elucidation of cancer cell epigenetic regulation. In fact, most stages of tumor progression, including tumorigenesis, promotion, progression, and recurrence are accompanied by epigenetic alterations, some of which can be reversed by epigenetic drugs. The main objective of epigenetic therapy in the era of personalized precision medicine is to detect cancer biomarkers to improve risk assessment, diagnosis, and targeted treatment interventions. Rapid technological advancements streamlining the characterization of molecular epigenetic changes associated with cancers have propelled epigenetic drug research and development. This review summarizes the main mechanisms of epigenetic dysregulation and discusses past and present examples of epigenetic inhibitors in cancer diagnosis and treatment, with an emphasis on the development of epigenetic enzyme inhibitors or drugs. In the final part, the prospect of precise diagnosis and treatment is considered based on a better understanding of epigenetic abnormalities in cancer.
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Affiliation(s)
- Xinyang Yu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, (Zhuhai People's Hospital Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Hao Zhao
- Department of Spinal Surgery, Yichang Central People's Hospital Affiliated with China Three Gorges University, Yichang, Hubei, 443000, China
| | - Ruiqi Wang
- Department of Pharmacy, Zhuhai People's Hospital, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, Guangdong, 519000, China
| | - Yingyin Chen
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, (Zhuhai People's Hospital Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Xumei Ouyang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, (Zhuhai People's Hospital Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Wenting Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, (Zhuhai People's Hospital Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Yihao Sun
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, (Zhuhai People's Hospital Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China.
| | - Anghui Peng
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, (Zhuhai People's Hospital Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China.
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9
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Waitman KB, de Almeida LC, Primi MC, Carlos JAEG, Ruiz C, Kronenberger T, Laufer S, Goettert MI, Poso A, Vassiliades SV, de Souza VAM, Toledo MFZJ, Hassimotto NMA, Cameron MD, Bannister TD, Costa-Lotufo LV, Machado-Neto JA, Tavares MT, Parise-Filho R. HDAC specificity and kinase off-targeting by purine-benzohydroxamate anti-hematological tumor agents. Eur J Med Chem 2024; 263:115935. [PMID: 37989057 DOI: 10.1016/j.ejmech.2023.115935] [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: 09/19/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023]
Abstract
A series of hybrid inhibitors, combining pharmacophores of known kinase inhibitors bearing anilino-purines (ruxolitinib, ibrutinib) and benzohydroxamate HDAC inhibitors (nexturastat A), were generated in the present study. The compounds have been synthesized and tested against solid and hematological tumor cell lines. Compounds 4d-f were the most promising in cytotoxicity assays (IC50 ≤ 50 nM) vs. hematological cells and displayed moderate activity in solid tumor models (EC50 = 9.3-21.7 μM). Compound 4d potently inhibited multiple kinase targets of interest for anticancer effects, including JAK2, JAK3, HDAC1, and HDAC6. Molecular dynamics simulations showed that 4d has stable interactions with HDAC and members of the JAK family, with differences in the hinge binding energy conferring selectivity for JAK3 and JAK2 over JAK1. The kinase inhibition profile of compounds 4d-f allows selective cytotoxicity, with minimal effects on non-tumorigenic cells. Moreover, these compounds have favorable pharmacokinetic profiles, with high stability in human liver microsomes (e.g., see t1/2: >120 min for 4f), low intrinsic clearance, and lack of significant inhibition of four major CYP450 isoforms.
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Affiliation(s)
- Karoline B Waitman
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Larissa C de Almeida
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marina C Primi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, United States
| | - Jorge A E G Carlos
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudia Ruiz
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, United States
| | - Thales Kronenberger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland; Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), 72076, Tübingen, Germany
| | - Stefan Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany
| | - Marcia Ines Goettert
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland; Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), 72076, Tübingen, Germany
| | - Sandra V Vassiliades
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vinícius A M de Souza
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mônica F Z J Toledo
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Neuza M A Hassimotto
- Food Research Center-(FoRC-CEPID) and Department of Food Science and Nutrition, Faculty of Pharmaceutical Science, University of São Paulo, São Paulo, SP, Brazil
| | - Michael D Cameron
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, United States
| | - Thomas D Bannister
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, United States
| | - Letícia V Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - João A Machado-Neto
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maurício T Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, United States.
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
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Tetens AR, Martin AM, Arnold A, Novak OV, Idrizi A, Tryggvadottir R, Craig-Schwartz J, Liapodimitri A, Lunsford K, Barbato MI, Eberhart CG, Resnick AC, Raabe EH, Koldobskiy MA. DNA methylation landscapes in DIPG reveal methylome variability that can be modified pharmacologically. Neurooncol Adv 2024; 6:vdae023. [PMID: 38468866 PMCID: PMC10926944 DOI: 10.1093/noajnl/vdae023] [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] [Indexed: 03/13/2024] Open
Abstract
Background Diffuse intrinsic pontine glioma (DIPG) is a uniformly lethal brainstem tumor of childhood, driven by histone H3 K27M mutation and resultant epigenetic dysregulation. Epigenomic analyses of DIPG have shown global loss of repressive chromatin marks accompanied by DNA hypomethylation. However, studies providing a static view of the epigenome do not adequately capture the regulatory underpinnings of DIPG cellular heterogeneity and plasticity. Methods To address this, we performed whole-genome bisulfite sequencing on a large panel of primary DIPG specimens and applied a novel framework for analysis of DNA methylation variability, permitting the derivation of comprehensive genome-wide DNA methylation potential energy landscapes that capture intrinsic epigenetic variation. Results We show that DIPG has a markedly disordered epigenome with increasingly stochastic DNA methylation at genes regulating pluripotency and developmental identity, potentially enabling cells to sample diverse transcriptional programs and differentiation states. The DIPG epigenetic landscape was responsive to treatment with the hypomethylating agent decitabine, which produced genome-wide demethylation and reduced the stochasticity of DNA methylation at active enhancers and bivalent promoters. Decitabine treatment elicited changes in gene expression, including upregulation of immune signaling such as the interferon response, STING, and MHC class I expression, and sensitized cells to the effects of histone deacetylase inhibition. Conclusions This study provides a resource for understanding the epigenetic instability that underlies DIPG heterogeneity. It suggests the application of epigenetic therapies to constrain the range of epigenetic states available to DIPG cells, as well as the use of decitabine in priming for immune-based therapies.
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Affiliation(s)
- Ashley R Tetens
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Allison M Martin
- Pediatric Hematology-Oncology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Antje Arnold
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Orlandi V Novak
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jordyn Craig-Schwartz
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Athanasia Liapodimitri
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kayleigh Lunsford
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael I Barbato
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charles G Eberhart
- Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Neurosurgery, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Eric H Raabe
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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11
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Zheng D, Long S, Xi M. A comprehensive pan-cancer analysis identifies a novel glycolysis score and its hub genes as prognostic and immunological biomarkers. Transl Cancer Res 2023; 12:2852-2874. [PMID: 37969385 PMCID: PMC10643978 DOI: 10.21037/tcr-23-325] [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: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 11/17/2023]
Abstract
Background Glycolysis plays significant roles in tumor progression and immune response. However, the exact role of glycolysis in prognosis and immune regulation has not been explored in all cancer types. This study first calculated a novel glycolysis score and screened out 12 glycolytic hub genes, and comprehensively analyzed molecular expression, clinical implications, and immune features of glycolysis among pan-cancer. Methods The glycolysis score was derived by the single sample gene set enrichment analysis (ssGSEA) algorithm. The correlations of glycolysis with clinical parameters were analyzed using "limma" package. Downstream pathways of glycolysis were identified by Gene Set Enrichment Analysis (GSEA). The immune cell infiltration was explored and validated by three databases. The association between glycolysis and some immunotherapy biomarkers was explored by Pearson correlation analysis. Single-nucleotide variation (SNV), copy number variation (CNV), DNA methylation, and drug sensitivity analyses of 12 glycolytic hub genes were investigated. IMvigor210 and GSE91061 immunotherapeutic cohorts were retrieved to assess the ability of glycolysis score to predict immunotherapy efficacy. The expression of glycolysis key genes was detected in normal and endometrial cancer cell lines. Results We found that glycolysis score was generally higher in tumor tissues compared to normal tissues and a high glycolysis score predominated as a risk prognostic factor. A high glycolysis score was associated with decreased immunostimulatory natural killer (NK) cells and CD8+ T cells infiltration, well increased immunosuppressive M2-tumor-associated macrophages (M2-TAM) cells infiltration. Tumor mutational burden (TMB), microsatellite instability (MSI), and immune checkpoints (ICPs) all closely interacted with glycolysis score and the frequency of gene mutation was confirmed to be higher in colon adenocarcinoma (COAD) patients with higher glycolysis score. The SNV, CNV, and DNA methylation of 12 glycolysis key genes occurred at different frequencies and showed different impacts on survival outcomes. The predictive and prognostic value of glycolysis score for immunotherapy outcomes was validated in two immunotherapy cohorts. The expression levels of key genes differ in normal endometrial and three endometrial cancer cell lines. Conclusions This work indicated that glycolysis score and 12 glycolytic hub genes were correlated with an immunosuppressive microenvironment. They could be served as promising biomarkers aiding diagnosis, predicting prognosis and immunotherapy response for some tumor patients.
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Affiliation(s)
- Danxi Zheng
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Siyu Long
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Mingrong Xi
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, China
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12
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Allegra A, Caserta S, Mirabile G, Gangemi S. Aging and Age-Related Epigenetic Drift in the Pathogenesis of Leukemia and Lymphomas: New Therapeutic Targets. Cells 2023; 12:2392. [PMID: 37830606 PMCID: PMC10572300 DOI: 10.3390/cells12192392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
One of the traits of cancer cells is abnormal DNA methylation patterns. The idea that age-related epigenetic changes may partially explain the increased risk of cancer in the elderly is based on the observation that aging is also accompanied by comparable changes in epigenetic patterns. Lineage bias and decreased stem cell function are signs of hematopoietic stem cell compartment aging. Additionally, aging in the hematopoietic system and the stem cell niche have a role in hematopoietic stem cell phenotypes linked with age, such as leukemia and lymphoma. Understanding these changes will open up promising pathways for therapies against age-related disorders because epigenetic mechanisms are reversible. Additionally, the development of high-throughput epigenome mapping technologies will make it possible to identify the "epigenomic identity card" of every hematological disease as well as every patient, opening up the possibility of finding novel molecular biomarkers that can be used for diagnosis, prediction, and prognosis.
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Affiliation(s)
- Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (S.C.); (G.M.)
| | - Santino Caserta
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (S.C.); (G.M.)
| | - Giuseppe Mirabile
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (S.C.); (G.M.)
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria, 98125 Messina, Italy;
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13
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Abdullahi A, Wong TWL, Ng SSM. Putative role of non-invasive vagus nerve stimulation in cancer pathology and immunotherapy: Can this be a hidden treasure, especially for the elderly? Cancer Med 2023; 12:19081-19090. [PMID: 37587897 PMCID: PMC10557911 DOI: 10.1002/cam4.6466] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/09/2023] [Accepted: 07/16/2023] [Indexed: 08/18/2023] Open
Abstract
Cancer is globally a disease of significant public health concern owing to its prevalence, and association with morbidity and mortality. Thus, cost-effective treatments for cancer are important to help reduce its significant morbidity and mortality. However, the current therapeutic options for cancer such as chemotherapy, radiotherapy, and surgery may produce serious adverse events such as nausea, vomiting, fatigue, and peripheral neuropathy, especially in the long term. In addition, these therapeutic options may not be well tolerated by the elderly especially those who are frail. The current article is aimed at discussing an alternative therapeutic option, non-invasive vagus nerve stimulation (VNS), and the roles it plays in cancer pathology and immunotherapy. The VNS does this by reducing oxidative stress via silent information regulator 1 (SIRT1); inhibiting inflammation via both hypothalamic-pituitary-axis (HPA) and the release of corticosteroid from the adrenal gland, and cholinergic anti-inflammatory pathway (CAP), and increasing vagal activity which helps in the regulation of cell proliferation, differentiation, apoptosis, and metabolism, and increase chance of survival. Furthermore, it helps with reducing complications due to cancer or its treatments such as postoperative ileus and severity of peripheral neuropathy induced by chemotherapy, and improves cancer-related fatigue, lymphopenia, and quality of life. These suggest that the importance of non-invasive VNS in cancer pathology and immunotherapy cannot be overemphasized. Therefore, considering the safety of non-invasive VNS and its cost-effectiveness, it is a therapeutic option worth trying for these patients, especially in combination with other therapies.
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Affiliation(s)
- Auwal Abdullahi
- Department of Rehabilitation SciencesThe Hong Kong Polytechnic UniversityKowloonHong Kong Special Administrative RegionChina
| | - Thomson W. L. Wong
- Department of Rehabilitation SciencesThe Hong Kong Polytechnic UniversityKowloonHong Kong Special Administrative RegionChina
| | - Shamay S. M. Ng
- Department of Rehabilitation SciencesThe Hong Kong Polytechnic UniversityKowloonHong Kong Special Administrative RegionChina
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14
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Kawaguchi K, Ohashi T, Kobayashi N, Kanemoto K, Nose M, Shinozaki R, Kataoka T, Fujii H. Aberrant DNA methylation-mediated NF-κB/fatty acid-binding protein 5 (FABP5) feed-forward loop promotes malignancy of colorectal cancer cells. Biochim Biophys Acta Mol Cell Biol Lipids 2023:159362. [PMID: 37414211 DOI: 10.1016/j.bbalip.2023.159362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/15/2023] [Accepted: 06/26/2023] [Indexed: 07/08/2023]
Abstract
Fatty acid-binding proteins (FABPs) are intracellular lipid-binding proteins that play roles in fatty acid transport and the regulation of gene expression. Dysregulated FABP expression and/or activity have been associated with cancer pathogenesis; in particular, epidermal-type FABP (FABP5) is upregulated in many types of cancer. However, the mechanisms regulating FABP5 expression and its involvement in cancer remain largely unknown. Here, we examined the regulation of FABP5 gene expression in non-metastatic and metastatic human colorectal cancer (CRC) cells. We found that FABP5 expression was upregulated in metastatic compared with non-metastatic CRC cells as well as in human CRC tissues compared with adjacent normal tissue. Analysis of the DNA methylation status of the FABP5 promoter showed that hypomethylation correlated with the malignant potential of the CRC cell lines. Moreover, FABP5 promoter hypomethylation also correlated with the expression pattern of splice variants of the DNA methyltransferase DNMT3B. ChIP assays and luciferase reporter assays demonstrated that the transcription factor nuclear factor-kappa B (NF-κB) was involved in regulating FABP5 expression. FABP5 expression could be upregulated in metastatic CRC cells by sequential promotion of DNA demethylation followed by activation of NF-κB. We also found that upregulated FABP5 in turn controlled NF-κB activity through IL-8 production. Collectively, these findings suggest the existence of a DNA methylation-dependent NF-κB /FABP5 positive feed-forward loop that may lead to constitutive activation of NF-κB signaling pathway and play a crucial role in CRC progression.
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Affiliation(s)
- Koichiro Kawaguchi
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Tsubasa Ohashi
- Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Narumi Kobayashi
- Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Kotoya Kanemoto
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Makoto Nose
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Rin Shinozaki
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Takao Kataoka
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; Biomedical Research Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hiroshi Fujii
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan.
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15
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Agustinus AS, Al-Rawi D, Dameracharla B, Raviram R, Jones BSCL, Stransky S, Scipioni L, Luebeck J, Di Bona M, Norkunaite D, Myers RM, Duran M, Choi S, Weigelt B, Yomtoubian S, McPherson A, Toufektchan E, Keuper K, Mischel PS, Mittal V, Shah SP, Maciejowski J, Storchova Z, Gratton E, Ly P, Landau D, Bakhoum MF, Koche RP, Sidoli S, Bafna V, David Y, Bakhoum SF. Epigenetic dysregulation from chromosomal transit in micronuclei. Nature 2023; 619:176-183. [PMID: 37286593 PMCID: PMC10322720 DOI: 10.1038/s41586-023-06084-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/14/2023] [Indexed: 06/09/2023]
Abstract
Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers1-4, but whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei5,6 and subsequent rupture of the micronuclear envelope7 profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice, as well as in cancer and non-transformed cells. Some of the changes in histone PTMs occur because of the rupture of the micronuclear envelope, whereas others are inherited from mitotic abnormalities before the micronucleus is formed. Using orthogonal approaches, we demonstrate that micronuclei exhibit extensive differences in chromatin accessibility, with a strong positional bias between promoters and distal or intergenic regions, in line with observed redistributions of histone PTMs. Inducing CIN causes widespread epigenetic dysregulation, and chromosomes that transit in micronuclei experience heritable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, as well as altering genomic copy number, CIN promotes epigenetic reprogramming and heterogeneity in cancer.
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Affiliation(s)
- Albert S Agustinus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Duaa Al-Rawi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bhargavi Dameracharla
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | | | - Bailey S C L Jones
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Lorenzo Scipioni
- School of Engineering, University of California, Irvine, Irvine, CA, USA
| | - Jens Luebeck
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | - Melody Di Bona
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Danguole Norkunaite
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert M Myers
- New York Genome Center, New York, NY, USA
- Tri-institutional MD-PhD Program, New York, NY, USA
| | - Mercedes Duran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Seongmin Choi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shira Yomtoubian
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eléonore Toufektchan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kristina Keuper
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Paul S Mischel
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Vivek Mittal
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Maciejowski
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zuzana Storchova
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Enrico Gratton
- School of Engineering, University of California, Irvine, Irvine, CA, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dan Landau
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Mathieu F Bakhoum
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Vineet Bafna
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | - Yael David
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA.
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-institutional PhD Program in Chemical Biology, New York, NY, USA.
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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16
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Wang B, Liu Y, Liao Z, Wu H, Zhang B, Zhang L. EZH2 in hepatocellular carcinoma: progression, immunity, and potential targeting therapies. Exp Hematol Oncol 2023; 12:52. [PMID: 37268997 DOI: 10.1186/s40164-023-00405-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/15/2023] [Indexed: 06/04/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the leading cause of cancer-related death. The accumulation of genetic and epigenetic changes is closely related to the occurrence and development of HCC. Enhancer of zeste homolog 2 (EZH2, a histone methyltransferase) is suggested to be one of the principal factors that mediates oncogenesis by acting as a driver of epigenetic alternation. Recent studies show that EZH2 is widely involved in proliferation and metastasis of HCC cells. In this review, the functions of EZH2 in HCC progression, the role of EZH2 in tumor immunity and the application of EZH2-related inhibitors in HCC therapy are summarized.
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Affiliation(s)
- Bohan Wang
- Hepatic Surgery Center, Institute of Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yachong Liu
- Hepatic Surgery Center, Institute of Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhibin Liao
- Hepatic Surgery Center, Institute of Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Haofeng Wu
- Hepatic Surgery Center, Institute of Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bixiang Zhang
- Hepatic Surgery Center, Institute of Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Lei Zhang
- Hepatic Surgery Center, Institute of Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Department of Hepatobiliary Surgery, Shanxi Tongji Hospital, Tongji Medical College, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Shanxi Medical University, Huazhong University of Science and Technology, Taiyuan, 030032, China.
- Key Laboratory of Hepatobiliary and Pancreatic Diseases of Shanxi Province (Preparatory), Shanxi Tongji Hospital, Tongji Medical College, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Shanxi Medical University, Huazhong University of Science and Technology, Taiyuan, 030032, China.
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17
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Zeng Z, Li Z, Xue J, Xue H, Liu Z, Zhang W, Liu H, Xu S. KDM4C silencing inhibits cell migration and enhances radiosensitivity by inducing CXCL2 transcription in hepatocellular carcinoma. Cell Death Discov 2023; 9:137. [PMID: 37117173 PMCID: PMC10147924 DOI: 10.1038/s41420-023-01418-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/30/2023] Open
Abstract
KDM4C, which is a histone lysine demethylase, has been proposed to participate in the malignant transformation and progression of several types of cancer. However, its roles in hepatocellular carcinoma (HCC) remain poorly understood. Here, we find that KDM4C protein expression is increased in HCC and promotes HCC cell growth, proliferation and migration. Furthermore, we provide evidence that depletion of KDM4C leads to a defective G2/M checkpoint, increases radiation-induced DNA damage, impairs DNA repair and enhances radiosensitivity in HCC cells. Using RNA sequencing, we identify that the chemokine CXCL2 is a downstream effector of KDM4C. KDM4C knockdown increases the binding of H3K36me3 to the promoter of CXCL2, thus upregulating CXCL2 expression and promoting CXCL2 secretion in HCC cells. Importantly, the observed effects of KDM4C depletion in HCC cells can be partially rescued by CXCL2 silencing. Thus, our findings reveal that KDM4C is involved in cell migration and radiosensitivity by modulating CXCL2 transcription, indicating that KDM4C may be a potential therapeutic target in HCC.
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Affiliation(s)
- Zhen Zeng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Zixuan Li
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Jun Xue
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Huichan Xue
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Zhiwei Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Wenxuan Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Hongli Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
| | - Shuangbing Xu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
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18
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Zhao Y, Peng F, Wang C, Murano T, Baba H, Ikematsu H, Li W, Goel A. A DNA Methylation-based Epigenetic Signature for the Identification of Lymph Node Metastasis in T1 Colorectal Cancer. Ann Surg 2023; 277:655-663. [PMID: 35837968 PMCID: PMC9840712 DOI: 10.1097/sla.0000000000005564] [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: 01/18/2023]
Abstract
OBJECTIVE This study aimed to unravel the lymph node metastasis (LNM)-related methylated DNA (mDNA) landscape and develop a mDNA signature to identify LNM in patients with T1 colorectal cancers (T1 CRC). BACKGROUND Considering the invasiveness of T1 CRC, current guidelines recommend endoscopic resection in patients with LNM-negative, and radical surgical resection only for high-risk LNM-positive patients. Unfortunately, the clinicopathological criteria for LNM risk stratification are imperfect, resulting in frequent misdiagnosis leading to unnecessary radical surgeries and postsurgical complications. METHODS We conducted genome-wide methylation profiling of 39 T1 CRC specimens to identify differentially methylated CpGs between LNM-positive and LNM-negative, and performed quantitative pyrosequencing analysis in 235 specimens from 3 independent patient cohorts, including 195 resected tissues (training cohort: n=128, validation cohort: n=67) and 40 pretreatment biopsies. RESULTS Using logistic regression analysis, we developed a 9-CpG signature to distinguish LNM-positive versus LNM-negative surgical specimens in the training cohort [area under the curve (AUC)=0.831, 95% confidence interval (CI)=0.755-0.892; P <0.0001], which was subsequently validated in additional surgical specimens (AUC=0.825; 95% CI=0.696-0.955; P =0.003) and pretreatment biopsies (AUC=0.836; 95% CI=0.640-1.000, P =0.0036). This diagnostic power was further improved by combining the signature with conventional clinicopathological features. CONCLUSIONS We established a novel epigenetic signature that can robustly identify LNM in surgical specimens and even pretreatment biopsies from patients with T1 CRC. Our signature has strong translational potential to improve the selection of high-risk patients who require radical surgery while sparing others from its complications and expense.
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Affiliation(s)
- Yinghui Zhao
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fuduan Peng
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
| | - Chuanxin Wang
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, China
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tatsuro Murano
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroaki Ikematsu
- Department of Gastroenterology and Endoscopy, National Cancer Center Hospital East, Chiba, Japan
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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Otsuka K, Iwasaki T. Insights into radiation carcinogenesis based on dose-rate effects in tissue stem cells. Int J Radiat Biol 2023; 99:1503-1521. [PMID: 36971595 DOI: 10.1080/09553002.2023.2194398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
PURPOSE Increasing epidemiological and biological evidence suggests that radiation exposure enhances cancer risk in a dose-dependent manner. This can be attributed to the 'dose-rate effect,' where the biological effect of low dose-rate radiation is lower than that of the same dose at a high dose-rate. This effect has been reported in epidemiological studies and experimental biology, although the underlying biological mechanisms are not completely understood. In this review, we aim to propose a suitable model for radiation carcinogenesis based on the dose-rate effect in tissue stem cells. METHODS We surveyed and summarized the latest studies on the mechanisms of carcinogenesis. Next, we summarized the radiosensitivity of intestinal stem cells and the role of dose-rate in the modulation of stem-cell dynamics after irradiation. RESULTS Consistently, driver mutations can be detected in most cancers from past to present, supporting the hypothesis that cancer progression is initiated by the accumulation of driver mutations. Recent reports demonstrated that driver mutations can be observed even in normal tissues, which suggests that the accumulation of mutations is a necessary condition for cancer progression. In addition, driver mutations in tissue stem cells can cause tumors, whereas they are not sufficient when they occur in non-stem cells. For non-stem cells, tissue remodeling induced by marked inflammation after the loss of tissue cells is important in addition to the accumulation of mutations. Therefore, the mechanism of carcinogenesis differs according to the cell type and magnitude of stress. In addition, our results indicated that non-irradiated stem cells tend to be eliminated from three-dimensional cultures of intestinal stem cells (organoids) composed of irradiated and non-irradiated stem cells, supporting the stem-cell competition. CONCLUSIONS We propose a unique scheme in which the dose-rate dependent response of intestinal stem cells incorporates the concept of the threshold of stem-cell competition and context-dependent target shift from stem cells to whole tissue. The concept highlights four key issues that should be considered in radiation carcinogenesis: i.e. accumulation of mutations; tissue reconstitution; stem-cell competition; and environmental factors like epigenetic modifications.
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Affiliation(s)
- Kensuke Otsuka
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry, Tokyo, Japan
| | - Toshiyasu Iwasaki
- Strategy and Planning Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry, Tokyo, Japan
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20
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Li Z, Fu Y, Hu Y, Zhu Y, Hu L, Shi C, Zhang Y, Zhang J, Zhou S. Low-dose arecoline regulates distinct core signaling pathways in oral submucous fibrosis and oral squamous cell carcinoma. BMC Oral Health 2023; 23:171. [PMID: 36966276 PMCID: PMC10039525 DOI: 10.1186/s12903-023-02887-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/15/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND Betel nut chewing plays a role in the pathogenesis of oral submucous fibrosis (OSF) and oral squamous cell carcinoma (OSCC). As the major active ingredient of the betel nut, the effect of arecoline and its underlying mechanism to OSF and OSCC pathogenesis remain unclear. METHODS Next-generation sequencing-based transcriptome and dRRBS analysis were performed on OSF and OSCC cells under low-dose arecoline exposure. Functional analyses were performed to compare the different roles of arecoline during OSF and OSCC pathogenesis, and key genes were identified. RESULTS In this study, we identified that low-dose arecoline promoted cell proliferation of both NFs and OSCC cells via the acceleration of cell cycle progression, while high-dose arecoline was cytotoxic to both NFs and OSCC cells. We performed for the first time the transcriptome and methylome landscapes of NFs and OSCC cells under low-dose arecoline exposure. We found distinct transcriptome and methylome profiles mediated by low-dose arecoline in OSF and OSCC cells, as well as specific genes and signaling pathways associated with metabolic disorders induced by low-dose arecoline exposure. Additionally, low-dose arecoline displayed different functions at different stages, participating in the modulation of the extracellular matrix via Wnt signaling in NFs and epigenetic regulation in OSCC cells. After exposure to low-dose arecoline, the node roles of FMOD in NFs and histone gene clusters in OSCC cells were found. Meanwhile, some key methylated genes induced by arecoline were also identified, like PTPRM and FOXD3 in NFs, SALL3 and IRF8 in OSCC cells, indicating early molecular events mediated by arecoline during OSF and OSCC pathogenesis. CONCLUSIONS This study elucidated the contribution of low-dose arecoline to OSF and OSCC pathogenesis and identified key molecular events that could be targeted for further functional studies and their potential as biomarkers.
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Affiliation(s)
- Zhenming Li
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - You Fu
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Yuhua Hu
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
- Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yun Zhu
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Longwei Hu
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Chaoji Shi
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Yi Zhang
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
- Department of Endodontics and Operative Dentistry, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Jianjun Zhang
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Shanghui Zhou
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China.
- National Center for Stomatology, Shanghai, 200011, China.
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China.
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China.
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China.
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Qiu T, Ding Y, Qin J, Ren D, Xie M, Qian Q, Wang Y, Ma L, Jing A, Yang J, Ma S, Wang X, Wang W, Ji J, Li G. Epigenetic reactivation of PEG3 by EZH2 inhibitors suppresses renal clear cell carcinoma progress. Cell Signal 2023; 107:110662. [PMID: 37001595 DOI: 10.1016/j.cellsig.2023.110662] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/01/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
PEG3 is a paternally imprinted gene located on chromosome 19q13.4 and one of the most common low-expression genes in human ovarian cancer. PEG3 plays an important role in p53-related cell death. However, whether PEG3 plays a role in renal clear cell carcinoma (ccRCC) remains unclear. Here, we found that PEG3 was epigenetic inactivated and played a tumor suppressor role in ccRCC. Overexpression of PEG3 inhibited ccRCC cell proliferation and colony formation, while removal of PEG3 significantly promoted cell proliferation in vitro and tumor formation in nude mice in vivo. EZH2-mediated H3K27me3 at the PEG3 promoter suppressed PEG3 expression. EZH2 specific inhibitors promote PEG3 transcriptional expression through the transition from H3K27me3 to H3K27ac at the PEG3 promoter region. Depletion of PEG3 inhibited the activation of the p53 signaling pathway, resulting in the resistance of ccRCC to EZH2 inhibitors treatment. Thus, our data show that EZH2-mediated epigenetic inactivation of PEG3 promotes the progress of ccRCC, and reactivation of PEG3 may be a promising strategy for ccRCC.
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Affiliation(s)
- Teng Qiu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yuanyuan Ding
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jingting Qin
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Dexu Ren
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Mengru Xie
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Qilan Qian
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yasong Wang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Ling Ma
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Aixin Jing
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jiayan Yang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Shaojie Ma
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiujun Wang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Weiling Wang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jing Ji
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China.
| | - Guanchu Li
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning Province, PR China
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Placental Galectins in Cancer: Why We Should Pay More Attention. Cells 2023; 12:cells12030437. [PMID: 36766779 PMCID: PMC9914345 DOI: 10.3390/cells12030437] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/15/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
The first studies suggesting that abnormal expression of galectins is associated with cancer were published more than 30 years ago. Today, the role of galectins in cancer is relatively well established. We know that galectins play an active role in many types of cancer by regulating cell growth, conferring cell death resistance, or inducing local and systemic immunosuppression, allowing tumor cells to escape the host immune response. However, most of these studies have focused on very few galectins, most notably galectin-1 and galectin-3, and more recently, galectin-7 and galectin-9. Whether other galectins play a role in cancer remains unclear. This is particularly true for placental galectins, a subgroup that includes galectin-13, -14, and -16. The role of these galectins in placental development has been well described, and excellent reviews on their role during pregnancy have been published. At first sight, it was considered unlikely that placental galectins were involved in cancer. Yet, placentation and cancer progression share several cellular and molecular features, including cell invasion, immune tolerance and vascular remodeling. The development of new research tools and the concomitant increase in database repositories for high throughput gene expression data of normal and cancer tissues provide a new opportunity to examine the potential involvement of placental galectins in cancer. In this review, we discuss the possible roles of placental galectins in cancer progression and why they should be considered in cancer studies. We also address challenges associated with developing novel research tools to investigate their protumorigenic functions and design highly specific therapeutic drugs.
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EZH2: An Accomplice of Gastric Cancer. Cancers (Basel) 2023; 15:cancers15020425. [PMID: 36672374 PMCID: PMC9856299 DOI: 10.3390/cancers15020425] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/10/2023] Open
Abstract
Gastric cancer is the fifth most common cancer and the third leading cause of cancer deaths worldwide. Understanding the factors influencing the therapeutic effects in gastric cancer patients and the molecular mechanism behind gastric cancer is still facing challenges. In addition to genetic alterations and environmental factors, it has been demonstrated that epigenetic mechanisms can also induce the occurrence and progression of gastric cancer. Enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of the polycomb repressor complex 2 (PRC2), which trimethylates histone 3 at Lys-27 and regulates the expression of downstream target genes through epigenetic mechanisms. It has been found that EZH2 is overexpressed in the stomach, which promotes the progression of gastric cancer through multiple pathways. In addition, targeted inhibition of EZH2 expression can effectively delay the progression of gastric cancer and improve its resistance to chemotherapeutic agents. Given the many effects of EZH2 in gastric cancer, there are no studies to comprehensively describe this mechanism. Therefore, in this review, we first introduce EZH2 and clarify the mechanisms of abnormal expression of EZH2 in cancer. Secondly, we summarize the role of EZH2 in gastric cancer, which includes the association of the EZH2 gene with genetic susceptibility to GC, the correlation of the EZH2 gene with gastric carcinogenesis and invasive metastasis, the resistance to chemotherapeutic drugs of gastric cancer mediated by EZH2 and the high expression of EZH2 leading to poor prognosis of gastric cancer patients. Finally, we also clarify some of the current statuses of drug development regarding targeted inhibition of EZH2/PRC2 activity.
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Yang YB, Wu CY, Wang XY, Deng J, Cao WJ, Tang YZ, Wan CC, Chen ZT, Zhan WY, Shan H, Kuang DM, Wei Y. Targeting inflammatory macrophages rebuilds therapeutic efficacy of DOT1L inhibition in hepatocellular carcinoma. Mol Ther 2023; 31:105-118. [PMID: 36183166 PMCID: PMC9840147 DOI: 10.1016/j.ymthe.2022.09.019] [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: 02/23/2022] [Revised: 09/01/2022] [Accepted: 09/28/2022] [Indexed: 01/26/2023] Open
Abstract
Epigenetic reprogramming is a promising therapeutic strategy for aggressive cancers, but its limitations in vivo remain unclear. Here, we showed, in detailed studies of data regarding 410 patients with human hepatocellular carcinoma (HCC), that increased histone methyltransferase DOT1L triggered epithelial-mesenchymal transition-mediated metastasis and served as a therapeutic target for human HCC. Unexpectedly, although targeting DOT1L in vitro abrogated the invasive potential of hepatoma cells, abrogation of DOT1L signals hardly affected the metastasis of hepatoma in vivo. Macrophages, which constitute the major cellular component of the stroma, abrogated the anti-metastatic effect of DOT1L targeting. Mechanistically, NF-κB signal elicited by macrophage inflammatory response operated via a non-epigenetic machinery to eliminate the therapeutic efficacy of DOT1L targeting. Importantly, therapeutic strategy combining DOT1L-targeted therapy with macrophage depletion or NF-κB inhibition in vivo effectively and successfully elicited cancer regression. Moreover, we found that the densities of macrophages in HCC determined malignant cell DOT1L-associated clinical outcome of the patients. Our results provide insight into the crosstalk between epigenetic reprogramming and cancer microenvironments and suggest that strategies to influence the functional activities of inflammatory cells may benefit epigenetic reprogramming therapy.
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Affiliation(s)
- Yi-Bin Yang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imaging, and The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Cai-Yuan Wu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Xu-Yan Wang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jia Deng
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imaging, and The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Wen-Jie Cao
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Yun-Zhi Tang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Chao-Chao Wan
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhi-Tian Chen
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Wan-Yu Zhan
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Hong Shan
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imaging, and The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China.
| | - Dong-Ming Kuang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China.
| | - Yuan Wei
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, China.
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25
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Morita S, Horii T, Hatada I. Regulation of Gene Expression Using dCas9-SunTag Platforms. Methods Mol Biol 2023; 2577:189-195. [PMID: 36173574 DOI: 10.1007/978-1-0716-2724-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Regulating gene expression is important for basic research and therapeutic applications. The epigenome is a record of genetic modifications such as DNA methylation and histone modifications, and epigenetic changes can play a key role in modifying gene expression. With the advent of genome editing technologies, it has become possible to manipulate the epigenome of specific genomic regions to control gene expression. In particular, CRISPR-Cas9 systems have been used widely for epigenome editing due to their high efficiency, versatility, specificity, and ease of use. Here, we describe a protocol for the upregulation of specific genes using the dCas9-SunTag system.
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Affiliation(s)
- Sumiyo Morita
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan.
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Porphyromonas gingivalis-Derived Lipopolysaccharide Promotes Glioma Cell Proliferation and Migration via Activating Akt Signaling Pathways. Cells 2022; 11:cells11244088. [PMID: 36552854 PMCID: PMC9777333 DOI: 10.3390/cells11244088] [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: 10/10/2022] [Revised: 12/11/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Periodontitis is significantly associated with the risk of cancers in the lung and the digestive system. Emerging evidence shows a plausible link between periodontitis and several types of brain diseases. However, the association between periodontal infection and glioma remains unclear. In the cultured GL261 glioma cells, P. gingivalis lipopolysaccharide (LPS) significantly promoted cell proliferation at concentrations ranging from 10 to 1000 ng/mL. It promoted cell migration at a higher concentration (100 and 1000 ng/mL). Additionally, exposure to 100 ng/mL P. gingivalis LPS induced a significant increase in the expression of TNF-α, TGF-β, MMP2, and MMP9, as well as the phosphorylation level of Akt at Ser473. These changes induced by P. gingivalis LPS were significantly antagonized by the Akt inhibitor. Furthermore, a total of 48 patients with brain tumors were enrolled to investigate their periodontal status before receiving tumor management. Poor periodontal status [probing depth (PD) ≥ 6 mm and attachment loss (AL) >5 mm] was found in 42.9% (9/21) of patients with glioma, which was significantly higher than that in patients with benign tumors and the relevant data in the 4th National Oral Health Survey in China. The glioma patients with both AL > 5 mm and PD ≥ 6 mm had a higher ki-67 labeling index than those with AL ≤ 5 mm or PD < 6 mm. These findings support the association between periodontal infection and glioma progression.
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27
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Langille E, Al-Zahrani KN, Ma Z, Liang M, Uuskula-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, El Ghamrasni S, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lü Y, Oh RH, Kozma KJ, Trcka D, Narimatsu M, Liu JC, Nguyen T, Barutcu S, Loganathan SK, Bremner R, Bader GD, Egan SE, Cescon DW, Sørlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D. Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer. Cancer Discov 2022; 12:2930-2953. [PMID: 36108220 PMCID: PMC9812400 DOI: 10.1158/2159-8290.cd-21-0865] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/15/2022] [Accepted: 09/13/2022] [Indexed: 01/21/2023]
Abstract
Systematically investigating the scores of genes mutated in cancer and discerning disease drivers from inconsequential bystanders is a prerequisite for precision medicine but remains challenging. Here, we developed a somatic CRISPR/Cas9 mutagenesis screen to study 215 recurrent "long-tail" breast cancer genes, which revealed epigenetic regulation as a major tumor-suppressive mechanism. We report that components of the BAP1 and COMPASS-like complexes, including KMT2C/D, KDM6A, BAP1, and ASXL1/2 ("EpiDrivers"), cooperate with PIK3CAH1047R to transform mouse and human breast epithelial cells. Mechanistically, we find that activation of PIK3CAH1047R and concomitant EpiDriver loss triggered an alveolar-like lineage conversion of basal mammary epithelial cells and accelerated formation of luminal-like tumors, suggesting a basal origin for luminal tumors. EpiDriver mutations are found in ∼39% of human breast cancers, and ∼50% of ductal carcinoma in situ express casein, suggesting that lineage infidelity and alveogenic mimicry may significantly contribute to early steps of breast cancer etiology. SIGNIFICANCE Infrequently mutated genes comprise most of the mutational burden in breast tumors but are poorly understood. In vivo CRISPR screening identified functional tumor suppressors that converged on epigenetic regulation. Loss of epigenetic regulators accelerated tumorigenesis and revealed lineage infidelity and aberrant expression of alveogenesis genes as potential early events in tumorigenesis. This article is highlighted in the In This Issue feature, p. 2711.
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Affiliation(s)
- Ellen Langille
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Khalid N. Al-Zahrani
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Zhibo Ma
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Minggao Liang
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | | | - Roderic Espin
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Spain
| | - Katie Teng
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ahmad Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Helga Bergholtz
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
| | - Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Somaieh Afiuni-Zadeh
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sana Alvi
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Andrew Elia
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - YiQing Lü
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Robin H. Oh
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Katelyn J. Kozma
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Daniel Trcka
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Masahiro Narimatsu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jeff C. Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Thomas Nguyen
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Seda Barutcu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sampath K. Loganathan
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Rod Bremner
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gary D. Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sean E. Egan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - David W. Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway
| | - Jeffrey L. Wrana
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hartland W. Jackson
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michael D. Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | | | - Erik S. Knudsen
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York
| | - Miguel Angel Pujana
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Spain
| | - Geoffrey M. Wahl
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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28
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Recillas-Targa F. Cancer Epigenetics: An Overview. Arch Med Res 2022; 53:732-740. [PMID: 36411173 DOI: 10.1016/j.arcmed.2022.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/18/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
Abstract
Cancer is a complex disease caused by genetic and epigenetic alterations in the control of cell division. Findings from the field of cancer genomics and epigenomics have increased our understanding of the origin and evolution of tumorigenic processes, greatly advancing our knowledge of the molecular etiology of cancer. Consequently, any contemporary view of cancer research must consider tumorigenesis as a cellular phenomenon that is a result of the interplay between genetic and epigenetic mutations and their interaction with environmental factors, including our microbiome, that influences cellular metabolism and proliferation rates. The integration and better knowledge of these processes will help us to improve diagnosis, prognosis, and future genetic and epigenetic therapies. Here, I present an overview of the epigenetic processes that are affected in cancer and how they contribute to the onset and progression of the disease. Finally, I discuss how the development of sophisticated experimental approaches and computational tools, including novel ways to exploit large data sets, could contribute to the better understanding and treatment of cancer.
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Affiliation(s)
- Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México.
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29
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Haque S, Raina R, Afroze N, Hussain A, Alsulimani A, Singh V, Mishra BN, Kaul S, Kharwar RN. Microbial dysbiosis and epigenetics modulation in cancer development - A chemopreventive approach. Semin Cancer Biol 2022; 86:666-681. [PMID: 34216789 DOI: 10.1016/j.semcancer.2021.06.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 01/27/2023]
Abstract
An overwhelming number of research articles have reported a strong relationship of the microbiome with cancer. Microbes have been observed more commonly in the body fluids like urine, stool, mucus of people with cancer compared to the healthy controls. The microbiota is responsible for both progression and suppression activities of various diseases. Thus, to maintain healthy human physiology, host and microbiota relationship should be in a balanced state. Any disturbance in this equilibrium, referred as microbiome dysbiosis becomes a prime cause for the human body to become more prone to immunodeficiency and cancer. It is well established that some of these microbes are the causative agents, whereas others may encourage the formation of tumours, but very little is known about how these microbial communications causing change at gene and epigenome level and trigger as well as encourage the tumour growth. Various studies have reported that microbes in the gut influence DNA methylation, DNA repair and DNA damage. The genes and pathways that are altered by gut microbes are also associated with cancer advancement, predominantly those implicated in cell growth and cell signalling pathways. This study exhaustively reviews the current research advancements in understanding of dysbiosis linked with colon, lung, ovarian, breast cancers and insights into the potential molecular targets of the microbiome promoting carcinogenesis, the epigenetic alterations of various potential targets by altered microbiota, as well as the role of various chemopreventive agents for timely prevention and customized treatment against various types of cancers.
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Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia; Bursa Uludağ University Faculty of Medicine, Görükle Campus, 16059, Nilüfer, Bursa, Turkey
| | - Ritu Raina
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
| | - Nazia Afroze
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
| | - Arif Hussain
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates.
| | - Ahmad Alsulimani
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Vineeta Singh
- Department of Biotechnology, Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, 226021, Uttar Pradesh, India
| | - Bhartendu Nath Mishra
- Department of Biotechnology, Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, 226021, Uttar Pradesh, India
| | - Sanjana Kaul
- School of Biotechnology, University of Jammu, Jammu, 180006, J&K, India
| | - Ravindra Nath Kharwar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, 221005, India
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30
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Hu Y, Hong X, Yuan Z, Mu J, Zhang X, Fang Z, Yuan Y, Zheng S, Guo C. Pan-cancer analysis of DNA epigenetic modifications by hydrophilic interaction liquid chromatography-tandem mass spectrometry. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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A critical review of datasets and computational suites for improving cancer theranostics and biomarker discovery. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:206. [PMID: 36175717 DOI: 10.1007/s12032-022-01815-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/29/2022] [Indexed: 10/14/2022]
Abstract
Cancer has been constantly evolving and so is the research pertaining to cancer diagnosis and therapeutic regimens. Early detection and specific therapeutics are the key features of modern cancer therapy. These requirements can only be fulfilled with the integration of diverse high-throughput technologies. Integration of advanced omics methodology involving genomics, epigenomics, proteomics, and transcriptomics provide a clear understanding of multi-faceted cancer. In the past few years, tremendous high-throughput data have been generated from cancer genomics and epigenomic analyses, which on further methodological analyses can yield better biological insights. The major epigenetic alterations reported in cancer are DNA methylation levels, histone post-translational modifications, and epi-miRNA regulating the oncogenes and tumor suppressor genes. While the genomic analyses like gene expression profiling, cancer gene prediction, and genome annotation divulge the genetic alterations in oncogenes or tumor suppressor genes. Also, systems biology approach using biological networks is being extensively used to identify novel cancer biomarkers. Therefore, integration of these multi-dimensional approaches will help to identify potential diagnostic and therapeutic biomarkers. Here, we reviewed the critical databases and tools dedicated to various epigenomic and genomic alterations in cancer. The review further focuses on the multi-omics resources available for further validating the identified cancer biomarkers. We also highlighted the tools for cancer biomarker discovery using a systems biology approach utilizing genomic and epigenomic data. Biomarkers predicted using such integrative approaches are shown to be more clinically relevant.
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32
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Unraveling Mitochondrial Determinants of Tumor Response to Radiation Therapy. Int J Mol Sci 2022; 23:ijms231911343. [PMID: 36232638 PMCID: PMC9569617 DOI: 10.3390/ijms231911343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/18/2022] Open
Abstract
Radiotherapy represents a highly targeted and efficient treatment choice in many cancer types, both with curative and palliative intents. Nevertheless, radioresistance, consisting in the adaptive response of the tumor to radiation-induced damage, represents a major clinical problem. A growing body of the literature suggests that mechanisms related to mitochondrial changes and metabolic remodeling might play a major role in radioresistance development. In this work, the main contributors to the acquired cellular radioresistance and their relation with mitochondrial changes in terms of reactive oxygen species, hypoxia, and epigenetic alterations have been discussed. We focused on recent findings pointing to a major role of mitochondria in response to radiotherapy, along with their implication in the mechanisms underlying radioresistance and radiosensitivity, and briefly summarized some of the recently proposed mitochondria-targeting strategies to overcome the radioresistant phenotype in cancer.
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33
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Davoodvandi A, Nikfar B, Reiter RJ, Asemi Z. Melatonin and cancer suppression: insights into its effects on DNA methylation. Cell Mol Biol Lett 2022; 27:73. [PMID: 36064311 PMCID: PMC9446540 DOI: 10.1186/s11658-022-00375-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
Melatonin is an important naturally occurring hormone in mammals. Melatonin-mediated biological effects include the regulation of circadian rhythms, which is important for optimal human health. Also, melatonin has a broad range of immunoenhancing actions. Moreover, its oncostatic properties, especially regarding breast cancer, involve a variety cancer-inhibitory processes and are well documented. Due to their promising effects on the prognosis of cancer patients, anti-cancer drugs with epigenetic actions have attracted a significant amount of attention in recent years. Epigenetic modifications of cancers are categorized into three major processes including non-coding RNAs, histone modification, and DNA methylation. Hence, the modification of the latter epigenetic event is currently considered an effective strategy for treatment of cancer patients. Thereby, this report summarizes the available evidence that investigated melatonin-induced effects in altering the status of DNA methylation in different cancer cells and models, e.g., malignant glioma and breast carcinoma. Also, we discuss the role of artificial light at night (ALAN)-mediated inhibitory effects on melatonin secretion and subsequent impact on global DNA methylation of cancer cells.
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Affiliation(s)
- Amirhossein Davoodvandi
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran.,Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Banafsheh Nikfar
- Pars Advanced and Minimally Invasive Medical Manners Research Center, Pars Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, UT Health. Long School of Medicine, San Antonio, TX, USA
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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34
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Espín-Pérez A, Brennan K, Ediriwickrema AS, Gevaert O, Lossos IS, Gentles AJ. Peripheral blood DNA methylation profiles predict future development of B-cell Non-Hodgkin Lymphoma. NPJ Precis Oncol 2022; 6:53. [PMID: 35864305 PMCID: PMC9304422 DOI: 10.1038/s41698-022-00295-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 06/28/2022] [Indexed: 11/09/2022] Open
Abstract
Lack of accurate methods for early lymphoma detection limits the ability to cure patients. Since patients with Non-Hodgkin lymphomas (NHL) who present with advanced disease have worse outcomes, accurate and sensitive methods for early detection are needed to improve patient care. We developed a DNA methylation-based prediction tool for NHL, based on blood samples collected prospectively from 278 apparently healthy patients who were followed for up to 16 years to monitor for NHL development. A predictive score was developed using machine learning methods in a robust training/validation framework. Our predictive score incorporates CpG DNA methylation at 135 genomic positions, with higher scores predicting higher risk. It was 85% and 78% accurate for identifying patients at risk of developing future NHL, in patients with high or low epigenetic mitotic clock respectively, in a validation cohort. It was also sensitive at detecting active NHL (96.3% accuracy) and healthy status (95.6% accuracy) in additional independent cohorts. Scores optimized for specific NHL subtypes showed significant but lower accuracy for predicting other subtypes. Our score incorporates hyper-methylation of Polycomb and HOX genes, which have roles in NHL development, as well as PAX5 - a master transcriptional regulator of B-cell fate. Subjects with higher risk scores showed higher regulatory T-cells, memory B-cells, but lower naïve T helper lymphocytes fractions in the blood. Future prospective studies will be required to confirm the utility of our signature for managing patients who are at high risk for developing future NHL.
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Affiliation(s)
- Almudena Espín-Pérez
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, 94035, USA.
| | - Kevin Brennan
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, 94035, USA
| | | | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, 94035, USA
| | - Izidore S Lossos
- Department of Medicine, Division of Hematology, Miller School of Medicine, University of Miami, 1600 NW 10th Avenue/1475 NW 12th Avenue (D8-4), Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.,Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Andrew J Gentles
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, 94035, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA, 94035, USA. .,Cancer Institute, Stanford University, Stanford, CA, 94035, USA.
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35
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Hozhabri H, Moghaddam MM, Moghaddam MM, Mohammadian A. A comprehensive bioinformatics analysis to identify potential prognostic biomarkers among CC and CXC chemokines in breast cancer. Sci Rep 2022; 12:10374. [PMID: 35725915 PMCID: PMC9209453 DOI: 10.1038/s41598-022-14610-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/06/2022] [Indexed: 11/09/2022] Open
Abstract
Breast cancer (BC) is a major human health problem due to its increasing incidence and mortality rate. CC and CXC chemokines are associated with tumorigenesis and the progression of many cancers. Since the prognostic values of CC and CXC families' expression in various types of cancers are becoming increasingly evident, we aimed to conduct a comprehensive bioinformatics analysis elucidating the prognostic values of the CC and CXC families in BC. Therefore, TCGA, UALCAN, Kaplan–Meier plotter, bc-GenExMiner, cBioPortal, STRING, Enrichr, and TIMER were utilized for analysis. We found that high levels of CCL4/5/14/19/21/22 were associated with better OS and RFS, while elevated expression of CCL24 was correlated with shorter OS in BC patients. Also, high levels of CXCL9/13 indicated longer OS, and enhanced expression of CXCL12/14 was linked with better OS and RFS in BC patients. Meanwhile, increased transcription levels of CXCL8 were associated with worse OS and RFS in BC patients. In addition, our results showed that CCL5, CCL8, CCL14, CCL20, CCL27, CXCL4, and CXCL14 were notably correlated with the clinical outcomes of BC patients. Our findings provide a new point of view that may help the clinical application of CC and CXC chemokines as prognostic biomarkers in BC.
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Affiliation(s)
- Hossein Hozhabri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | | | - Madiheh Mazaheri Moghaddam
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Ali Mohammadian
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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Bellanger A, Madsen-Østerbye J, Galigniana NM, Collas P. Restructuring of Lamina-Associated Domains in Senescence and Cancer. Cells 2022; 11:cells11111846. [PMID: 35681541 PMCID: PMC9180887 DOI: 10.3390/cells11111846] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 01/01/2023] Open
Abstract
Induction of cellular senescence or cancer is associated with a reshaping of the nuclear envelope and a broad reorganization of heterochromatin. At the periphery of mammalian nuclei, heterochromatin is stabilized at the nuclear lamina via lamina-associated domains (LADs). Alterations in the composition of the nuclear lamina during senescence lead to a loss of peripheral heterochromatin, repositioning of LADs, and changes in epigenetic states of LADs. Cancer initiation and progression are also accompanied by a massive reprogramming of the epigenome, particularly in domains coinciding with LADs. Here, we review recent knowledge on alterations in chromatin organization and in the epigenome that affect LADs and related genomic domains in senescence and cancer.
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Affiliation(s)
- Aurélie Bellanger
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
| | - Julia Madsen-Østerbye
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
| | - Natalia M. Galigniana
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (A.B.); (J.M.-Ø.); (N.M.G.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
- Correspondence:
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Sedillo JC, Cryns VL. Targeting the methionine addiction of cancer. Am J Cancer Res 2022; 12:2249-2276. [PMID: 35693095 PMCID: PMC9185618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023] Open
Abstract
Methionine is the initiator amino acid for protein synthesis, the methyl source for most nucleotide, chromatin, and protein methylation, and the carbon backbone for various aspects of the cellular antioxidant response and nucleotide biosynthesis. Methionine is provided in the diet and serum methionine levels fluctuate based on dietary methionine content. Within the cell, methionine is recycled from homocysteine via the methionine cycle, which is linked to nutrient status via one-carbon metabolism. Unlike normal cells, many cancer cells, both in vitro and in vivo, show high methionine cycle activity and are dependent on exogenous methionine for continued growth. However, the molecular mechanisms underlying the methionine dependence of diverse malignancies are poorly understood. Methionine deprivation initiates widespread metabolic alterations in cancer cells that enable them to survive despite limited methionine availability, and these adaptive alterations can be specifically targeted to enhance the activity of methionine deprivation, a strategy we have termed "metabolic priming". Chemotherapy-resistant cell populations such as cancer stem cells, which drive treatment-resistance, are also sensitive to methionine deprivation, suggesting dietary methionine restriction may inhibit metastasis and recurrence. Several clinical trials in cancer are investigating methionine restriction in combination with other agents. This review will explore new insights into the mechanisms of methionine dependence in cancer and therapeutic efforts to translate these insights into enhanced clinical activity of methionine restriction in cancer.
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Affiliation(s)
- Joni C Sedillo
- Department of Medicine, University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health Madison, WI, USA
| | - Vincent L Cryns
- Department of Medicine, University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health Madison, WI, USA
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New kinase and HDAC hybrid inhibitors: recent advances and perspectives. Future Med Chem 2022; 14:745-766. [PMID: 35543381 DOI: 10.4155/fmc-2021-0276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cancer is the second most common cause of death worldwide. It can easily acquire resistance to treatments, demanding new therapeutic strategies, such as simultaneous inhibition of kinase and HDAC enzymes with hybrid inhibitors. Different approaches to this have varied according to their targets, with a few common trends, such as the usage of heterocycle scaffolds for kinase interaction, especially pyrimidine and quinazolines, and hydroxamic acids and benzamides for HDAC inhibition. Besides the hybrid compounds developed focusing on the inhibition tyrosine kinase and receptor tyrosine kinase, many advances have occurred in the development of serine-threonine kinase/HDAC and lipid kinase/HDAC novel compounds. Here, the latest strategies employed in this research area will be reviewed, alongside trends in inhibitor design, and observed gaps will be punctuated.
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H3K4 demethylase KDM5B regulates cancer cell identity and epigenetic plasticity. Oncogene 2022; 41:2958-2972. [PMID: 35440714 DOI: 10.1038/s41388-022-02311-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/08/2022]
Abstract
The H3K4 demethylase KDM5B is overexpressed in multiple cancer types, and elevated expression levels of KDM5B is associated with decreased survival. However, the underlying mechanistic contribution of dysregulated expression of KDM5B and H3K4 demethylation in cancer is poorly understood. Our results show that loss of KDM5B in multiple types of cancer cells leads to increased proliferation and elevated expression of cancer stem cell markers. In addition, we observed enhanced tumor formation following KDM5B depletion in a subset of representative cancer cell lines. Our findings also support a role for KDM5B in regulating epigenetic plasticity, where loss of KDM5B in cancer cells with elevated KDM5B expression leads to alterations in activity of chromatin states, which facilitate activation or repression of alternative transcriptional programs. In addition, we define KDM5B-centric epigenetic and transcriptional patterns that support cancer cell plasticity, where KDM5B depleted cancer cells exhibit altered epigenetic and transcriptional profiles resembling a more primitive cellular state. This study also provides a resource for evaluating associations between alterations in epigenetic patterning upon depletion of KDM5B and gene expression in a diverse set of cancer cells.
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LaFave LM, Savage RE, Buenrostro JD. Single-Cell Epigenomics Reveals Mechanisms of Cancer Progression. ANNUAL REVIEW OF CANCER BIOLOGY 2022. [DOI: 10.1146/annurev-cancerbio-070620-094453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cancer initiation is driven by the cooperation between genetic and epigenetic aberrations that disrupt gene regulatory programs critical to maintaining specialized cellular functions. After initiation, cells acquire additional genetic and epigenetic alterations influenced by tumor-intrinsic and -extrinsic mechanisms, which increase intratumoral heterogeneity, reshape the cell's underlying gene regulatory networks and promote cancer evolution. Furthermore, environmental or therapeutic insults drive the selection of heterogeneous cell states, with implications for cancer initiation, maintenance, and drug resistance. The advancement of single-cell genomics has begun to uncover the full repertoire of chromatin and gene expression states (cell states) that exist within individual tumors. These single-cell analyses suggest that cells diversify in their regulatory states upon transformation by co-opting damage-induced and nonlineage regulatory programs that can lead to epigenomic plasticity. Here, we review these recent studies related to regulatory state changes in cancer progression and highlight the growing single-cell epigenomics toolkit poised to address unresolved questions in the field.
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Affiliation(s)
- Lindsay M. LaFave
- Department of Cell Biology and Albert Einstein Cancer Center, Albert Einstein College of Medicine, Montefiore Health System, Bronx, NY, USA
| | - Rachel E. Savage
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jason D. Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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MAT2A facilitates PDCD6 methylation and promotes cell growth under glucose deprivation in cervical cancer. Cell Death Dis 2022; 8:176. [PMID: 35396512 PMCID: PMC8993843 DOI: 10.1038/s41420-022-00987-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 11/08/2022]
Abstract
The underlying mechanisms of methionine adenosyltransferase 2 A (MAT2A)-mediated cervical cancer progression under nutrient stress are largely elusive. Therefore, our study aims to investigate molecular mechanism by which MAT2A-indcued cervical oncogenesis. The interaction between MAT2A and programmed cell death protein 6 (PDCD6) in cervical cancer cell lines was detected by immunoprecipitation, immunoblotting and mass spectrometric analysis. A panel of inhibitors that are linked to stress responsive kinases were utilized to detect related pathways by immunoblotting. Cell proliferation and apoptosis were investigated by CCK-8 and flow cytometry. Apoptosis related protein level of Bcl-2, Bax and Caspase-3 was also analyzed in cells with PDCD6 K90 methylation mutation. The association between MAT2A and PDCD6 was detected by immunohistochemistry and clinicopathological characteristics were further analyzed. We found that the interaction between MAT2A and PDCD6 is mediated by AMPK activation and facilitates PDCD6 K90 methylation and further promotes protein stability of PDCD6. Physiologically, expression of PDCD6 K90R leads to increased apoptosis and thus suppresses growth of cervical cancer cells under glucose deprivation. Furthermore, the clinical analysis indicates that the MAT2A protein level is positively associated with the PDCD6 level, and the high level of PDCD6 significantly correlates with poor prognosis and advanced stages of cervical cancer patients. We conclude that MAT2A facilitates PDCD6 methylation to promote cervical cancer growth under glucose deprivation, suggesting the regulatory role of MAT2A in cellular response to nutrient stress and cervical cancer progression.
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Abstract
Although tumourigenesis occurs due to genetic mutations, the role of epigenetic dysregulations in cancer is also well established. Epigenetic dysregulations in cancer may occur as a result of mutations in genes encoding histone/DNA-modifying enzymes and chromatin remodellers or mutations in histone protein itself. It is also true that misregulated gene expression without genetic mutations in these factors could also support tumour initiation and progression. Interestingly, metabolic rewiring has emerged as a hallmark of cancer due to gene mutations in specific metabolic enzymes or dietary/environmental factors. Recent studies report an intricate cross-talk between epigenetic and metabolic reprogramming in cancer. This review discusses the role of epigenetic and metabolic dysregulations and their cross-talk in tumourigenesis with a special focus on gliomagenesis. We also discuss the role of recently developed human embryonic stem cells/induced pluripotent stem cells-derived organoid models of gliomas and how these models are proving instrumental in uncovering human-specific cellular and molecular complexities of gliomagenesis.
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Affiliation(s)
- Bismi Phasaludeen
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Suraiya Anjum Ansari
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
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Integrating mutational and nonmutational mechanisms of acquired therapy resistance within the Darwinian paradigm. Trends Cancer 2022; 8:456-466. [DOI: 10.1016/j.trecan.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023]
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Wu Z, Zhang X, Chen D, Li Z, Wu X, Wang J, Deng Y. N6-Methyladenosine-Related LncRNAs Are Potential Remodeling Indicators in the Tumor Microenvironment and Prognostic Markers in Osteosarcoma. Front Immunol 2022; 12:806189. [PMID: 35095893 PMCID: PMC8790065 DOI: 10.3389/fimmu.2021.806189] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/06/2021] [Indexed: 12/23/2022] Open
Abstract
N6-Adenosine methylation, yielding N6-methyladenosine (m6A), is a reversible epigenetic modification found in messenger RNAs and long non-coding RNAs (lncRNAs), which affects the fate of modified RNA molecules and is essential for the development and differentiation of immune cells in the tumor microenvironment (TME). Osteosarcoma (OS) is the most common primary bone tumor in children and adolescents, and is characterized by high mortality. Currently, the possible role of m6A modifications in the prognosis of OS is unclear. In the present study, we investigated the correlation between m6A-related lncRNA expression and the clinical outcomes of OS patients via a comprehensive analysis. Clinical and workflow-type data were obtained from the Genotype-Tissue Expression Program and The Cancer Genome Atlas. We examined the relationship between m6A modifications and lncRNA expression, conducted Kyoto Encyclopedia of Genes analysis and also gene set enrichment analysis (GSEA), implemented survival analysis to investigate the association of clinical survival data with the expression of m6A-related lncRNAs, and utilized Lasso regression to model the prognosis of OS. Furthermore, we performed immune correlation analysis and TME differential analysis to investigate the infiltration levels of immune cells and their relationship with clinical prognosis. LncRNA expression and m6A levels were closely associated in co-expression analysis. The expression of m6A-related lncRNAs was quite low in tumor tissues; this appeared to be a predicting factor of OS in a prognostic model, independent of other clinical features. The NOD-like receptor signaling pathway was the most significantly enriched pathway in GSEA. In tumor tissues, SPAG4 was overexpressed while ZBTB32 and DEPTOR were downregulated. Tissues in cluster 2 were highly infiltrated by plasma cells. Cluster 2 presented higher ESTIMATE scores and stromal scores, showing a lower tumor cell purity in the TME. In conclusion, m6A-related lncRNA expression is strongly associated with the occurrence and development of OS, and can be used to as a prognostic factor of OS. Moreover, m6A-related lncRNAs and infiltrating immune cells in the TME could serve as new therapeutic targets and prognostic biomarkers for OS.
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Affiliation(s)
- Zhongguang Wu
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaobo Zhang
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Dongjie Chen
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zian Li
- Department of Clinical Laboratory, Qinghai Provincial People's Hospital, Xining, China
| | - Xin Wu
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Jianlong Wang
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Youwen Deng
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
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Abstract
The importance of the microbiota in the development of colorectal cancer (CRC) is increasingly evident, but identifying specific microbial features that influence CRC initiation and progression remains a central task for investigators. Studies determining the microbial mechanisms that directly contribute to CRC development or progression are revealing bacterial factors such as toxins that contribute to colorectal carcinogenesis. However, even when investigators have identified bacteria that express toxins, questions remain about the host determinants of a toxin's cancer-potentiating effects. For other cancer-correlating bacteria that lack toxins, the challenge is to define cancer-relevant virulence factors. Herein, we evaluate three CRC-correlating bacteria, colibactin-producing Escherichia coli, enterotoxigenic Bacteroides fragilis, and Fusobacterium nucleatum, for their virulence features relevant to CRC. We also consider the beneficial bioactivity of gut microbes by highlighting a microbial metabolite that may enhance CRC antitumor immunity. In doing so, we aim to elucidate unique and shared mechanisms underlying the microbiota's contributions to CRC and to accelerate investigation from target validation to CRC therapeutic discovery.
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Affiliation(s)
- Slater L. Clay
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
| | - Diogo Fonseca-Pereira
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
| | - Wendy S. Garrett
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Bošković M, Roje B, Chung FFL, Gelemanović A, Cahais V, Cuenin C, Khoueiry R, Vilović K, Herceg Z, Terzić J. DNA Methylome Changes of Muscle- and Neuronal-Related Processes Precede Bladder Cancer Invasiveness. Cancers (Basel) 2022; 14:487. [PMID: 35158756 PMCID: PMC8833512 DOI: 10.3390/cancers14030487] [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: 12/22/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) is the ninth leading cause of cancer death with one of the highest recurrence rates among all cancers. One of the main risks for BC development is exposure to nitrosamines present in tobacco smoke or in other products. Aberrant epigenetic (DNA methylation) changes accompanied by deregulated gene expression are an important element of cancer pathogenesis. Therefore, we aimed to determine DNA methylation signatures and their impacts on gene expression in mice treated with N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN), a carcinogen similar to compounds found in tobacco smoke. Following BBN administration mice developed non-invasive or invasive bladder cancers. Surprisingly, muscle- and neuronal-related pathways emerged as the most affected in those tumors. Hypo- and hypermethylation changes were present within non-invasive BC, across CpGs mapping to the genes involved in muscle- and neuronal-related pathways, however, methylation differences were not sufficient to affect the expression of the majority of associated genes. Conversely, invasive tumors displayed hypermethylation changes that were linked with alterations in gene expression profiles. Together, these findings indicate that bladder cancer progression could be revealed through methylation profiling at the pre-invasive cancer stage that could assist monitoring of cancer patients and guide novel therapeutic approaches.
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Affiliation(s)
- Maria Bošković
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
| | - Blanka Roje
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
| | - Felicia Fei-Lei Chung
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia
| | - Andrea Gelemanović
- Biology of Robustness Group, Mediterranean Institute for Life Sciences (MedILS), Šetalište Ivana Meštrovića 45, 21000 Split, Croatia;
| | - Vincent Cahais
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Rita Khoueiry
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Katarina Vilović
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; (F.F.-L.C.); (V.C.); (C.C.); (R.K.)
| | - Janoš Terzić
- Laboratory for Cancer Research, University of Split School of Medicine, Šoltanska 2, 21000 Split, Croatia; (M.B.); (B.R.); (K.V.)
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Prokop J, Maršálek P, Sengul I, Pelikán A, Janoutová J, Horyl P, Roman J, Sengul D, Junior JMS. Evaluation of breast stiffness pathology based on breast compression during mammography: Proposal for novel breast stiffness scale classification. Clinics (Sao Paulo) 2022; 77:100100. [PMID: 36137345 PMCID: PMC9493386 DOI: 10.1016/j.clinsp.2022.100100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022] Open
Abstract
Breast cancer is diagnosed through a patient's Breast Self-Examination (BSE), Clinical Breast Examination (CBE), or para-clinical methods. False negativity of PCM in breast cancer diagnostics leads to a persisting problem associated with breast tumors diagnosed only in advanced stages. As the tumor volume/size at which it becomes invasive is not clear, BSE and CBE play an exceedingly important role in the early diagnosis of breast cancer. The quality and effectiveness of BSE and CBE depend on several factors, among which breast stiffness is the most important one. In this study, the authors present four methods for evaluating breast stiffness pathology during mammography examination based on the outputs obtained during the breast compression process, id est, without exposing the patient to X-Ray radiation. Based on the subjective assessment of breast stiffness by experienced medical examiners, a novel breast stiffness classification was designed, and the best method of its objective measurement was calibrated to fit the scale. Hence, this study provides an objective tool for the identification of patients who, being unable to perform valid BSE, could benefit from an increased frequency of mammography screening. Dum vivimus servimus.
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Affiliation(s)
- Jiří Prokop
- Department of Epidemiology and Public Health, Faculty of Medicine, University of Ostrava, Czechia; Department of Surgery, University Hospital Ostrava, Czechia; Department of Surgical Studies, Faculty of Medicine, University of Ostrava, Czechia
| | - Pavel Maršálek
- Department of Applied Mechanics, Faculty of Mechanical Engineering, VŠB-Technical University of Ostrava, Czechia
| | - Ilker Sengul
- Division of Endocrine Surgery, Faculty of Medicine, Giresun University, Turkey; Department of General Surgery, Faculty of Medicine, Giresun University, Turkey.
| | - Anton Pelikán
- Department of Surgery, University Hospital Ostrava, Czechia; Department of Surgical Studies, Faculty of Medicine, University of Ostrava, Czechia; Department of Health Care Sciences, Faculty of Humanities, Tomas Bata University in Zlin, Czechia
| | - Jana Janoutová
- Department of Public Health, Faculty of Medicine and Dentistry, Palacký University Olomouc, Czechia
| | - Petr Horyl
- Department of Applied Mechanics, Faculty of Mechanical Engineering, VŠB-Technical University of Ostrava, Czechia
| | - Jan Roman
- Department of Surgery, University Hospital Ostrava, Czechia; Department of Surgical Studies, Faculty of Medicine, University of Ostrava, Czechia
| | - Demet Sengul
- Department of Pathology, Faculty of Medicine, Giresun University, Turkey
| | - José Maria Soares Junior
- Universidade Federal de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Departamento de Obstetrícia e Ginecologia, Disciplina de Ginecologia São Paulo (SP), Brasil
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Correlation Analysis of Protein Expression of 10 HDAC/Sirtuin Isoenzymes with Sensitivities of 23 Anticancer Drugs in 17 Cancer Cell Lines and Potentiation of Drug Activity by Co-Treatment with HDAC Inhibitors. Cancers (Basel) 2021; 14:cancers14010187. [PMID: 35008351 PMCID: PMC8750037 DOI: 10.3390/cancers14010187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Protein expression profiles of 10 HDAC/Sirtuin isoenzymes in two panels of human cancer cell lines were compared with each other and with the potencies of various anticancer drugs by Pearson and Spearman correlation analysis to identify patterns of enzyme expression and anticancer activity. Furthermore, the NCI COMPARE database was used to identify possible correlations between the mRNA expression in a 60 cancer cell panel and the potency of the same anticancer drugs. While several interesting correlations were found within both data sets, none of these correlations were identical in the two sets of data, suggesting that protein and mRNA expression profiles are not comparable. Combination treatments with several HDAC inhibitors with a number of the anticancer drugs revealed interesting synergistic effects that were in keeping with some of the correlations predicted by our protein expression analysis. Abstract Inhibiting the activity of histone deacetylase (HDAC) is an ongoing strategy in anticancer therapy. However, to our knowledge, the relationships between the expression of HDAC proteins and the antitumor drug sensitivity of cancer cells have not been studied until now. In the current work, we investigated the relative expression profiles of 10 HDAC isoenzymes comprising the classes I–III (HDAC1/2/4/6; Sirt1/2/3/5/6/7) in a panel of 17 cancer cell lines, including the breast, cervix, oesophageal, lung, oral squamous, pancreas, as well as urinary bladder carcinoma cells. Correlations between the data of mRNA expression for these enzymes obtained from the National Cancer Institute (NCI) 60 cancer cell line program were also examined. Next, we performed univariate analysis between the expression patterns of HDAC/Sirt isoenzymes with the sensitivity of a 16 cell panel of cancer cell lines towards several antitumor drugs. In a univariate correlation analysis, we found a strong relation between Sirt2 expression and cytotoxicity caused by busulfan, etoposide, and hydroxyurea. Moreover, it was identified that Sirt5 correlates with the effects exerted by oxaliplatin or topotecan, as well as between HDAC4 expression and these two drugs. Correlations between the data of mRNA expression for enzymes with the potencies of the same anticancer agents obtained from the NCI 60 cancer cell line program were also found, but none were the same as those we found with our protein expression data. Additionally, we report here the effects upon combination of the approved HDAC inhibitor vorinostat and one other known inhibitor trichostatin A as well as newer hetero-stilbene and diazeno based sirtuin inhibitors on the potency of cisplatin, lomustine, and topotecan. For these three anticancer drugs, we found a significantly enhanced cytotoxicity when co-incubated with HDAC inhibitors, demonstrating a potentially beneficial influence of HDAC inhibition on anticancer drug treatment.
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Zhang J, Chen W, Ma W, Song K, Lee S, Han C, Wu T. Epigenetic Silencing of 15-Hydroxyprostaglandin Dehydrogenase by Histone Methyltransferase EHMT2/G9a in Cholangiocarcinoma. Mol Cancer Res 2021; 20:350-360. [PMID: 34880125 DOI: 10.1158/1541-7786.mcr-21-0536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022]
Abstract
Cholangiocarcinoma (CCA) is a lethal malignancy with few therapeutic options. NAD+-dependent 15-hydroxyprostaglandin dehydrogenase (15-PGDH) has been shown to inhibit CCA cell growth in vitro and in xenograft models. However, the role of 15-PGDH in CCA development has not been investigated and the mechanism for 15-PGDH gene regulation remains unclear. Here, we evaluated the role of 15-PGDH in CCA development by using a mouse model with hydrodynamic tail vein injection of transposase-based plasmids expressing Notch1 intracellular domain and myr-Akt, with or without co-injection of 15-PGDH expression plasmids. Our results reveal that 15-PGDH overexpression effectively prevents CCA development. Through patient data mining and experimental approaches, we provide novel evidences that 15-PGDH is epigenetically silenced by histone methyltransferase G9a. We observe that 15-PGDH and G9a expressions are inversely correlated in both human and mouse CCAs. By using CCA cells and mouse models, we show that G9a inhibition restores 15-PGDH expression and inhibited CCA in vitro and in vivo. Mechanistically, our data indicate that G9a is recruited to 15-PGDH gene promoter via protein-protein interaction with the E-box binding Myc/Max heterodimer. The recruited G9a then silences 15-PGDH gene through enhanced methylation of H3K9. Our further experiments have led to the identification of STAT4 as a key transcription factor involved in the regulation of 15-PGDH by G9a. Collectively, our findings disclose a novel G9a-15PGDH signaling axis which is importantly implicated in CCA development and progression. Implications: The current study describes a novel G9a-15PGDH signaling axis which is importantly implicated in cholangiocarcinoma (CCA) development and progression.
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Affiliation(s)
- Jinqiang Zhang
- Pathology and Laboratory Medicine, Tulane University School of Medicine
| | | | - Wenbo Ma
- Tulane University School of Medicine
| | - Kyoungsub Song
- Pathology and Laboratory Medicine, Tulane University School of Medicine
| | - Sean Lee
- Pathology and Laboratory Medicine, Tulane University School of Medicine
| | - Chang Han
- Pathology and Laboratory Medicine, Tulane University School of Medicine
| | - Tong Wu
- Pathology and Laboratory Medicine, Tulane University
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Batoon L, McCauley LK. Cross Talk Between Macrophages and Cancer Cells in the Bone Metastatic Environment. Front Endocrinol (Lausanne) 2021; 12:763846. [PMID: 34803925 PMCID: PMC8597897 DOI: 10.3389/fendo.2021.763846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
The skeleton is a common site for cancer metastases with the bone microenvironment providing the appropriate conditions for cancer cell colonization. Once in bone, cancer cells effectively manipulate their microenvironment to support their growth and survival. Despite previous efforts to improve treatment modalities, skeletal metastases remain with poor prognoses. This warrants an improved understanding of the mechanisms leading to bone metastasis that will aid development of effective treatments. Macrophages in the tumor microenvironment are termed tumor associated macrophages (TAMs) and their crosstalk with cancer cells is critical in regulating tumorigenicity in multiple cancers. In bone metastases, this crosstalk is also being increasingly implicated but the specific signaling pathways remain incompletely understood. Here, we summarize the reported functions, interactions, and signaling of macrophages with cancer cells during the metastatic cascade to bone. Specifically, we review and discuss how these specific interactions impact macrophages and their profiles to promote tumor development. We also discuss the potential of targeting this crosstalk to inhibit disease progression. Finally, we identify the remaining knowledge gaps that will need to be addressed in order to fully consider therapeutic targeting to improve clinical outcomes in cancer patients.
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Affiliation(s)
- Lena Batoon
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, United States
- Bones and Immunology Group, Mater Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Laurie K. McCauley
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, United States
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