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Zhang Z, Jin H, Zhang X, Bai M, Zheng K, Tian J, Deng B, Mao L, Qiu P, Huang B. Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression. Front Immunol 2024; 15:1369311. [PMID: 38601162 PMCID: PMC11004287 DOI: 10.3389/fimmu.2024.1369311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Background Coronavirus disease (COVID-19), caused by SARS-CoV-2, has emerged as a infectious disease, coexisting with widespread seasonal and sporadic influenza epidemics globally. Individuals living with HIV, characterized by compromised immune systems, face an elevated risk of severe outcomes and increased mortality when affected by COVID-19. Despite this connection, the molecular intricacies linking COVID-19, influenza, and HIV remain unclear. Our research endeavors to elucidate the shared pathways and molecular markers in individuals with HIV concurrently infected with COVID-19 and influenza. Furthermore, we aim to identify potential medications that may prove beneficial in managing these three interconnected illnesses. Methods Sequencing data for COVID-19 (GSE157103), influenza (GSE185576), and HIV (GSE195434) were retrieved from the GEO database. Commonly expressed differentially expressed genes (DEGs) were identified across the three datasets, followed by immune infiltration analysis and diagnostic ROC analysis on the DEGs. Functional enrichment analysis was performed using GO/KEGG and Gene Set Enrichment Analysis (GSEA). Hub genes were screened through a Protein-Protein Interaction networks (PPIs) analysis among DEGs. Analysis of miRNAs, transcription factors, drug chemicals, diseases, and RNA-binding proteins was conducted based on the identified hub genes. Finally, quantitative PCR (qPCR) expression verification was undertaken for selected hub genes. Results The analysis of the three datasets revealed a total of 22 shared DEGs, with the majority exhibiting an area under the curve value exceeding 0.7. Functional enrichment analysis with GO/KEGG and GSEA primarily highlighted signaling pathways associated with ribosomes and tumors. The ten identified hub genes included IFI44L, IFI44, RSAD2, ISG15, IFIT3, OAS1, EIF2AK2, IFI27, OASL, and EPSTI1. Additionally, five crucial miRNAs (hsa-miR-8060, hsa-miR-6890-5p, hsa-miR-5003-3p, hsa-miR-6893-3p, and hsa-miR-6069), five essential transcription factors (CREB1, CEBPB, EGR1, EP300, and IRF1), and the top ten significant drug chemicals (estradiol, progesterone, tretinoin, calcitriol, fluorouracil, methotrexate, lipopolysaccharide, valproic acid, silicon dioxide, cyclosporine) were identified. Conclusion This research provides valuable insights into shared molecular targets, signaling pathways, drug chemicals, and potential biomarkers for individuals facing the complex intersection of COVID-19, influenza, and HIV. These findings hold promise for enhancing the precision of diagnosis and treatment for individuals with HIV co-infected with COVID-19 and influenza.
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Affiliation(s)
- Zhen Zhang
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Hao Jin
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Xu Zhang
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Mei Bai
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Kexin Zheng
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Jing Tian
- Department of Immunology, School of Basic Medical Science, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Bin Deng
- Laboratory Department, Jinzhou Central Hospital, Jinzhou, Liaoning, China
| | - Lingling Mao
- Institute for Prevention and Control of Infection and Infectious Diseases, Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Pengcheng Qiu
- Thoracic Surgery Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Bo Huang
- Thoracic Surgery Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
- Thoracic Surgery Department, Yingkou Central Hospital, Yingkou, Liaoning, China
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Liu HM, Zhou Y, Chen HX, Wu JW, Ji SK, Shen L, Wang SP, Liu HM, Liu Y, Dai XJ, Zheng YC. LSD1 in drug discovery: From biological function to clinical application. Med Res Rev 2024; 44:833-866. [PMID: 38014919 DOI: 10.1002/med.22000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/18/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) is a flavin adenine dinucleotide (FAD) dependent monoamine oxidase (MAO) that erases the mono-, and dimethylation of histone 3 lysine 4 (H3K4), resulting in the suppression of target gene transcriptions. Besides, it can also demethylate some nonhistone substrates to regulate their biological functions. As reported, LSD1 is widely upregulated and plays a key role in several kinds of cancers, pharmacological or genetic ablation of LSD1 in cancer cells suppresses cell aggressiveness by several distinct mechanisms. Therefore, numerous LSD1 inhibitors, including covalent and noncovalent, have been developed and several of them have entered clinical trials. Herein, we systemically reviewed and discussed the biological function of LSD1 in tumors, lymphocytes as well as LSD1-targeting inhibitors in clinical trials, hoping to benefit the field of LSD1 and its inhibitors.
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Affiliation(s)
- Hui-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ying Zhou
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - He-Xiang Chen
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiang-Wan Wu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Shi-Kun Ji
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Liang Shen
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Shao-Peng Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Hong-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ying Liu
- Department of Pharmacy, Henan Engineering Research Center for Application & Translation of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xing-Jie Dai
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yi-Chao Zheng
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
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Bandini C, Mereu E, Paradzik T, Labrador M, Maccagno M, Cumerlato M, Oreglia F, Prever L, Manicardi V, Taiana E, Ronchetti D, D’Agostino M, Gay F, Larocca A, Besse L, Merlo GR, Hirsch E, Ciarrocchi A, Inghirami G, Neri A, Piva R. Lysin (K)-specific demethylase 1 inhibition enhances proteasome inhibitor response and overcomes drug resistance in multiple myeloma. Exp Hematol Oncol 2023; 12:71. [PMID: 37563685 PMCID: PMC10413620 DOI: 10.1186/s40164-023-00434-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Multiple myeloma (MM) is an incurable plasma cell malignancy, accounting for approximately 1% of all cancers. Despite recent advances in the treatment of MM, due to the introduction of proteasome inhibitors (PIs) such as bortezomib (BTZ) and carfilzomib (CFZ), relapses and disease progression remain common. Therefore, a major challenge is the development of novel therapeutic approaches to overcome drug resistance, improve patient outcomes, and broaden PIs applicability to other pathologies. METHODS We performed genetic and drug screens to identify new synthetic lethal partners to PIs, and validated candidates in PI-sensitive and -resistant MM cells. We also tested best synthetic lethal interactions in other B-cell malignancies, such as mantle cell, Burkitt's and diffuse large B-cell lymphomas. We evaluated the toxicity of combination treatments in normal peripheral blood mononuclear cells (PBMCs) and bone marrow stromal cells (BMSCs). We confirmed the combo treatment' synergistic effects ex vivo in primary CD138+ cells from MM patients, and in different MM xenograft models. We exploited RNA-sequencing and Reverse-Phase Protein Arrays (RPPA) to investigate the molecular mechanisms of the synergy. RESULTS We identified lysine (K)-specific demethylase 1 (LSD1) as a top candidate whose inhibition can synergize with CFZ treatment. LSD1 silencing enhanced CFZ sensitivity in both PI-resistant and -sensitive MM cells, resulting in increased tumor cell death. Several LSD1 inhibitors (SP2509, SP2577, and CC-90011) triggered synergistic cytotoxicity in combination with different PIs in MM and other B-cell neoplasms. CFZ/SP2509 treatment exhibited a favorable cytotoxicity profile toward PBMCs and BMSCs. We confirmed the clinical potential of LSD1-proteasome inhibition in primary CD138+ cells of MM patients, and in MM xenograft models, leading to the inhibition of tumor progression. DNA damage response (DDR) and proliferation machinery were the most affected pathways by CFZ/SP2509 combo treatment, responsible for the anti-tumoral effects. CONCLUSIONS The present study preclinically demonstrated that LSD1 inhibition could provide a valuable strategy to enhance PI sensitivity and overcome drug resistance in MM patients and that this combination might be exploited for the treatment of other B-cell malignancies, thus extending the therapeutic impact of the project.
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Affiliation(s)
- Cecilia Bandini
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Elisabetta Mereu
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Tina Paradzik
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Department of Physical Chemistry, Rudjer Boskovic Insitute, Zagreb, Croatia
| | - Maria Labrador
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Monica Maccagno
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Michela Cumerlato
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Federico Oreglia
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Lorenzo Prever
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Veronica Manicardi
- Laboratory of Translational Research, Azienda USL-IRCCS Reggio Emilia, Reggio Emilia, Italy
| | - Elisa Taiana
- Hematology, Fondazione Cà Granda IRCCS Policlinico, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Domenica Ronchetti
- Hematology, Fondazione Cà Granda IRCCS Policlinico, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Mattia D’Agostino
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Città Della Salute e della Scienza Hospital, Turin, Italy
| | - Francesca Gay
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Città Della Salute e della Scienza Hospital, Turin, Italy
| | - Alessandra Larocca
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Città Della Salute e della Scienza Hospital, Turin, Italy
| | - Lenka Besse
- Experimental Oncology and Hematology, Department of Oncology and Hematology, St. Gallen Cantonal Hospital, St. Gallen, Switzerland
- Scientific Directorate, Azienda-USL IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Giorgio Roberto Merlo
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Emilio Hirsch
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS Reggio Emilia, Reggio Emilia, Italy
| | - Giorgio Inghirami
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Antonino Neri
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY USA
| | - Roberto Piva
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Città Della Salute e della Scienza Hospital, Turin, Italy
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Antona A, Leo G, Favero F, Varalda M, Venetucci J, Faletti S, Todaro M, Mazzucco E, Soligo E, Saglietti C, Stassi G, Manfredi M, Pelicci G, Corà D, Valente G, Capello D. Targeting lysine-specific demethylase 1 (KDM1A/LSD1) impairs colorectal cancer tumorigenesis by affecting cancer cells stemness, motility, and differentiation. Cell Death Discov 2023; 9:201. [PMID: 37385999 DOI: 10.1038/s41420-023-01502-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/12/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
Among all cancers, colorectal cancer (CRC) is the 3rd most common and the 2nd leading cause of death worldwide. New therapeutic strategies are required to target cancer stem cells (CSCs), a subset of tumor cells highly resistant to present-day therapy and responsible for tumor relapse. CSCs display dynamic genetic and epigenetic alterations that allow quick adaptations to perturbations. Lysine-specific histone demethylase 1A (KDM1A also known as LSD1), a FAD-dependent H3K4me1/2 and H3K9me1/2 demethylase, was found to be upregulated in several tumors and associated with a poor prognosis due to its ability to maintain CSCs staminal features. Here, we explored the potential role of KDM1A targeting in CRC by characterizing the effect of KDM1A silencing in differentiated and CRC stem cells (CRC-SCs). In CRC samples, KDM1A overexpression was associated with a worse prognosis, confirming its role as an independent negative prognostic factor of CRC. Consistently, biological assays such as methylcellulose colony formation, invasion, and migration assays demonstrated a significantly decreased self-renewal potential, as well as migration and invasion potential upon KDM1A silencing. Our untargeted multi-omics approach (transcriptomic and proteomic) revealed the association of KDM1A silencing with CRC-SCs cytoskeletal and metabolism remodeling towards a differentiated phenotype, supporting the role of KDM1A in CRC cells stemness maintenance. Also, KDM1A silencing resulted in up-regulation of miR-506-3p, previously reported to play a tumor-suppressive role in CRC. Lastly, loss of KDM1A markedly reduced 53BP1 DNA repair foci, implying the involvement of KDM1A in the DNA damage response. Overall, our results indicate that KDM1A impacts CRC progression in several non-overlapping ways, and therefore it represents a promising epigenetic target to prevent tumor relapse.
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Affiliation(s)
- Annamaria Antona
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy.
| | - Giovanni Leo
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Francesco Favero
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, Department of Translational Medicine, Università del Piemonte Orientale, Corso Trieste 15/A, 28100, Novara, Italy
| | - Marco Varalda
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Jacopo Venetucci
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Stefania Faletti
- Department of Experimental Oncology, IRCCS, European Institute of Oncology, Via Adamello 16, 20139, Milano, Italy
| | - Matilde Todaro
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Piazza delle Cliniche 2, 90127, Palermo, Italy
| | - Eleonora Mazzucco
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Enrica Soligo
- Pathology Unit, Ospedale Sant'Andrea, Corso Mario Abbiate 21, 13100, Vercelli, Italy
| | - Chiara Saglietti
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
| | - Giorgio Stassi
- Department of Surgical, Oncological and Stomatological Sciences, Università di Palermo, Via del Vespro 131, 90127, Palermo, Italy
| | - Marcello Manfredi
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, Department of Translational Medicine, Università del Piemonte Orientale, Corso Trieste 15/A, 28100, Novara, Italy
| | - Giuliana Pelicci
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
- Department of Experimental Oncology, IRCCS, European Institute of Oncology, Via Adamello 16, 20139, Milano, Italy
| | - Davide Corà
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, Department of Translational Medicine, Università del Piemonte Orientale, Corso Trieste 15/A, 28100, Novara, Italy
| | - Guido Valente
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
- Pathology Unit, Ospedale Sant'Andrea, Corso Mario Abbiate 21, 13100, Vercelli, Italy
| | - Daniela Capello
- Department of Translational Medicine, Centre of Excellence in Aging Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100, Novara, Italy
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Zhou X, Matskova L, Zheng S, Wang X, Wang Y, Xiao X, Mo Y, Wölke M, Li L, Zheng Q, Huang G, Zhang Z, Ernberg I. Mechanisms of Anergic Inflammatory Response in Nasopharyngeal Carcinoma Cells Despite Ubiquitous Constitutive NF-κB Activation. Front Cell Dev Biol 2022; 10:861916. [PMID: 35938161 PMCID: PMC9353648 DOI: 10.3389/fcell.2022.861916] [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: 01/25/2022] [Accepted: 06/15/2022] [Indexed: 11/29/2022] Open
Abstract
Commensal microbes cross talk with their colonized mucosa. We show that microbes and their cell wall components induce an inflammatory response in cultured human mucosal cells derived from the nonmalignant nasopharyngeal epithelium (NNE) cells in vitro. NNE cells show significant induction of NF-κB with nuclear shuttling and inflammatory gene response when exposed to Gram-positive bacteria (streptococci) or peptidoglycan (PGN), a component of the Gram-positive bacterial cell wall. This response is abrogated in nasopharyngeal carcinoma (NPC)–derived cell lines. The inflammatory response induced by NF-κB signaling was blocked at two levels in the tumor-derived cells. We found that NF-κB was largely trapped in lipid droplets (LDs) in the cytoplasm of the NPC-derived cells, while the increased expression of lysine-specific histone demethylase 1 (LSD1, a repressive nuclear factor) reduces the response mediated by remaining NF-κB at the promoters responding to inflammatory stimuli. This refractory response in NPC cells might be a consequence of long-term exposure to microbes in vivo during carcinogenic progression. It may contribute to the decreased antitumor immune responses in NPC, among others despite heavy T-helper cell infiltration, and thus facilitate tumor progression.
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Affiliation(s)
- Xiaoying Zhou
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- Life Science Institute, Guangxi Medical University, Nanning, China
- Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Liudmila Matskova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Shixing Zheng
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, Fudan University, Shanghai, China
| | - Xiaoxia Wang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Yifang Wang
- Life Science Institute, Guangxi Medical University, Nanning, China
- Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Xue Xiao
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yingxi Mo
- Department of Research, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Marleen Wölke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Limei Li
- Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Qian Zheng
- Life Science Institute, Guangxi Medical University, Nanning, China
- Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Guangwu Huang
- Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhe Zhang
- Key Laboratory of Early Prevention and Treatment for Regional High-Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, Fudan University, Shanghai, China
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- *Correspondence: Ingemar Ernberg,
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Moreno-Andrés D, Bhattacharyya A, Scheufen A, Stegmaier J. LiveCellMiner: A new tool to analyze mitotic progression. PLoS One 2022; 17:e0270923. [PMID: 35797385 PMCID: PMC9262191 DOI: 10.1371/journal.pone.0270923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Live-cell imaging has become state of the art to accurately identify the nature of mitotic and cell cycle defects. Low- and high-throughput microscopy setups have yield huge data amounts of cells recorded in different experimental and pathological conditions. Tailored semi-automated and automated image analysis approaches allow the analysis of high-content screening data sets, saving time and avoiding bias. However, they were mostly designed for very specific experimental setups, which restricts their flexibility and usability. The general need for dedicated experiment-specific user-annotated training sets and experiment-specific user-defined segmentation parameters remains a major bottleneck for fully automating the analysis process. In this work we present LiveCellMiner, a highly flexible open-source software tool to automatically extract, analyze and visualize both aggregated and time-resolved image features with potential biological relevance. The software tool allows analysis across high-content data sets obtained in different platforms, in a quantitative and unbiased manner. As proof of principle application, we analyze here the dynamic chromatin and tubulin cytoskeleton features in human cells passing through mitosis highlighting the versatile and flexible potential of this tool set.
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Affiliation(s)
- Daniel Moreno-Andrés
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
- * E-mail: (DMA), (JS)
| | - Anuk Bhattacharyya
- Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
| | - Anja Scheufen
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Johannes Stegmaier
- Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
- * E-mail: (DMA), (JS)
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Adhikari S, Bhattacharya A, Adhikary S, Singh V, Gadad S, Roy S, Das C. The paradigm of drug resistance in cancer: an epigenetic perspective. Biosci Rep 2022; 42:BSR20211812. [PMID: 35438143 PMCID: PMC9069444 DOI: 10.1042/bsr20211812] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 12/12/2022] Open
Abstract
Innate and acquired resistance towards the conventional therapeutic regimen imposes a significant challenge for the successful management of cancer for decades. In patients with advanced carcinomas, acquisition of drug resistance often leads to tumor recurrence and poor prognosis after the first therapeutic cycle. In this context, cancer stem cells (CSCs) are considered as the prime drivers of therapy resistance in cancer due to their 'non-targetable' nature. Drug resistance in cancer is immensely influenced by different properties of CSCs such as epithelial-to-mesenchymal transition (EMT), a profound expression of drug efflux pump genes, detoxification genes, quiescence, and evasion of apoptosis, has been highlighted in this review article. The crucial epigenetic alterations that are intricately associated with regulating different mechanisms of drug resistance, have been discussed thoroughly. Additionally, special attention is drawn towards the epigenetic mechanisms behind the interaction between the cancer cells and their microenvironment which assists in tumor progression and therapy resistance. Finally, we have provided a cumulative overview of the alternative treatment strategies and epigenome-modifying therapies that show the potential of sensitizing the resistant cells towards the conventional treatment strategies. Thus, this review summarizes the epigenetic and molecular background behind therapy resistance, the prime hindrance of present day anti-cancer therapies, and provides an account of the novel complementary epi-drug-based therapeutic strategies to combat drug resistance.
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Affiliation(s)
- Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhaba National Institute, Mumbai 400094, India
| | - Apoorva Bhattacharya
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Vipin Singh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhaba National Institute, Mumbai 400094, India
| | - Shrikanth S. Gadad
- Department of Molecular and Translational Medicine, Center of Emphasis in Cancer, Texas Tech University Health Sciences Center El Paso, El Paso, TX, U.S.A
- Mays Cancer Center, UT Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229, U.S.A
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhaba National Institute, Mumbai 400094, India
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8
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Agboyibor C, Dong J, Effah CY, Drokow EK, Pervaiz W, Li D, Kang L, Ma X, Li J, Liu Z, Liu HM. Systematic Review and Meta-Analysis of Lysine-Specific Demethylase 1 Expression as a Prognostic Biomarker of Cancer Survival and Disease Progression. Cancer Control 2021; 28:10732748211051557. [PMID: 34802287 PMCID: PMC8727833 DOI: 10.1177/10732748211051557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Numerous studies on the prognostic significance of lysine-specific demethylase 1 (LSD1) up-regulation in tumors have different outcomes. The inconsistency originated from various studies looking into the association between LSD1 and tumor cells has prompted the decision of this quantitative systematic review to decipher how up-regulated LSD1 and overall survival (OS) or recurrence-free survival (RFS) or disease-free survival (DFS) are linked in tumor patients. Methods Articles were searched from online databases such as Embase, Web of Science Core, PubMed, Google Scholar, and Scopus. The extraction of the hazard ratios (HR) with their 95% confidence intervals (CIs) was attained and survival data of 3151 tumor patients from 17 pieces of related research were used for this meta-analysis. Results To shed light on the link between LSD1 up-regulation and the prognosis of diverse tumors, the pooled hazard ratios (HRs) with their 95% confidence intervals (CIs) were determined. In this meta-analysis, it was observed that LSD1 up-regulation is linked with poor OS (HR = 2.08, 95% CI: 1.66–2.61, P < .01) and RFS (HR = 3.09, 95% CI: 1.81–5.26, P < .01) in tumor patients. However, LSD1 up-regulation was not linked to DFS (HR = 1.49, 95% CI: .83–2.69, P = .18) in tumor patients. The subcategory examination grouped by tumor type and ethnicity showed that LSD1 up-regulation was linked with a poor outcome in the esophageal tumor and hepatocellular carcinoma and Asian patients, respectively. For clinical-pathological factors, up-regulated LSD1 was significantly linked with Lymph node status. Conclusion Despite the shortfall of the present work, this meta-analysis proposes that LSD1 up-regulation may be a prognostic biomarker for patients with tumors including esophageal tumors and hepatocellular carcinoma. We propose that large-scale studies are vital to substantiate these outcomes.
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Affiliation(s)
- Clement Agboyibor
- School of Pharmaceutical Sciences, 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, 12636Zhengzhou University, Zhengzhou, China.,Institute of Drug Discovery and Development; 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Henan Province for Drug Quality Control and Evaluation, 12636Zhengzhou University, Zhengzhou, China.,Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province; 12636Zhengzhou University, Zhengzhou, China
| | - Jianshu Dong
- School of Pharmaceutical Sciences, 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, 12636Zhengzhou University, Zhengzhou, China.,Institute of Drug Discovery and Development; 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Henan Province for Drug Quality Control and Evaluation, 12636Zhengzhou University, Zhengzhou, China.,Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province; 12636Zhengzhou University, Zhengzhou, China
| | - Clement Y Effah
- College of Public Health, 12636Zhengzhou University, Zhengzhou, China
| | - Emmanuel K Drokow
- Department of Oncology, 89632Zhengzhou University People's Hospital and Henan Provincial People's Hospital Henan, Zhengzhou, China
| | - Waqar Pervaiz
- School of Pharmaceutical Sciences, 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, 12636Zhengzhou University, Zhengzhou, China.,Institute of Drug Discovery and Development; 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Henan Province for Drug Quality Control and Evaluation, 12636Zhengzhou University, Zhengzhou, China.,Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province; 12636Zhengzhou University, Zhengzhou, China
| | - Dié Li
- School of Pharmaceutical Sciences, 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, 12636Zhengzhou University, Zhengzhou, China.,Institute of Drug Discovery and Development; 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Henan Province for Drug Quality Control and Evaluation, 12636Zhengzhou University, Zhengzhou, China.,Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province; 12636Zhengzhou University, Zhengzhou, China
| | - Lei Kang
- School of Pharmaceutical Sciences, 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, 12636Zhengzhou University, Zhengzhou, China.,Institute of Drug Discovery and Development; 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Henan Province for Drug Quality Control and Evaluation, 12636Zhengzhou University, Zhengzhou, China.,Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province; 12636Zhengzhou University, Zhengzhou, China
| | - Xinli Ma
- China-US(Henan) Hormel Cancer Institute, Zhengzhou, China
| | - Jian Li
- China-US(Henan) Hormel Cancer Institute, Zhengzhou, China
| | - Zhenzhen Liu
- 12636The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, 12636Zhengzhou University, Zhengzhou, China.,Institute of Drug Discovery and Development; 12636Zhengzhou University, Zhengzhou, China.,Key Laboratory of Henan Province for Drug Quality Control and Evaluation, 12636Zhengzhou University, Zhengzhou, China.,Collaborative Innovation Center of New Drug Research and Safety Evaluation of Henan Province; 12636Zhengzhou University, Zhengzhou, China
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9
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Deng S, Lu X, Zhang Z, Meng R, Li M, Xia S. Identification and assessment of PLK1/2/3/4 in lung adenocarcinoma and lung squamous cell carcinoma: Evidence from methylation profile. J Cell Mol Med 2021; 25:6652-6663. [PMID: 34080290 PMCID: PMC8278123 DOI: 10.1111/jcmm.16668] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/25/2021] [Accepted: 05/13/2021] [Indexed: 12/25/2022] Open
Abstract
Lung cancer is a very aggressive cancer characterized with molecular heterogeneities in different subtypes, including lung adenocarcinoma and lung squamous cell carcinoma. However, few related molecular signatures have been established for the treatment of lung cancer subtypes. Polo-like kinase (PLK) family is a crucial regulator during cell division. Aberrant genetic and epigenetic alteration of PLK members plays a controversial role among different cancers. In this study, we performed an analysis of transcriptional and protein expression to identify overexpressed PLK1/4 and under-expressed PLK2/3 in lung cancer subtypes. We then analysed biological function of PLKs and related genes. Besides, we estimated a correlation of PLKs with patient's genders and TP53 mutation in lung cancer. Higher PLK1/4 expression was significantly associated with male patient and TP53 mutant status, separately. Moreover, we carried out a methylation profile analysis including methylation level, DNA methyltransferases correlation and survival analysis of global methylation. Global methylation survival analysis showed that prognostic value of PLK1/2/4 methylation remained the same significant trend between two lung cancer subtypes, whereas prognostic value of PLK3 methylation lacked consistency. Taken together, these results provided instructive insights into a comprehensive evaluation for advanced therapeutic strategy based on epigenetic evidences.
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Affiliation(s)
- Sisi Deng
- Cancer CenterTongji Medical CollegeUnion HospitalHuazhong University of Science and TechnologyWuhanChina
| | - Xiaoli Lu
- Cancer CenterTongji Medical CollegeUnion HospitalHuazhong University of Science and TechnologyWuhanChina
| | - Zhi Zhang
- Cancer CenterTongji Medical CollegeUnion HospitalHuazhong University of Science and TechnologyWuhanChina
| | - Rui Meng
- Cancer CenterTongji Medical CollegeUnion HospitalHuazhong University of Science and TechnologyWuhanChina
| | - Mi Li
- Department of OrthopedicsTongji Medical CollegeTongji HospitalHuazhong University of Science and TechnologyWuhanChina
- Shenzhen Huazhong University of Science and Technology Research InstituteShenzhenChina
| | - Shilin Xia
- Clinical Laboratory of Integrative MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
- Department of Palliative MedicineGraduate School of MedicineJuntendo UniversityTokyoJapan
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10
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Hong Y, Li X, Zhu J. LSD1-mediated stabilization of SEPT6 protein activates the TGF-β1 pathway and regulates non-small-cell lung cancer metastasis. Cancer Gene Ther 2021; 29:189-201. [PMID: 33664458 DOI: 10.1038/s41417-021-00297-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 12/30/2020] [Accepted: 01/13/2021] [Indexed: 01/21/2023]
Abstract
Non-small cell lung cancer (NSCLC) is a prevalent cancer with unfavorable prognosis. Over the past decade accumulating studies have reported an involvement of lysine-specific histone demethylase 1 (LSD1) in NSCLC development. Here, we aimed to explore whether LSD1 affects the metastasis of NSCLC by mediating Septin 6 (SEPT6) through the TGF-β1 pathway. RT-qPCR was used to determine LSD1 and SEPT6 expression in NSCLC tissues and cells. Interactions between LSD1, SEPT6, and TGF-β1 were detected using lentivirus-mediated silencing of LSD1 and overexpression of SEPT6. The role of LSD1 and SEPT6 in mediating the biological behavior of NSCLC cells was determined using the EdU proliferation assay, Transwell assay, and flow cytometry. Thereafter, transplanted cell tumors into nude mice were used to explore the in vivo effects of LSD1 and SEPT6 on metastasis of NSCLC. LSD1 and SEPT6 were overexpressed in NSCLC tissue and cell samples. LSD1 could demethylate the promoter of the SEPT6 to positively regulate SEPT6 expression. LSD1 promoted proliferation, migration, and invasion, while suppressing the apoptosis of NSCLC cells by increasing SEPT6 expression. LSD1-mediated SEPT6 accelerated in vivo NSCLC metastasis through the TGF-β1/Smad pathway. Collectively, LSD1 demethylates SEPT6 promoter to upregulate SEPT6, which activates TGF-β1 pathway, thereby promoting metastasis of NSCLC.
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Affiliation(s)
- Yanni Hong
- Department of Oncology, Quanzhou First Hospital Affiliated Fujian Medical University, Quanzhou, P.R. China.
| | - Xiaofeng Li
- Department of Oncology, Quanzhou First Hospital Affiliated Fujian Medical University, Quanzhou, P.R. China
| | - Jinfeng Zhu
- Department of Oncology, Quanzhou First Hospital Affiliated Fujian Medical University, Quanzhou, P.R. China
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11
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Zhang S, Zhang H, Li H, Guo J, Wang J, Zhang L. Potential role of glucosamine-phosphate N-acetyltransferase 1 in the development of lung adenocarcinoma. Aging (Albany NY) 2021; 13:7430-7453. [PMID: 33686019 PMCID: PMC7993716 DOI: 10.18632/aging.202604] [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: 09/29/2020] [Accepted: 12/23/2020] [Indexed: 12/18/2022]
Abstract
Glucosamine-phosphate N-acetyltransferase 1 (GNPNAT1) is a key enzyme associated with glucose metabolism and uridine diphosphate-N-acetylglucosamine biosynthesis. Abnormal GNPNAT1 expression might be associated with carcinogenesis. We analyzed multiple lung adenocarcinoma (LUAD) gene expression databases and verified GNPNAT1 higher expression in LUAD tumor tissues than in normal tissues. Moreover, we analyzed the survival relationship between LUAD patients’ clinical status and GNPNAT1 expression, and found higher GNPNAT1 expression in LUAD patients with unfavorable prognosis. We built GNPNAT1 gene co-expression networks and further annotated the co-expressed genes’ Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and various associated regulatory factors. These co-expression genes’ functional networks mainly participate in chromosome segregation, RNA metabolic process, and RNA transport. We analyzed GNPNAT1 genetic alterations and co-occurrence networks, and the functional networks of these genes showed that GNPNAT1 participates in multiple steps of cell cycle transition and in the development of some cancers. We assessed the correlation between GNPNAT1 expression and cancer immune infiltrates and showed that GNPNAT1 expression is correlated with several immune cells, chemokines, and immunomodulators in LUAD. We found that GNPNAT1 correlates with LUAD development and prognosis, laying a foundation for further research, especially in immunotherapy.
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Affiliation(s)
- Shengqiang Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, People's Republic of China
| | - Hongyan Zhang
- Department of Physiology and Neurobiology, Mudanjiang Medical University, Mudanjiang 157000, Heilongjiang, People's Republic of China
| | - Huawei Li
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, People's Republic of China
| | - Jida Guo
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, People's Republic of China
| | - Jun Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, People's Republic of China
| | - Linyou Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, People's Republic of China
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12
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Fu DJ, Li J, Yu B. Annual review of LSD1/KDM1A inhibitors in 2020. Eur J Med Chem 2021; 214:113254. [PMID: 33581557 DOI: 10.1016/j.ejmech.2021.113254] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/24/2021] [Accepted: 01/30/2021] [Indexed: 02/07/2023]
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) has emerged as a promising target for the discovery of specific inhibitors as antitumor drugs. Based on the source of compounds, all LSD1 inhibitors in this review are divided into two categories: natural LSD1 inhibitors and synthetic LSD1 inhibitors. This review highlights the research progress of LSD1 inhibitors with the potential to treat cancer covering articles published in 2020. Design strategies, structure-activity relationships, co-crystal structure analysis and action mechanisms are also highlighted.
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Affiliation(s)
- Dong-Jun Fu
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jun Li
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China.
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13
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Krushkal J, Silvers T, Reinhold WC, Sonkin D, Vural S, Connelly J, Varma S, Meltzer PS, Kunkel M, Rapisarda A, Evans D, Pommier Y, Teicher BA. Epigenome-wide DNA methylation analysis of small cell lung cancer cell lines suggests potential chemotherapy targets. Clin Epigenetics 2020; 12:93. [PMID: 32586373 PMCID: PMC7318526 DOI: 10.1186/s13148-020-00876-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/26/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Small cell lung cancer (SCLC) is an aggressive neuroendocrine lung cancer. SCLC progression and treatment resistance involve epigenetic processes. However, links between SCLC DNA methylation and drug response remain unclear. We performed an epigenome-wide study of 66 human SCLC cell lines using the Illumina Infinium MethylationEPIC BeadChip array. Correlations of SCLC DNA methylation and gene expression with in vitro response to 526 antitumor agents were examined. RESULTS We found multiple significant correlations between DNA methylation and chemosensitivity. A potentially important association was observed for TREX1, which encodes the 3' exonuclease I that serves as a STING antagonist in the regulation of a cytosolic DNA-sensing pathway. Increased methylation and low expression of TREX1 were associated with the sensitivity to Aurora kinase inhibitors AZD-1152, SCH-1473759, SNS-314, and TAK-901; the CDK inhibitor R-547; the Vertex ATR inhibitor Cpd 45; and the mitotic spindle disruptor vinorelbine. Compared with cell lines of other cancer types, TREX1 had low mRNA expression and increased upstream region methylation in SCLC, suggesting a possible relationship with SCLC sensitivity to Aurora kinase inhibitors. We also identified multiple additional correlations indicative of potential mechanisms of chemosensitivity. Methylation of the 3'UTR of CEP350 and MLPH, involved in centrosome machinery and microtubule tracking, respectively, was associated with response to Aurora kinase inhibitors and other agents. EPAS1 methylation was associated with response to Aurora kinase inhibitors, a PLK-1 inhibitor and a Bcl-2 inhibitor. KDM1A methylation was associated with PLK-1 inhibitors and a KSP inhibitor. Increased promoter methylation of SLFN11 was correlated with resistance to DNA damaging agents, as a result of low or no SLFN11 expression. The 5' UTR of the epigenetic modifier EZH2 was associated with response to Aurora kinase inhibitors and a FGFR inhibitor. Methylation and expression of YAP1 were correlated with response to an mTOR inhibitor. Among non-neuroendocrine markers, EPHA2 was associated with response to Aurora kinase inhibitors and a PLK-1 inhibitor and CD151 with Bcl-2 inhibitors. CONCLUSIONS Multiple associations indicate potential epigenetic mechanisms affecting SCLC response to chemotherapy and suggest targets for combination therapies. While many correlations were not specific to SCLC lineages, several lineage markers were associated with specific agents.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Dr., Rockville, MD, 20850, USA.
| | - Thomas Silvers
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - Suleyman Vural
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - John Connelly
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Mark Kunkel
- Drug Synthesis and Chemistry Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Annamaria Rapisarda
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - David Evans
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Beverly A Teicher
- Molecular Pharmacology Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, 20892, USA.
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14
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Quagliano A, Gopalakrishnapillai A, Barwe SP. Understanding the Mechanisms by Which Epigenetic Modifiers Avert Therapy Resistance in Cancer. Front Oncol 2020; 10:992. [PMID: 32670880 PMCID: PMC7326773 DOI: 10.3389/fonc.2020.00992] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
The development of resistance to anti-cancer therapeutics remains one of the core issues preventing the improvement of survival rates in cancer. Therapy resistance can arise in a multitude of ways, including the accumulation of epigenetic alterations in cancer cells. By remodeling DNA methylation patterns or modifying histone proteins during oncogenesis, cancer cells reorient their epigenomic landscapes in order to aggressively resist anti-cancer therapy. To combat these chemoresistant effects, epigenetic modifiers such as DNA hypomethylating agents, histone deacetylase inhibitors, histone demethylase inhibitors, along with others have been used. While these modifiers have achieved moderate success when used either alone or in combination with one another, the most positive outcomes were achieved when they were used in conjunction with conventional anti-cancer therapies. Epigenome modifying drugs have succeeded in sensitizing cancer cells to anti-cancer therapy via a variety of mechanisms: disrupting pro-survival/anti-apoptotic signaling, restoring cell cycle control and preventing DNA damage repair, suppressing immune system evasion, regulating altered metabolism, disengaging pro-survival microenvironmental interactions and increasing protein expression for targeted therapies. In this review, we explore different mechanisms by which epigenetic modifiers induce sensitivity to anti-cancer therapies and encourage the further identification of the specific genes involved with sensitization to facilitate development of clinical trials.
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Affiliation(s)
- Anthony Quagliano
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Anilkumar Gopalakrishnapillai
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Sonali P. Barwe
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
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15
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Design, synthesis and biological evaluation of tetrahydroquinoline-based reversible LSD1 inhibitors. Eur J Med Chem 2020; 194:112243. [PMID: 32229389 DOI: 10.1016/j.ejmech.2020.112243] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/08/2020] [Accepted: 03/16/2020] [Indexed: 11/22/2022]
Abstract
The targeted regulation of LSD1, which is highly expressed in a variety of tumor cells, is a promising cancer therapy strategy. Several LSD1 inhibitors are currently under clinical evaluation, and most of these inhibitors are irreversible. Here, we report the design, synthesis and biochemical evaluation of novel tetrahydroquinoline-based reversible LSD1 inhibitors. Compounds 18s and 18x, which are selective to LSD1 over MAO-A/B, exhibit excellent LSD1 inhibition at the molecular levels with IC50 = 55 nM and 540 nM, respectively. The classic Lineweaver-Burk plots revealed that compound 18s could reversibly bind the LSD1 enzyme in a noncompetitive manner. Molecular docking was used to reveal the potential binding-mode of the compounds and interpret the structure-activity relationships. Furthermore, compounds 18s and 18x significantly inhibited proliferation (IC50 = 1.13 μM and 1.15 μM, respectively) and induced apoptosis in MGC-803 cells with high expression of LSD1. Compound 18x showed acceptable liver microsomal stability. Meanwhile, 18x did not appear to inhibit CYPs at 10 μM in vitro. Remarkably, the oral administration of compound 18x can inhibit the growth of MGC-803 xenograft tumors without significant side effects. Our findings suggest that tetrahydroquinoline-based LSD1 inhibitors deserve further investigation for the treatment of LSD1 overexpressing cancer.
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16
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Analysis of the Expression of Cell Division Cycle-Associated Genes and Its Prognostic Significance in Human Lung Carcinoma: A Review of the Literature Databases. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6412593. [PMID: 32104702 PMCID: PMC7037569 DOI: 10.1155/2020/6412593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022]
Abstract
Background Lung cancer (LC) has become the top cause responsible for cancer-related deaths. Cell division cycle-associated (CDCA) genes exert an important role in the life process. Dysregulation in the process of cell division may lead to malignancy. Methods Transcriptional data on CDCA gene family and patient survival data were examined for lung cancer (LC) patients from the GEPIA, Oncomine, cBioPortal, and Kaplan-Meier Plotter databases. Results CDCA1/2/3/4/5/7/8 expression levels were higher in lung adenocarcinoma tissues, and the CDCA1/2/3/4/5/6/7/8 expression levels were increased in squamous cell LC tissues compared with those in noncarcinoma lung tissues. The expression levels of CDCA1/2/3/4/5/8 showed correlation with tumor classification. The Kaplan-Meier Plotter database was employed to carry out survival analysis, indicating that increased CDCA1/2/3/4/5/6/7/8 expression levels were increased in squamous cell LC tissues compared with those in noncarcinoma lung tissues. The expression levels of P < 0.05). Only LC patients with increased CDCA3/4/5/8 expression were significantly related to lower post-progression survival (PPS) (P < 0.05). Only LC patients with increased CDCA gene family and patient survival data were examined for lung cancer (LC) patients from the GEPIA, Oncomine, cBioPortal, and Kaplan-Meier Plotter databases. CDCA8, INCENP, AURKB, and BIRC5); CORUM: 127: NDC80 kinetochore complex; M129: the PID PLK1 pathway; and GO: 0007080: mitotic metaphase plate congression, all of which were remarkably modulated since the alterations affected CDCA gene family and patient survival data were examined for lung cancer (LC) patients from the GEPIA, Oncomine, cBioPortal, and Kaplan-Meier Plotter databases. Conclusions Upregulated CDCA genes' expression levels in LC tissues probably play a crucial part in LC oncogenesis. The upregulated CDCA genes' expression levels are used as the potential prognostic markers to improve patient survival and the LC prognostic accuracy. CDCA genes probably exert their functions in tumorigenesis through the PLK1 pathway.CDCA gene family and patient survival data were examined for lung cancer (LC) patients from the GEPIA, Oncomine, cBioPortal, and Kaplan-Meier Plotter databases. CDCA gene family and patient survival data were examined for lung cancer (LC) patients from the GEPIA, Oncomine, cBioPortal, and Kaplan-Meier Plotter databases. CDCA gene family and patient survival data were examined for lung cancer (LC) patients from the GEPIA, Oncomine, cBioPortal, and Kaplan-Meier Plotter databases.
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17
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Xi X, Chu Y, Liu N, Wang Q, Yin Z, Lu Y, Chen Y. Joint bioinformatics analysis of underlying potential functions of hsa-let-7b-5p and core genes in human glioma. J Transl Med 2019; 17:129. [PMID: 30995921 PMCID: PMC6471881 DOI: 10.1186/s12967-019-1882-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/11/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Glioma accounts for a large proportion of cancer, and an effective treatment for this disease is still lacking because of the absence of specific driver molecules. Current challenges in the treatment of glioma are the accurate and timely diagnosis of brain glioma and targeted treatment plans. To investigate the diagnostic biomarkers and prospective role of miRNAs in the tumorigenesis and progression of glioma, we analyzed the expression of miRNAs and key genes in glioma based on The Cancer Genome Atlas database. METHODS Of the 701 cases that were downloaded, five were normal and 696 were glioma. Then, 1626 differentially expressed genes were identified, and 173 aberrantly expressed miRNAs were calculated by edgeR. GO and KEGG pathway enrichment analyses were performed using Cytoscape software. A coexpression network was built by weighted correlation network analysis (WGCNA). A cell scratch test and transwell, cell apoptosis and cell cycle assays were performed to validate the function of hsa-let-7b-5p. RESULTS Based on crosstalk genes in the KEGG, PPI network, and WGCNA analyses, PLK1, CCNA2, cyclin B2 (CCNB2), and AURKA were screened as candidate diagnostic marker genes. The survival analysis revealed that high mRNA expression of PLK1, CCNA2, and AURKA was significantly associated with poor overall survival. Furthermore, hsa-let-7b-5p was identified as a core miRNA in the regulation of candidate genes involved in glioma development. We confirmed that hsa-let-7b-5p could inhibit the migration, invasion, and cell cycle of glioma cells. CONCLUSIONS This study provides four potential biomarkers for the diagnosis of glioma, offers a potential explanation of its pathogenesis, and proposes hsa-let-7b-5p as a therapeutic target.
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Affiliation(s)
- Xiaonan Xi
- College of Pharmacy, Nankai University, Tianjin, 300350 People’s Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Yahui Chu
- College of Pharmacy, Nankai University, Tianjin, 300350 People’s Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Ning Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Qianqian Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Zheng Yin
- College of Pharmacy, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Yaxin Lu
- College of Pharmacy, Nankai University, Tianjin, 300350 People’s Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
| | - Yue Chen
- College of Pharmacy, Nankai University, Tianjin, 300350 People’s Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350 People’s Republic of China
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