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Nel AE, Pavlisko EN, Roggli VL. The Interplay Between the Immune System, Tumor Suppressor Genes, and Immune Senescence in Mesothelioma Development and Response to Immunotherapy. J Thorac Oncol 2024; 19:551-564. [PMID: 38000500 DOI: 10.1016/j.jtho.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/30/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]
Abstract
Despite efforts to ban asbestos mining and manufacturing, mesothelioma deaths in the United States have remained stable at approximately 2500 cases annually. This trend is not unique to the United States but is also a global phenomenon, associated with increased aging of populations worldwide. Although geoeconomic factors such as lack of regulations and continued asbestos manufacturing in resource-poor countries play a role, it is essential to consider biological factors such as immune senescence and increased genetic instability associated with aging. Recognizing that mesothelioma shares genetic instability and immune system effects with other age-related cancers is crucial because the impact of aging on mesothelioma is frequently assessed in the context of disease latency after asbestos exposure. Nevertheless, the long latency period, often cited as a reason for mesothelioma's elderly predominance, should not overshadow the shared mechanisms. This communication focuses on the role of immune surveillance in mesothelioma, particularly exploring the impact of immune escape resulting from altered TSG function during aging, contributing to the phylogenetic development of gene mutations and mesothelioma oncogenesis. The interplay between the immune system, TSGs, and aging not only shapes the immune landscape in mesothelioma but also contributes to the development of heterogeneous tumor microenvironments, significantly influencing responses to immunotherapy approaches and survival rates. By understanding the complex interplay between aging, TSG decline, and immune senescence, health care professionals can pave the way for more effective and personalized immunotherapies, ultimately offering hope for better outcomes in the fight against mesothelioma.
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Affiliation(s)
- Andre E Nel
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California; Division of NanoMedicine, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California.
| | | | - Victor L Roggli
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
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Zhou Y, Qin Y, Ma J, Li Z, Heng W, Zhang L, Liu H, Li R, Zhang M, Peng Q, Ye P, Duan N, Liu T, Wang W, Wang X. Heat-killed Prevotella intermedia promotes the progression of oral squamous cell carcinoma by inhibiting the expression of tumor suppressors and affecting the tumor microenvironment. Exp Hematol Oncol 2024; 13:33. [PMID: 38515216 PMCID: PMC10956211 DOI: 10.1186/s40164-024-00500-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Oral microbial dysbiosis contributes to the development of oral squamous cell carcinoma (OSCC). Our previous study showed that Prevotella intermedia (P. intermedia) were enriched in the oral mucosal surface, plaque, and saliva of patients with OSCC. Intratumoral microbiome could reshape the immune system and influence the development of various tumors. However, the invasion status of human OSCC tissues by P. intermedia and the pathway through which intratumoral P. intermedia potentiates tumor progression remain unexplored. METHODS P. intermedia in human OSCC or normal tissues was detected by FISH. A mouse OSCC cell line SCC7 was adopted to investigate the effects of heat-killed P. intermedia treatment on cell proliferation, invasion, and cytokine release by using CCK-8 assay, transwell invasion assay and ELISA. Moreover, we established a mouse transplanted tumor model by using SCC7 cells, injected heat-killed P. intermedia into tumor tissues, and investigated the effects of heat-killed P. intermedia on tumor growth, invasion, cytokine levels, immune cell infiltrations, and expression levels by using gross observation, H&E staining, ELISA, immunohistochemistry, mRNA sequencing, and transcriptomic analysis. RESULTS Our results indicated that P. intermedia were abundant in OSCC and surrounding muscle tissues. Heat-killed P. intermedia promoted SCC7 cell proliferation, invasion and proinflammatory cytokine secretions, accelerated transplanted tumor growth in mice, exacerbate muscle and perineural invasion of OSCC, elevated the serum levels of IL-17A, IL-6, TNF-α, IFN-γ, and PD-L1, induced Treg cells M2 type macrophages in mouse transplanted tumors. The data of transcriptomic analysis revealed that heat-killed P. intermedia increased the expression levels of inflammatory cytokines and chemokines while reduced the expression levels of some tumor suppressor genes in mouse transplanted tumors. Additionally, IL-17 signaling pathway was upregulated whereas GABAergic system was downregulated by heat-killed P. intermedia treatment. CONCLUSIONS Taken together, our results suggest that P. intermedia could inhibit the expression of tumor suppressors, alter the tumor microenvironment, and promote the progression of OSCC.
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Affiliation(s)
- Yifan Zhou
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Yao Qin
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Jingjing Ma
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Zhiyuan Li
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Weiwei Heng
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Lei Zhang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Hong Liu
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Ruowei Li
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Miaomiao Zhang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Qiao Peng
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Pei Ye
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Ning Duan
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Ting Liu
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China.
| | - Wenmei Wang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China.
| | - Xiang Wang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China.
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Jiménez N, Garcia de Herreros M, Reig Ò, Marín-Aguilera M, Aversa C, Ferrer-Mileo L, García-Esteve S, Rodríguez-Carunchio L, Trias I, Font A, Rodriguez-Vida A, Climent MÁ, Cros S, Chirivella I, Domènech M, Figols M, Carles J, Suárez C, Herrero Rivera D, González-Billalabeitia E, Cívico C, Sala-González N, Ruiz de Porras V, Ribal MJ, Prat A, Mellado B. Development and Independent Validation of a Prognostic Gene Expression Signature Based on RB1, PTEN, and TP53 in Metastatic Hormone-sensitive Prostate Cancer Patients. Eur Urol Oncol 2024:S2588-9311(24)00025-7. [PMID: 38429210 DOI: 10.1016/j.euo.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/29/2023] [Indexed: 03/03/2024]
Abstract
BACKGROUND Androgen deprivation therapy (ADT) with docetaxel (D) and/or antiandrogen receptor therapies (ARTs) are the standard therapies in metastatic hormone-sensitive prostate cancer (mHSPC). Alterations in the tumor suppressor genes (TSGs) RB1, PTEN, and TP53 are associated with an aggressive evolution and treatment resistance in castration-resistant prostate cancer (CRPC). OBJECTIVE To study the clinical implications of TSG mRNA expression in mHSPC patients. DESIGN, SETTING, AND PARTICIPANTS This is a multicenter retrospective biomarker study in mHSPC patients. TSGlow status was defined when two or more out of the three TSGs presented low RNA expression by nCounter in formalin-fixed paraffin-embedded samples and TSGwt for the remaining cases. The microarray data from the CHAARTED trial were analyzed as an independent validation cohort. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Molecular data were correlated with CRPC-free survival (CRPC-FS) and overall survival (OS) by the Kaplan-Meier method and multivariate Cox analysis. RESULTS AND LIMITATIONS A total of 226 patients were included, of whom 218 were eligible: 93 were treated with ADT and 125 with ADT + D; 75.7% presented de novo stage IV and 67.9% high-volume disease. TSGlow (19.2%) was independently correlated with shorter CRPC-FS (hazard ratio [HR] 1.8, p = 0.002) and OS (HR 2, p = 0.002). In the CHAARTED trial, TSGlow was independently correlated with lower CRPC-FS (HR 2.2, p = 0.02); no differences in clinical outcomes according to treatment were observed in TSGlow patients, while a significant benefit was observed for ADT + D in the TSGwt group for CRPC-FS (HR 0.4, p < 0.001) and OS (HR 0.4, p = 0.001). However, no interaction was observed between TSG signature and treatment in either series. Study limitations are the retrospective design, small sample size, and lack of inclusion of patients treated with ADT + ART. CONCLUSIONS TSGlow expression correlates with adverse outcomes in patients with mHSPC. The investigation of new therapeutic strategies in these patients is warranted. PATIENT SUMMARY The low RNA expression of tumor suppressor genes in the tumors is correlated with adverse outcomes in patients with metastatic hormone-sensitive prostate cancer.
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Affiliation(s)
- Natalia Jiménez
- Translational Genomics and Targeted Therapeutics in Solid Tumors Lab, Fundació de Recerca Clínic Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Marta Garcia de Herreros
- Translational Genomics and Targeted Therapeutics in Solid Tumors Lab, Fundació de Recerca Clínic Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain; Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - Òscar Reig
- Translational Genomics and Targeted Therapeutics in Solid Tumors Lab, Fundació de Recerca Clínic Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain; Medical Oncology Department, Hospital Clínic, Barcelona, Spain; Uro-Oncology Unit, Hospital Clínic, University of Barcelona, Barcelona, Spain; Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Mercedes Marín-Aguilera
- Translational Genomics and Targeted Therapeutics in Solid Tumors Lab, Fundació de Recerca Clínic Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain; Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - Caterina Aversa
- Translational Genomics and Targeted Therapeutics in Solid Tumors Lab, Fundació de Recerca Clínic Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain; Medical Oncology Department, Hospital Clínic, Barcelona, Spain; Uro-Oncology Unit, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Laura Ferrer-Mileo
- Translational Genomics and Targeted Therapeutics in Solid Tumors Lab, Fundació de Recerca Clínic Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain; Medical Oncology Department, Hospital Clínic, Barcelona, Spain; Uro-Oncology Unit, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Samuel García-Esteve
- Translational Genomics and Targeted Therapeutics in Solid Tumors Lab, Fundació de Recerca Clínic Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain; Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Leonardo Rodríguez-Carunchio
- Uro-Oncology Unit, Hospital Clínic, University of Barcelona, Barcelona, Spain; Department of Pathology, Hospital Clínic, Barcelona, Spain
| | - Isabel Trias
- Uro-Oncology Unit, Hospital Clínic, University of Barcelona, Barcelona, Spain; Department of Pathology, Hospital Clínic, Barcelona, Spain
| | - Albert Font
- Medical Oncology Department, Institut Català d'Oncologia, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Alejo Rodriguez-Vida
- Medical Oncology Department, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Hospital del Mar, Barcelona, Spain
| | - Miguel Ángel Climent
- Medical Oncology Service, Instituto Valenciano de Oncología (IVO), Valencia, Spain
| | - Sara Cros
- Medical Oncology Department, Hospital General de Granollers, Barcelona, Spain
| | - Isabel Chirivella
- Oncology Department, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Montserrat Domènech
- Medical Oncology Department, Fundació Althaia, Xarxa Assistencial Universitària de Manresa, Spain
| | - Mariona Figols
- Medical Oncology Department, Fundació Althaia, Xarxa Assistencial Universitària de Manresa, Spain
| | - Joan Carles
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Cristina Suárez
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | - Claudia Cívico
- Department of Hematology and Medical Oncology, Hospital Universitario Morales Meseguer, IMIB-Universidad de Murcia, Murcia, Spain
| | | | - Vicenç Ruiz de Porras
- Badalona Applied Research Group in Oncology (B-ARGO), Institut Català d'Oncologia - Germans Trias i Pujol Research Institute, Badalona, Spain
| | - Maria J Ribal
- Department of Urology, Hospital Clínic, Barcelona, Spain
| | - Aleix Prat
- Translational Genomics and Targeted Therapeutics in Solid Tumors Lab, Fundació de Recerca Clínic Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain; Medical Oncology Department, Hospital Clínic, Barcelona, Spain; Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Begoña Mellado
- Translational Genomics and Targeted Therapeutics in Solid Tumors Lab, Fundació de Recerca Clínic Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain; Medical Oncology Department, Hospital Clínic, Barcelona, Spain; Uro-Oncology Unit, Hospital Clínic, University of Barcelona, Barcelona, Spain; Department of Medicine, University of Barcelona, Barcelona, Spain.
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Stockhammer P, Grant M, Wurtz A, Foggetti G, Expósito F, Gu J, Zhao H, Choi J, Chung S, Li F, Walther Z, Dietz J, Duffield E, Gettinger S, Politi K, Goldberg SB. Co-Occurring Alterations in Multiple Tumor Suppressor Genes Are Associated With Worse Outcomes in Patients With EGFR-Mutant Lung Cancer. J Thorac Oncol 2024; 19:240-251. [PMID: 37806385 DOI: 10.1016/j.jtho.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/10/2023] [Accepted: 10/01/2023] [Indexed: 10/10/2023]
Abstract
INTRODUCTION Patients with metastatic EGFR-mutant NSCLC inevitably have disease progression while on tyrosine kinase inhibitor (TKI) therapy. Co-occurring tumor suppressor gene (TSG) alterations have been associated with poor outcomes, however, detailed analyses of their impact on patient outcomes are limited. METHODS Patients with EGFR-mutant NSCLC treated with EGFR TKIs who had tumor genomic profiling were included. Alterations in TP53 and five additional TSGs (RB1, NF1, ARID1A, BRCA1, and PTEN) were used to stratify the cohort into the following three subgroups: patients with tumors harboring a TP53 mutation plus a mutation in at least one additional TSG (TP53mut/TSGmut), those having a TP53 mutation without additional TSG mutations (TP53mut/TSGwt), and those with TP53wt. Patient characteristics and clinical outcomes were assessed in two independent cohorts. RESULTS A total of 101 patients from the Yale Cancer Center and 182 patients from the American Association for Cancer Research Project GENIE database were included. In the Yale cohort, TP53 mutations were identified in 65 cases (64%), of which 23 were TP53mut/TSGmut and 42 were TP53mut/TSGwt. Although the presence of a TP53 mutation was associated with worse outcomes, the additional TSG alteration in TP53mut tumors identified a subset of patients associated with particularly aggressive disease and inferior clinical outcome in both the Yale and the GENIE cohorts. Specifically, in the Yale cohort for patients receiving first-line TKIs, those with TP53mut/TSGmut tumors had shorter progression-free survival (PFS) and overall survival (OS) than TP53mut/TSGwt (PFS: hazard ratio [HR] = 2.03, confidence interval [CI]: 1.12-3.69, p < 0.01, OS: HR = 1.58, CI: 0.82-3.04, p = 0.12) or TP53wt cases (PFS: HR 2.4, CI: 1.28-4.47, p < 0.001, OS: HR = 2.54, CI: 1.21-5.34, p < 0.005). Inferior outcomes in patients with TP53mut/TSGmut tumors were also found in those receiving osimertinib as second-line therapy. Similar findings were seen in patients in the GENIE cohort. CONCLUSIONS Patients with TP53mut/TSGmut tumors represent a patient subgroup characterized by an aggressive disease phenotype and inferior outcomes on EGFR TKIs. This information is important for understanding the biological underpinnings of differential outcomes with TKI treatment and has implications for identifying patients who may benefit from additional therapeutic interventions beyond osimertinib monotherapy.
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Affiliation(s)
- Paul Stockhammer
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Michael Grant
- Section of Medical Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Anna Wurtz
- Section of Medical Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Giorgia Foggetti
- Section of Medical Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut; Vita-Salute San Raffaele University, Milano, Italy; Medical Oncology Department, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milano, Italy
| | - Francisco Expósito
- Section of Medical Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Jianlei Gu
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Sangyun Chung
- Section of Medical Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Fangyong Li
- Section of Medical Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Zenta Walther
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
| | - Julia Dietz
- Section of Medical Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Emily Duffield
- Yale New Haven Hospital, Smilow Cancer Hospital, New Haven, Connecticut
| | - Scott Gettinger
- Section of Medical Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Katerina Politi
- Section of Medical Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut; Department of Pathology, Yale School of Medicine, New Haven, Connecticut
| | - Sarah B Goldberg
- Section of Medical Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut.
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Hua T, Xue Y, Sarker DB, Kiran S, Li Y, Sang QXA. Modeling human brain rhabdoid tumor by inactivating tumor suppressor genes in induced pluripotent stem cells. Bioact Mater 2024; 31:136-150. [PMID: 37637078 PMCID: PMC10448240 DOI: 10.1016/j.bioactmat.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023] Open
Abstract
Atypical teratoid/rhabdoid tumor (ATRT) is a rare childhood malignancy that originates in the central nervous system. Over ninety-five percent of ATRT patients have biallelic inactivation of the tumor suppressor gene SMARCB1. ATRT has no standard treatment, and a major limiting factor in therapeutic development is the lack of reliable ATRT models. We employed CRISPR/Cas9 gene-editing technology to knock out SMARCB1 and TP53 genes in human episomal induced pluripotent stem cells (Epi-iPSCs), followed by brief neural induction, to generate an ATRT-like model. The dual knockout Epi-iPSCs retained their stemness with the capacity to differentiate into three germ layers. High expression of OCT4 and NANOG in neurally induced knockout spheroids was comparable to that in two ATRT cell lines. Beta-catenin protein expression was higher in SMARCB1-deficient cells and spheroids than in normal Epi-iPSC-derived spheroids. Nucleophosmin, Osteopontin, and Ki-67 proteins were also expressed by the SMARCB1-deficient spheroids. In summary, the tumor model resembled embryonal features of ATRT and expressed ATRT biomarkers at mRNA and protein levels. Ribociclib, PTC-209, and the combination of clofilium tosylate and pazopanib decreased the viability of the ATRT-like cells. This disease modeling scheme may enable the establishment of individualized tumor models with patient-specific mutations and facilitate high-throughput drug testing.
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Affiliation(s)
- Timothy Hua
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306-4390, USA
| | - Yu Xue
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306-4390, USA
| | - Drishty B. Sarker
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306-4390, USA
| | - Sonia Kiran
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306-4390, USA
| | - Yan Li
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL, 32310-6046, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
| | - Qing-Xiang Amy Sang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306-4390, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
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Singh SP, Tewari M, Singh AK, Mishra RR, Shukla HS. Epigenetic Silencing of p16INK4a gene in Sporadic Breast Cancer. Indian J Surg Oncol 2023; 14:822-828. [PMID: 38187858 PMCID: PMC10766924 DOI: 10.1007/s13193-023-01780-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 06/06/2023] [Indexed: 01/09/2024] Open
Abstract
Epigenetic alterations of tumor suppressor genes (TSG) involved in the onset and progression of Breast Cancer (BC) may serve as biomarkers for early detection and prediction of disease prognosis. We have herein tried to determine the methylation status of TSG, p16INK4a, in our 50 BC patients and their association with clinicopathological parameters. The methylation status of the p16INK4a gene in fresh tissue samples from 50 patients with BC was assessed by methylation-specific polymerase chain reaction (MS-PCR). The mean age of BC patients was 49.30 ± 9.75 years. Of 50 BC samples tested, 21 (42%) had methylated p16INK4a gene. p16INK4a gene hypermethylation was significantly associated with age ≤ 50 years, premenopausal status and advanced BC stage. Multivariate analysis revealed a strong association between advanced BC stage (Stage III and Stage IV) and p16INK4a hypermethylation (P = 0.008, RR = 5.996, 95% CI = 1.581-22.739). p16INK4a methylation was significantly associated with Triple Negative BC (TNBC) (P = 0.045, OR = 4.181, 95% CI = 1.030-16.981). These findings indicate that p16INK4a hypermethylation frequently occurs in BC. Hypermethylation of p16INK4a in young, premenopausal, TNBC and with advance stage in BC patients suggests its association with aggressive BC.
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Affiliation(s)
- Satya P. Singh
- Department of Surgical Oncology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India 221005
| | - Mallika Tewari
- Department of Surgical Oncology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India 221005
| | - Alok K. Singh
- Department of Geriatric Medicine, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India 221005
| | - Raghvendra R. Mishra
- Medical Lab Technology, DDU Kaushal Kendra, Banaras Hindu University, Varanasi, India
| | - Hari S. Shukla
- Department of Surgical Oncology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India 221005
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Yadav R, Das PP, Sharma S, Sengupta S, Kumar D, Sagar R. Recent advancement of nanomedicine-based targeted delivery for cervical cancer treatment. Med Oncol 2023; 40:347. [PMID: 37930458 DOI: 10.1007/s12032-023-02195-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023]
Abstract
Cervical cancer is a huge worldwide health burden, impacting women in impoverished nations in particular. Traditional therapeutic approaches, such as surgery, radiation therapy, and chemotherapy, frequently result in systemic toxicity and ineffectiveness. Nanomedicine has emerged as a viable strategy for targeted delivery of therapeutic drugs to cancer cells while decreasing off-target effects and increasing treatment success in recent years. Nanomedicine for cervical cancer introduces several novel aspects that distinguish it from previous treatment options such as tailored delivery system, precision targeting, combination therapies, real-time monitoring and diverse nanocarriers to overcome the limitations of one another. This abstract presents recent advances in nanomedicine-based tailored delivery systems for the treatment of cervical cancer. Liposomes, polymeric nanoparticles, dendrimers, and carbon nanotubes have all been intensively studied for their ability to transport chemotherapeutic medicines, nucleic acids, and imaging agents to cervical cancer cells. Because of the way these nanocarriers are designed, they may cross biological barriers and preferentially aggregate at the tumor site, boosting medicine concentration and lowering negative effects on healthy tissues. Surface modification of nanocarriers with targeting ligands like antibodies, peptides, or aptamers improves specificity for cancer cells by identifying overexpressed receptors or antigens on the tumor surface. Furthermore, nanomedicine-based techniques have made it possible to co-deliver numerous therapeutic drugs, allowing for synergistic effects and overcoming drug resistance. In preclinical and clinical investigations, combination treatments comprising chemotherapeutic medicines, gene therapy, immunotherapy, and photodynamic therapy have showed encouraging results, opening up new avenues for individualized and multimodal treatment regimens. Furthermore, the inclusion of contrast agents and imaging probes into nanocarrier systems has enabled real-time monitoring and imaging of treatment response. This enables the assessment of therapy efficacy, the early diagnosis of recurrence, and the optimization of treatment regimens.
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Affiliation(s)
- Rakhi Yadav
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Priyanku Pradip Das
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Sunil Sharma
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sounok Sengupta
- Department of Pharmacology, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India.
| | - Ram Sagar
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Tariq N, Mirza T, Ansari M, Nazir S. Role of Human Papilloma Virus 16/18 In Laryngeal Carcinoma with Correlation to the Expression of Cyclin D1, p53, p16 and EGFR. Pak J Med Sci 2023; 39:1768-1773. [PMID: 37936777 PMCID: PMC10626090 DOI: 10.12669/pjms.39.6.8220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/24/2023] [Accepted: 07/18/2023] [Indexed: 11/09/2023] Open
Abstract
Objective To investigate the role of Human Papilloma Virus (HPV) (16/18) in relation to the molecular genetic mechanisms of Cyclin D1, p53, p16, and Epidermal growth factor receptor (EGFR) in Laryngeal Squamous Cell Carcinoma (LSSC). Methods A cross-sectional study of 88 (Formalin-fixed Paraffin Embedded) FFPE laryngeal biopsies were done at Basic Medical Sciences Institute, Jinnah Postgraduate Centre, Karachi from 2010 to 2019 with the application of Polymerase chain reaction (PCR) for HPV 16/18and Immuno-histochemical staining for molecular genetic expression of proteins, Cyclin D1, p53, p16, and EGFR. Results Out of 88 cases of Laryngeal Squamous Cell Carcinoma (LSSC) there was female preponderance. Mean age of the participants was found as 50.7±12.8 years. High risk HPV 16/18 was positive in 28 cases (31.8%), largely related to Grade-II and Grade-III. Immunohistochemically, Cyclin D1 (87.5%) appeared as the most important driver mutation followed by p16 (86.4%), EGFR (65.9%), and, p53 was positive in (61.4%) of cases. Conclusion The role of high-risk HPV 16/18 is concurred in the present study strongly in correlation to p16 as a surrogate marker. Moreover, the other driver mutations of Cyclin D1, p53, and EGFR are also implicated as cumulative molecular events in tumor progression as mostly seen in higher Grades.
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Affiliation(s)
- Naila Tariq
- Naila Tariq HOD, Laboratory National Medical Center, Karachi, Pakistan
| | - Talat Mirza
- Talat Mirza Meritorious Professor of Pathology Department of Research & Molecular Medicine Ziauddin University, Karachi, Pakistan
| | - Maqsood Ansari
- Maqsood Ali Ansari. Professor & HOD, Department of Genetics, University of Karachi, Karachi, Pakistan
| | - Sobia Nazir
- Sobia Nazir, MPhil. Molecular Pathology Reliance Laboratory, Karachi, Pakistan
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Sgro A, Cursons J, Waryah C, Woodward EA, Foroutan M, Lyu R, Yeoh GCT, Leedman PJ, Blancafort P. Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma. Clin Epigenetics 2023; 15:73. [PMID: 37120619 PMCID: PMC10149030 DOI: 10.1186/s13148-023-01482-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/09/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Epigenetic silencing of tumor suppressor genes (TSGs) is a key feature of oncogenesis in hepatocellular carcinoma (HCC). Liver-targeted delivery of CRISPR-activation (CRISPRa) systems makes it possible to exploit chromatin plasticity, by reprogramming transcriptional dysregulation. RESULTS Using The Cancer Genome Atlas HCC data, we identify 12 putative TSGs with negative associations between promoter DNA methylation and transcript abundance, with limited genetic alterations. All HCC samples harbor at least one silenced TSG, suggesting that combining a specific panel of genomic targets could maximize efficacy, and potentially improve outcomes as a personalized treatment strategy for HCC patients. Unlike epigenetic modifying drugs lacking locus selectivity, CRISPRa systems enable potent and precise reactivation of at least 4 TSGs tailored to representative HCC lines. Concerted reactivation of HHIP, MT1M, PZP, and TTC36 in Hep3B cells inhibits multiple facets of HCC pathogenesis, such as cell viability, proliferation, and migration. CONCLUSIONS By combining multiple effector domains, we demonstrate the utility of a CRISPRa toolbox of epigenetic effectors and gRNAs for patient-specific treatment of aggressive HCC.
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Affiliation(s)
- Agustin Sgro
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- School of Human Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Joseph Cursons
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Charlene Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Eleanor A Woodward
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Momeneh Foroutan
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Ruqian Lyu
- Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Melbourne, VIC, 3065, Australia
- Melbourne Integrative Genomics/School of Mathematics and Statistics, Faculty of Science, The University of Melbourne, Royal Parade, Parkville, VIC, 3010, Australia
| | - George C T Yeoh
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- School of Molecular Sciences, University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Peter J Leedman
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, Perth, WA, 6009, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia.
- Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
- School of Human Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia.
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Kumari S, Mishra S, Anand N, Hadi R, Rastogi M, Husain N. Circulating free DNA integrity index and promoter methylation of tumor suppressor gene P16, DAPK and RASSF1A as a biomarker for oropharyngeal squamous cell carcinoma. Pathol Res Pract 2023; 246:154489. [PMID: 37150134 DOI: 10.1016/j.prp.2023.154489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
Circulating free DNA (cfDNA) is in use for the non-invasive diagnosis of tumors. Methylation of tumor suppressor genes (TSGs) is an early event in carcinogenesis and may serve as tumor biomarker. We have investigated cfDNA integrity and methylation of tumor suppressor genes P16, DAPK and RASSF1A in serum cfDNA of oropharyngeal squamous cell carcinoma (OPSCC) comparing paired serum and tumor tissue samples to evaluate their diagnostic use. Prospective case-control study, paired serum and tissue samples from 56 OPSCC, and 15 normal controls (NC). Sybr green Quantitate real time PCR was used for cfDNA quantification through amplification ALU 115 and 247 fragments. Promoter methylation of was analyzed in paired samples using methylation specific PCR. There was significantly high cfDNA integrity in OPSCC compared to normal control (p = < 0.0001). The cfDNA integrity values were significantly higher and associated with nodal status (p = 0.016). The AUC for cfDNA integrity was 0.967. The P16, DAPK and RASSF1 promoters were significantly hypermethylated in serum of OPSCC compared to NC with high concordance in tissue (up to 96.55 %). The gene promoter methylation of P16 was associated with smoking (p = 0.030), RASSF1A with stage (p = 0.011). The combination of ALU115 with cfDNA integrity and combination of gene methylation increases diagnostic sensitivity. In followup samples the cfDNA change was not different. Liquid biopsy approach including cfDNA integrity, methylation profiling in cfDNA, in combination or separately can assist in the diagnosis of OPSCC along with radio diagnostic scan. Serum changes represent changes in tissue with very high concordance.
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Affiliation(s)
- Swati Kumari
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Sridhar Mishra
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Nidhi Anand
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Rahat Hadi
- Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Madhup Rastogi
- Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Nuzhat Husain
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India.
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Du X, Zhao Z, Zhao X, Wang H, Jiang L, Tang W. Risk signature identification and NPRL2 affects sunitinib sensitivity in clear cell renal cell carcinoma. Biochem Biophys Res Commun 2023; 663:122-131. [PMID: 37121122 DOI: 10.1016/j.bbrc.2023.04.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/09/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
Tumor suppressor genes (TSGs) play a crucial role in tumorigenesis and drug resistance. We analyzed the subtypes of clear cell renal cell carcinoma (ccRCC) mediated by 8 genes contained in the 3p21.3 tumor suppressor gene cluster and their effects on TME cell infiltration based on the TCGA database. The risk score model was established by principal component analysis. The hub gene NPRL2 was selected by protein-protein interactions (PPI) analysis. The effect of NPRL2 on sunitinib sensitivity of ccRCC was verified by using CCK-8, colony formation assay, wound healing assay, transwell assay and xenograft tumor model. Changes in protein expression were detected by Western blotting. We found that 8 TSGs were all differentially expressed in ccRCC samples, which could divide ccRCC into two subtypes. The constructed risk score model could predict the prognosis and drug sensitivity of ccRCC patients, and was an independent prognostic factor for ccRCC. Over-expression of NPRL2 promoted apoptosis, inhibited EMT, decreased the phosphorylation of the PI3K/AKT/mTOR signaling pathway to inhibit its activity, and promoted the sensitivity of sunitinib to ccRCC cells. Collectively, our findings increased the understanding of TSGs in ccRCC, suggesting that NPRL2 as a TSG could enhance sunitinib sensitivity to ccRCC cells.
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Affiliation(s)
- Xiaoyi Du
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhipeng Zhao
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Zhao
- Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Hexi Wang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Jiang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Wei Tang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Dube G, Tiamiou A, Bizet M, Boumahd Y, Gasmi I, Crake R, Bellier J, Nokin MJ, Calonne E, Deplus R, Wissocq T, Peulen O, Castronovo V, Fuks F, Bellahcène A. Methylglyoxal: a novel upstream regulator of DNA methylation. J Exp Clin Cancer Res 2023; 42:78. [PMID: 36998085 PMCID: PMC10064647 DOI: 10.1186/s13046-023-02637-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/02/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Aerobic glycolysis, also known as the Warburg effect, is predominantly upregulated in a variety of solid tumors, including breast cancer. We have previously reported that methylglyoxal (MG), a very reactive by-product of glycolysis, unexpectedly enhanced the metastatic potential in triple negative breast cancer (TNBC) cells. MG and MG-derived glycation products have been associated with various diseases, such as diabetes, neurodegenerative disorders, and cancer. Glyoxalase 1 (GLO1) exerts an anti-glycation defense by detoxifying MG to D-lactate. METHODS Here, we used our validated model consisting of stable GLO1 depletion to induce MG stress in TNBC cells. Using genome-scale DNA methylation analysis, we report that this condition resulted in DNA hypermethylation in TNBC cells and xenografts. RESULTS GLO1-depleted breast cancer cells showed elevated expression of DNMT3B methyltransferase and significant loss of metastasis-related tumor suppressor genes, as assessed using integrated analysis of methylome and transcriptome data. Interestingly, MG scavengers revealed to be as potent as typical DNA demethylating agents at triggering the re-expression of representative silenced genes. Importantly, we delineated an epigenomic MG signature that effectively stratified TNBC patients based on survival. CONCLUSION This study emphasizes the importance of MG oncometabolite, occurring downstream of the Warburg effect, as a novel epigenetic regulator and proposes MG scavengers to reverse altered patterns of gene expression in TNBC.
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Affiliation(s)
- Gaurav Dube
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Assia Tiamiou
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Yasmine Boumahd
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Imène Gasmi
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Rebekah Crake
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Justine Bellier
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Marie-Julie Nokin
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Tom Wissocq
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Olivier Peulen
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Vincent Castronovo
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
- WELBIO (Walloon Excellence in Lifesciences & Biotechnology), Brussels, Belgium
| | - Akeila Bellahcène
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium.
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13
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Peng Y, Tang R, Ding L, Zheng R, Liu Y, Yin L, Fu Y, Deng T, Li X. Diosgenin inhibits prostate cancer progression by inducing UHRF1 protein degradation. Eur J Pharmacol 2023; 942:175522. [PMID: 36681316 DOI: 10.1016/j.ejphar.2023.175522] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/25/2022] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
Prostate cancer (PCa) represents the second cause of cancer death in adult men. Aberrant overexpression of UHRF1 has been reported in several cancer types, and is regarded as a novel drug target for cancer therapy. Nevertheless, no UHRF1-targeted small molecule inhibitor has been testing in clinical trials. Traditional Chinese medicine (TCM) prescriptions have a long history for the treatment of PCa in China, and Chinese herbal extracts are important resources for new drug discovery. In the present study, we first screened the potentially effective components from the commonly used TCMs for PCa treatment in clinic by using network pharmacology together with molecular docking. We identified diosgenin (DSG) as a small molecule natural compound specifically targeting UHRF1 protein. Furthermore, we validated the results by using the wet lab experiments. DSG, by directly binding UHRF1 protein, induced UHRF1 protein degradation through the ubiquitin-proteasome pathway. Importantly, DSG induced UHRF1 protein degradation by reducing the protein interaction with a deubiquitinase USP7. DSG reduced the level of genomic DNA methylation, and elevated the expression of such tumor suppressor genes as p21, p16 and LXN, thereby resulting in cell cycle arrest, cellular senescence and the inhibition of xenograft tumor growth. We here presented the first report that DSG specifically induced UHRF1 protein degradation, thereby revealing a novel anticancer mechanism of DSG. Altogether, this present study provided a promising strategy to discover new molecule-targeted drugs from small-molecule natural products.
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Affiliation(s)
- Yuchong Peng
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Rong Tang
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Liuyang Ding
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Rirong Zheng
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Youhong Liu
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Linglong Yin
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China; School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Yongming Fu
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Tanggang Deng
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Xiong Li
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510699, China; NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China; School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China.
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Zhang L, Liu C, Zhang B, Zheng J, Singh PK, Bshara W, Wang J, Gomez EC, Zhang X, Wang Y, Zhu X, Goodrich DW. PTEN Loss Expands the Histopathologic Diversity and Lineage Plasticity of Lung Cancers Initiated by Rb1/Trp53 Deletion. J Thorac Oncol 2023; 18:324-338. [PMID: 36473627 PMCID: PMC9974779 DOI: 10.1016/j.jtho.2022.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION High-grade neuroendocrine tumors of the lung such as SCLC are recalcitrant cancers for which more effective systemic therapies are needed. Despite their histopathologic and molecular heterogeneity, they are generally treated as a single disease entity with similar chemotherapy regimens. Whereas marked clinical responses can be observed, they are short-lived. Inter- and intratumoral heterogeneity is considered a confounding factor in these unsatisfactory clinical outcomes, yet the origin of this heterogeneity and its impact on therapeutic responses is not well understood. METHODS New genetically engineered mouse models are used to test the effects of PTEN loss on the development of lung tumors initiated by Rb1 and Trp53 tumor suppressor gene deletion. RESULTS Complete PTEN loss drives more rapid tumor development with a greater diversity of tumor histopathology ranging from adenocarcinoma to SCLC. PTEN loss also drives transcriptional heterogeneity as marked lineage plasticity is observed within histopathologic subtypes. Spatial profiling indicates transcriptional heterogeneity exists both within and among tumor foci with transcriptional patterns correlating with spatial position, implying that the growth environment influences gene expression. CONCLUSIONS These results identify PTEN loss as a clinically relevant genetic alteration driving the molecular and histopathologic heterogeneity of neuroendocrine lung tumors initiated by Rb1/Trp53 mutations.
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Affiliation(s)
- Letian Zhang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York; Department of Pathology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Congrong Liu
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, People's Republic of China
| | - Bo Zhang
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, People's Republic of China
| | - Jie Zheng
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, People's Republic of China
| | - Prashant K Singh
- Department of Cancer Genetics & Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Wiam Bshara
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Xiaojing Zhang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Yanqing Wang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Xiang Zhu
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, People's Republic of China
| | - David W Goodrich
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
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González-Villaseñor CO, Ramírez-Guerrero AA, Moreno-Ortiz JM, Leal-Ugarte E, Peralta-Leal V, Macías-Gómez NM. A novel mutation in the TSC2 gene protects against colorectal cancer in the Mexican population. GAC MED MEX 2022; 158:283-288. [PMID: 36572026 DOI: 10.24875/gmm.m22000696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Colorectal cancer (CRC) is a complex disease due to the large number of factors that influence its development, including variants in tumor suppressor genes. OBJECTIVE To estimate allelic and genotypic frequencies of c.3915G>A and c.5371G>A variants of the TSC2 gene in a Mexican population with CRC, as well as to analyze their association with the development of CRC. METHODS 126 peripheral blood samples from patients diagnosed with sporadic CRC and 134 from healthy individuals, regarded as the control group, were included. Identification of genotypes was carried out using traditional PCR and enzymatic digestion. All individuals signed an informed consent letter. RESULTS The A allele of the c.3915G>A variant (OR = 0.31, 95% CI = 0.15-0.69, p = 0.004), as well as A/G haplotype of the c.3915G>A and c.5371G>A variants (OR = 0.28, 95% CI = 0.12-0.68, p = 0.005) showed a possible protective effect against sporadic CRC. In silico analysis indicated that both variants generate modifications in the splicing process. CONCLUSION The presence of TSC2 gene c.3915G>A variant suggests a possible protective effect against sporadic CRC in the Mexican population; however, no association was observed with the c.5371G>A variant.
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Affiliation(s)
| | | | | | - Evelia Leal-Ugarte
- Faculty of Medicine and Computational Systems Engineering of Matamoros, Universidad Autónoma de Tamaulipas, Tamaulipas. Mexico
| | - Valeria Peralta-Leal
- Faculty of Medicine and Computational Systems Engineering of Matamoros, Universidad Autónoma de Tamaulipas, Tamaulipas. Mexico
| | - Nelly M Macías-Gómez
- Human Genetics Laboratory, University Center of the South, Universidad de Guadalajara, Jalisco
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Sahu DK, Singh N, Das M, Rawat J, Gupta DK. Differential expression profiling of onco and tumor-suppressor genes from major-signaling pathways in Wilms' tumor. Pediatr Surg Int 2022; 38:1601-17. [PMID: 36107237 DOI: 10.1007/s00383-022-05202-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/22/2022] [Indexed: 10/14/2022]
Abstract
PURPOSE Wilms' tumor is the most-frequent malignant-kidney tumor in children under 3-4 years of age and is caused by genetic alterations of oncogenes (OG) and tumor-suppressor genes (TG). Wilms' tumor has been linked to many OG-&-TG. However, only WT1 has a proven role in the development of this embryonic-tumor. METHODS The study investigates the level of mRNA expression of 16 OGs and 20 TGs involved in key-signaling pathways, including chromatin modification; RAS; APC; Cell Cycle/Apoptosis; Transcriptional Regulation; PI3K; NOTCH-&-HH; PI3K & RAS of 24-fresh Wilms'-tumor cases by capture-and-reporter probe Code-Sets chemistry, as CNVs in these pathway genes have been reported. RESULTS Upon extensively investigating, MEN1, MLL2, MLL3, PBRM1, PRDM1, SMARCB1, SETD2, WT1, PTPN11, KRAS, HRAS, NF1, APC, RB1, FUBP1, BCOR, U2AF1, PIK3CA, PTEN, EBXW7, SMO, ALK, CBL, EP300-and-GATA1 were found to be significantly up-regulated in 58.34, 62.5, 79.17, 91.67, 58, 66.66,54, 58.34, 66.67, 75, 62.5, 62.5, 58, 79.17, 79.17, 75, 70.84, 50, 50, 75, 66.66, 62.50, 61.66, 58.34-and-62.50% of cases respectively, whereas BRAF, NF2, CDH1, BCL2, FGFR3, ERBB2, MET, RET, EGFR-and-GATA2 were significantly down regulated in 58, 87.50, 79.16, 54.16, 79.17, 91.66, 66.66, 58.33, 91.66-and-62.50% of cases, respectively. Interestingly, the WT1 gene was five-fold down regulated in 41.66% of cases only. CONCLUSION Hence, extensive profiling of OGs and TGs association of major-signaling pathways in Wilms' tumor cases may aid in disease diagnosis. PBRM1 (up-regulated in 91.67% of cases), ERBB2 and EGFR (down-regulated in 91.66 and 91.66% of cases, respectively) could be marker genes. However, validation of all relevant results in a larger number of samples is required.
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17
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Lin RK, Su CM, Lin SY, Thi Anh Thu L, Liew PL, Chen JY, Tzeng HE, Liu YR, Chang TH, Lee CY, Hung CS. Hypermethylation of TMEM240 predicts poor hormone therapy response and disease progression in breast cancer. Mol Med 2022; 28:67. [PMID: 35715741 PMCID: PMC9204905 DOI: 10.1186/s10020-022-00474-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/13/2022] [Indexed: 12/16/2022] Open
Abstract
Background Approximately 25% of patients with early-stage breast cancer experience cancer progression throughout the disease course. Alterations in TMEM240 in breast cancer were identified and investigated to monitor treatment response and disease progression. Methods Circulating methylated TMEM240 in the plasma of breast cancer patients was used to monitor treatment response and disease progression. The Cancer Genome Atlas (TCGA) data in Western countries and Illumina methylation arrays in Taiwanese breast cancer patients were used to identify novel hypermethylated CpG sites and genes related to poor hormone therapy response. Quantitative methylation-specific PCR (QMSP), real-time reverse transcription PCR, and immunohistochemical analyses were performed to measure DNA methylation and mRNA and protein expression levels in 394 samples from Taiwanese and Korean breast cancer patients. TMEM240 gene manipulation, viability, migration assays, RNA-seq, and MetaCore were performed to determine its biological functions and relationship to hormone drug treatment response in breast cancer cells. Results Aberrant methylated TMEM240 was identified in breast cancer patients with poor hormone therapy response using genome-wide methylation analysis in the Taiwan and TCGA breast cancer cohorts. A cell model showed that TMEM240, which is localized to the cell membrane and cytoplasm, represses breast cancer cell proliferation and migration and regulates the expression levels of enzymes involved in estrone and estradiol metabolism. TMEM240 protein expression was observed in normal breast tissues but was not detected in 88.2% (67/76) of breast tumors and in 90.0% (9/10) of metastatic tumors from breast cancer patients. QMSP revealed that in 54.5% (55/101) of Taiwanese breast cancer patients, the methylation level of TMEM240 was at least twofold higher in tumor tissues than in matched normal breast tissues. Patients with hypermethylation of TMEM240 had poor 10-year overall survival (p = 0.003) and poor treatment response, especially hormone therapy response (p < 0.001). Circulating methylated TMEM240 dramatically and gradually decreased and then diminished in patients without disease progression, whereas it returned and its levels in plasma rose again in patients with disease progression. Prediction of disease progression based on circulating methylated TMEM240 was found to have 87.5% sensitivity, 93.1% specificity, and 90.2% accuracy. Conclusions Hypermethylation of TMEM240 is a potential biomarker for treatment response and disease progression monitoring in breast cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-022-00474-9.
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Affiliation(s)
- Ruo-Kai Lin
- Program in Drug Discovery and Development Industry, Program in Clinical Drug Development of Herbal Medicine, Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Graduate Institute of Pharmacognosy, Taipei Medical University, 250 Wu-Hsing Street, Taipei, Taiwan.,Clinical Trial Center, Taipei Medical University Hospital, 252 Wu-Hsing Street, Taipei, Taiwan
| | - Chih-Ming Su
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Shih-Yun Lin
- Program in Drug Discovery and Development Industry, Program in Clinical Drug Development of Herbal Medicine, Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Graduate Institute of Pharmacognosy, Taipei Medical University, 250 Wu-Hsing Street, Taipei, Taiwan
| | - Le Thi Anh Thu
- Quang Tri Medical College, Dien Bien Phu Str., Dong Luong District, Dong Ha City, Quang Tri, Vietnam
| | - Phui-Ly Liew
- Department of Pathology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan.,Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jian-Yu Chen
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Huey-En Tzeng
- Division of Hematology and Oncology, Department of Medicine, Taipei Medical University Hospital, Taipei, Taiwan.,Department of Medical Research, Division of Hematology/Medical Oncology, Department of Medicine, Taichung Veterans General Hospital, Taichung City, Taiwan.,Program for Cancer Molecular Biology and Drug Discovery, and Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yun-Ru Liu
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Cheng-Yang Lee
- Bioinformatics Center, Office of Data Science, Taipei Medical University, Taipei, Taiwan
| | - Chin-Sheng Hung
- Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan. .,Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan. .,Division of General Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei, Taiwan.
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18
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Markou Α, Londra D, Tserpeli V, Kollias Ι, Tsaroucha E, Vamvakaris I, Potaris K, Pateras I, Kotsakis Α, Georgoulias V, Lianidou Ε. DNA methylation analysis of tumor suppressor genes in liquid biopsy components of early stage NSCLC: a promising tool for early detection. Clin Epigenetics 2022; 14:61. [PMID: 35538556 PMCID: PMC9092693 DOI: 10.1186/s13148-022-01283-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/27/2022] [Indexed: 12/02/2022] Open
Abstract
Purpose Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) analysis represents a liquid biopsy approach for real-time monitoring of tumor evolution. DNA methylation is considered to be an early event in the process of cancer development and progression. The aim of the present study was to evaluate whether detection of DNA methylation of selected tumor suppressor genes in CTC and matched ctDNA provides prognostic information in early stage NSCLC. Experimental design The methylation status of five selected gene promoters (APC, RASSFIA1, FOXA1, SLFN11, SHOX2) was examined by highly specific and sensitive real-time methylation specific PCR assays in: (a) a training group of 35 primary tumors and their corresponding adjacent non-cancerous tissues of early stage NSCLC patients, (b) a validation group of 22 primary tumor tissues (FFPEs) and 42 peripheral blood samples of early stage NSCLC patients. gDNA was isolated from FFPEs, CTCs (size-based enriched by Parsortix; Angle and plasma, and (c) a control group of healthy blood donors (n = 12). Results All five gene promoters tested were highly methylated in the training group; methylation of SHOX2 promoter in primary tumors was associated with unfavorable outcome. RASSFIA and APC were found methylated in plasma-cfDNA samples at 14.3% and 11.9%, respectively, whereas in the corresponding CTCs SLFN11 and APC promoters were methylated in 7.1%. The incidence of relapses was higher in patients with a) promoter methylation of APC and SLFN11 in plasma-cfDNA (P = 0.037 and P = 0.042 respectively) and b) at least one detected methylated gene promoter in CTC or plasma-cfDNA (P = 0.015). Conclusions DNA methylation of these five gene promoters was significantly lower in CTCs and plasma-cfDNA than in the primary tumors. Combination of DNA methylation analysis in CTC and plasma-cfDNA was associated with worse DFI of NSCLC patients. Additional studies are required to validate our findings in a large cohort of early stage NSCLC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01283-x.
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Affiliation(s)
- Α Markou
- Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
| | - D Londra
- Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - V Tserpeli
- Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Ι Kollias
- Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - E Tsaroucha
- 8th Department of Pulmonary Diseases, 'Sotiria' General Hospital for Chest Diseases, Athens, Greece
| | - I Vamvakaris
- 8th Department of Pulmonary Diseases, 'Sotiria' General Hospital for Chest Diseases, Athens, Greece
| | - K Potaris
- 8th Department of Pulmonary Diseases, 'Sotiria' General Hospital for Chest Diseases, Athens, Greece
| | - I Pateras
- Laboratory of Histology-Embryology, Molecular Carcinogenesis Group, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Α Kotsakis
- Department of Medical Oncology, University General Hospital of Larissa, Thessaly, Greece
| | - V Georgoulias
- First Department of Medical Oncology, Metropolitan General Hospital of Athens, Cholargos, Greece
| | - Ε Lianidou
- Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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19
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Sanaei M, Kavoosi F. Effect of Sodium Butyrate on p16INK4a, p14ARF, p15INK4b, Class I HDACs (HDACs 1, 2, 3) Class II HDACs (HDACs 4, 5, 6), Cell Growth Inhibition and Apoptosis Induction in Pancreatic Cancer AsPC-1 and Colon Cancer HCT-116 Cell Lines. Asian Pac J Cancer Prev 2022; 23:795-802. [PMID: 35345349 PMCID: PMC9360940 DOI: 10.31557/apjcp.2022.23.3.795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND In higher eukaryotes, cell-cycle transitions are regulated by different cyclin-dependent kinases (Cdks) and Cdk inhibitors (CKIs). CKIs include two groups, the Ink4 (p16INK4a, p15INK4b, p18INK4c, and p19INK4d) and the Cip/Kip (p21Cip1, p27Kip1, and p57Kip2) families. The hyperactivity of histone deacetylases (HDACs) is associated with cancer induction. Histone deacetylase inhibitors (HDACIs) such as sodium butyrate (NaBT) can inhibit HDAC activity resulting in apoptosis induction. The present study was designed to investigate the effect of sodium butyrate on p16INK4a, p14ARF, p15INK4b, class I HDACs (HDACs 1, 2, 3), and class II HDACs (HDACs 4, 5, 6), cell growth inhibition, and apoptosis induction in pancreatic cancer AsPC-1 and colon cancer HCT-116 cell lines. In fact, we want to know whether sodium butyrate can reactivate Ink4 and Cip/Kip families by HDACs inhibition. MATERIALS AND METHODS The AsPC-1 and HCT-116 cells were treated with sodium butyrate at different periods. Then, the MTT assay, cell apoptosis assay, and qRT-PCR were done to determine viability, apoptosis, and the relative expression level of the genes respectively. RESULTS The sodium butyrate increased p16INK4a, p14ARF, and p15INK4b and decreased class I and II HDACs significantly. Besides, HCT-116 cell was more sensitive to sodium butyrate in comparison to AsPC-1 cell. CONCLUSION The sodium butyrate can reactivate the p16INK4a, p14ARF, and p15INK4b through inhibition of HDACs in AsPC-1 and HCT-116 cell lines.
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Affiliation(s)
- Masumeh Sanaei
- Research Center for Non-Communicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Fraidoon Kavoosi
- Research Center for Non-Communicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
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20
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El makawy AI, Mabrouk DM, Mohammed SE, Abdel-Aziem SH, EL-Kader HAA, Sharaf HA, Youssef DA, Ibrahim FM. The suppressive role of nanoencapsulated chia oil against DMBA-induced breast cancer through oxidative stress repression and tumor genes expression modulation in rats. Mol Biol Rep 2022; 49:10217-10228. [PMID: 36063350 PMCID: PMC9618492 DOI: 10.1007/s11033-022-07885-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/17/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Chia oil is high in omega-3 fatty acids, which have been linked to a lower risk of many diseases, including cancer. Oil encapsulation is a method that holds promise for maintaining oil content while enhancing solubility and stability. The purpose of this study is to prepare nanoencapsulated Chia oil and investigate its suppressive effects on rat chemically induced breast cancer. METHODS The oil was extracted from commercial Chia seeds and their fatty acids were analyzed using Gas Chromatography-mass spectrometry (GC/MS). Sodium alginate was used as a loading agent to create the Chia oil nanocapsules. The DPPH assay was used to assess the oil nanocapsules' capacity to scavenge free radicals. Breast cancer induction was done by single dose subcutaneously administration of 80 mg/kg dimethylbenz (a) anthracene (DMBA). Models of breast cancer were given Chia oil nanocapsules orally for one month at doses of 100 and 200 mg/kg. Through measuring intracellular reactive oxygen species (ROS) and protein carbonyl, assessing the gene expression of tumor suppressor genes (BRCA 1 & 2, TP53), and conducting histopathological analysis, the suppressive effect of Chia oil nanocapsules was examined. RESULTS The increase in ROS and PC levels brought on by DMBA was significantly decreased by the administration of Chia oil nanocapsules. In tumor tissue from rats given Chia oil nanocapsules, the mRNA expression levels of BRCA1, BRCA2, and TP53 were controlled Histopathological analysis clarified that the tissue architecture of breast tumors was improved by nanocapsules management. CONCLUSIONS These findings demonstrate the ability of Chia oil nanocapsules to inhibit cancer cells in the rat breast.
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Affiliation(s)
- Aida I. El makawy
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Giza, P.O.12622, Egypt
| | - Dalia M. Mabrouk
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Giza, P.O.12622, Egypt
| | - Shaimaa E. Mohammed
- Nutrition and Food Sciences Department, Food Industries and Nutrition Research Institute, National Research Centre, Giza, P.O.12622, Egypt
| | - Sekena H. Abdel-Aziem
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Giza, P.O.12622, Egypt
| | - Heba A. Abd EL-Kader
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Giza, P.O.12622, Egypt
| | - Hafiza A. Sharaf
- Pathology Department, Medical Research and Clinical Studies Institute, National Research Centre, Giza, P.O.12622, Egypt
| | - Dalia A. Youssef
- Pests and Plant Protection Department, Agricultural and Biology Research Institute, National Research Centre, Giza, P.O.12622, Egypt
| | - Faten M. Ibrahim
- Medicinal and Aromatic Plants Research Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Giza, P.O.12622, Egypt
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21
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Wuputra K, Ku CC, Kato K, Wu DC, Saito S, Yokoyama KK. Translational models of 3-D organoids and cancer stem cells in gastric cancer research. Stem Cell Res Ther 2021; 12:492. [PMID: 34488885 PMCID: PMC8420044 DOI: 10.1186/s13287-021-02521-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/18/2021] [Indexed: 12/11/2022] Open
Abstract
It is postulated as a general concept of cancer stem cells (CSCs) that they can produce cancer cells overtly and repopulate cancer progenitor cells indefinitely. The CSC niche is part of a specialized cancer microenvironment that is important to keep the phenotypes of CSCs. Stem cell- and induced pluripotent stem cell (iPSC)-derived organoids with genetic manipulation are beneficial to the investigation of the regulation of the microenvironment of CSCs. It would be useful to assess the efficiency of the cancer microenvironment on initiation and progression of cancers. To identify CSCs in cancer tissues, normal cell organoids and gastric cancer organoids from the cancerous areas, as well as iPSCs, were established several years ago. However, many questions remain about the extent to which these cultures recapitulate the development of the gastrointestinal tract and the mechanism of Helicobacter pylori-induced cancer progression. To clarify the fidelity of human organoid models, we have noted several key issues for the cultivation of, and differences between, normal and cancerous organoids. We developed precise culture conditions for gastric organoids in vitro to improve the accuracy of the generation of organoid models for therapeutic and medical applications. In addition, the current knowledge on gastrointestinal CSC research, including the topic of CSC markers, cancer cell reprogramming, and application to target cancer cell plasticity through niches, should be reinforced. We discuss the progression of cancers derived from human gastric organoids and the identification of CSCs.
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Affiliation(s)
- Kenly Wuputra
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan
| | - Chia-Chen Ku
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan
| | - Kohsuke Kato
- Department of Infection Biology, Graduate School of Comprehensive Human Sciences, The University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Deng-Chyang Wu
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan.,Department of Gastroenterology, Department of Internal Medicines, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan
| | - Shigeo Saito
- Waseda Research Institute of Science and Engineering, Waseda University, Tokyo, 169-0051, Japan. .,Saito Laboratory of Cell Technology, Yaita, Tochigi, 329-1571, Japan.
| | - Kazunari K Yokoyama
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan. .,Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan. .,Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan. .,Waseda Research Institute of Science and Engineering, Waseda University, Tokyo, 169-0051, Japan.
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22
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Beacon TH, Delcuve GP, López C, Nardocci G, Kovalchuk I, van Wijnen AJ, Davie JR. The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes. Clin Epigenetics 2021; 13:138. [PMID: 34238359 PMCID: PMC8264473 DOI: 10.1186/s13148-021-01126-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4 (H3K4me3) located after first exons and around transcription start sites. This epigenetic mark is typically restricted to narrow regions at the 5`end of the gene body, though a small subset of genes have a broad H3K4me3 domain which extensively covers the coding region. Although most studies focus on the H3K4me3 mark, the broad H3K4me3 domain is associated with a plethora of histone modifications (e.g., H3 acetylated at K27) and is therein termed broad epigenetic domain. Genes marked with the broad epigenetic domain are involved in cell identity and essential cell functions and have clinical potential as biomarkers for patient stratification. Reducing expression of genes with the broad epigenetic domain may increase the metastatic potential of cancer cells. Enhancers and super-enhancers interact with the broad epigenetic domain marked genes forming a hub of interactions involving nucleosome-depleted regions. Together, the regulatory elements coalesce with transcription factors, chromatin modifying/remodeling enzymes, coactivators, and the Mediator and/or Integrator complex into a transcription factory which may be analogous to a liquid–liquid phase-separated condensate. The broad epigenetic domain has a dynamic chromatin structure which supports frequent transcription bursts. In this review, we present the current knowledge of broad epigenetic domains.
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Affiliation(s)
- Tasnim H Beacon
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Geneviève P Delcuve
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Camila López
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Gino Nardocci
- Faculty of Medicine, Universidad de Los Andes, Santiago, Chile.,Molecular Biology and Bioinformatics Lab, Program in Molecular Biology and Bioinformatics, Center for Biomedical Research and Innovation (CIIB), Universidad de Los Andes, Santiago, Chile
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - James R Davie
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada. .,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada.
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23
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Khalifa MK, Bakr NM, Ramadan A, Abd Elwahab KM, Desoky E, Nageeb AM, Swellam M. Implications of targeted next-generation sequencing for bladder cancer: report of four cases. J Genet Eng Biotechnol 2021; 19:91. [PMID: 34152511 PMCID: PMC8217481 DOI: 10.1186/s43141-021-00182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/17/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Bladder cancer is considered heterogeneous diseases with two major subgroups: non-muscle- invasive bladder cancer (NMIBC) and muscle invasive bladder cancer (MIBC). It is a major healthcare problem, and it is one of the leading causes of mortality worldwide. Genetic mutations are not only a cause for carcinogenesis but are also a way for treatment strategy. The present study aimed to investigate breast cancer (BRCA genes) tumor suppressor gene mutations in bladder cancer tissue and combined blood samples for patients who developed secondary tumor after or during trimodal therapy. Fresh tissue samples and their matched blood samples were collected from four patients with bladder cancer. The objective regions for the examined genes (BRCA1 and BRCA2) were sequenced using next-generation sequencing (NGS); generated BAM files were uploaded to the cloud-based Ionreporter server, and the Oncomine BRCA-specific plugin was used to analyze the paired normal and tumor sample for each patient using the default plugin parameters. RESULTS Intronic BRCA1 mutation c.5050-104 C >T was reported among the four investigated bladder cancer patients, and three somatic mutations were reported as follows: two of them were found to be benign rs1064793056 and rs28897679 on the Clinivar database and one nonsense pathogenic variant rs80357006. BRCA 2 gene mutation reported an exonic synonymous mutation rs397507876 in the tissue and germline DNA. Patients were treated with trimodal; however, three bladder cancer patients who reported BRCA mutations developed secondary tumors. CONCLUSION Identification of mutational BRCA changes in bladder cancer is a promising marker for better treatment strategy. Further studies are encouraged on a large cohort of bladder cancer patients to confirm our findings.
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Affiliation(s)
| | - Noha M Bakr
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
| | - Amal Ramadan
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
| | | | - Esam Desoky
- Urology Department, Zagazig University, Zagazig, Egypt
| | - Amira M Nageeb
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt
| | - Menha Swellam
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt.
- High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, El-Bohouth Street, Dokki, Giza, 12622, Egypt.
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24
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Gao L, Wu ZX, Assaraf YG, Chen ZS, Wang L. Overcoming anti-cancer drug resistance via restoration of tumor suppressor gene function. Drug Resist Updat 2021; 57:100770. [PMID: 34175687 DOI: 10.1016/j.drup.2021.100770] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 06/08/2021] [Accepted: 06/13/2021] [Indexed: 02/07/2023]
Abstract
The cytotoxic anti-cancer drugs cisplatin, paclitaxel, doxorubicin, 5-fluorouracil (5-FU), as well as targeted drugs including imatinib, erlotinib, and nivolumab, play key roles in clinical cancer treatment. However, the frequent emergence of drug resistance severely comprosises their anti-cancer efficacy. A number of studies indicated that loss of function of tumor suppressor genes (TSGs) is involved in the development of cancer drug resistance, apart from decreased drug influx, increased drug efflux, induction of anti-apoptosis mechanisms, alterations in tumor microenvironment, drug compartmentalization, enhanced DNA repair and drug inactivation. TSGs are involved in the pathogenesis of tumor formation through regulation of DNA damage repair, cell apoptosis, autophagy, proliferation, cell cycle progression, and signal transduction. Our increased understanding of TSGs in the past decades demonstrates that gene mutation is not the only reason that leads to the inactivation of TSGs. Loss of function of TSGs may be based on the ubiquitin-proteasome pathway, epigenetic and transcriptional regualtion, post-translation modifications like phosphorylation as well as cellular translocation of TSGs. As the above processes can constitute"druggable targets", these mechanisms provide novel therapeutic approaches in targeting TSGs. Some small molecule compounds targeting these approaches re-activated TSGs and reversed cancer drug resistance. Along this vein, functional restoration of TSGs is a novel and promising approach to surmount cancer drug resistance. In the current review, we draw a scenario based on the role of loss of function of TSGs in drug resistance, on mechanisms leading to inactivation of TSGs and on pharmacological agents acting on these mechanisms to overcome cancer drug resistance. This review discusses novel therapeutic strategies targeting TSGs and offers possible modalities to conquer cancer drug resistance.
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Affiliation(s)
- Lingyue Gao
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, PR China; Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Shenyang, PR China
| | - Zhuo-Xun Wu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, NY, 11439, USA
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, NY, 11439, USA.
| | - Lihui Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, PR China; Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Shenyang, PR China.
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Chernov AN, Alaverdian DA, Galimova ES, Renieri A, Frullanti E, Meloni I, Shamova OV. The phenomenon of multidrug resistance in glioblastomas. Hematol Oncol Stem Cell Ther 2021; 15:1-7. [PMID: 34216549 DOI: 10.1016/j.hemonc.2021.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/30/2021] [Indexed: 12/21/2022] Open
Abstract
The most common and aggressive brain tumor in the adult population is glioblastoma (GBM). The lifespan of patients does not exceed 22 months. One of the reasons for the low effectiveness of GBM treatment is its radioresistance and chemoresistance. In the current review, we discuss the phenomenon of multidrug resistance of GBM in the context of the expression of ABC family transporter proteins and the mechanisms of proliferation, angiogenesis, and recurrence. We focused on the search of molecular targets among growth factors, receptors, signal transduction proteins, microRNAs, transcription factors, proto-oncogenes, tumor suppressor genes, and their single-nucleotide polymorphisms.
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Affiliation(s)
- Alexandr N Chernov
- Institute of Experimental Medicine, Russian Academy of Medical Sciences, Saint-Petersburg, Russia.
| | - Diana A Alaverdian
- MedicalGenetics, Department of Medical Biotechnologies, University of Siena, Siena, Italy; MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elvira S Galimova
- I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Alessandra Renieri
- MedicalGenetics, Department of Medical Biotechnologies, University of Siena, Siena, Italy; MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Elisa Frullanti
- MedicalGenetics, Department of Medical Biotechnologies, University of Siena, Siena, Italy; MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Ilaria Meloni
- MedicalGenetics, Department of Medical Biotechnologies, University of Siena, Siena, Italy; MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Olga V Shamova
- Institute of Experimental Medicine, Russian Academy of Medical Sciences, Saint-Petersburg, Russia
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Ali MAM. The DEAD-box protein family of RNA helicases: sentinels for a myriad of cellular functions with emerging roles in tumorigenesis. Int J Clin Oncol 2021; 26:795-825. [PMID: 33656655 DOI: 10.1007/s10147-021-01892-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/20/2021] [Indexed: 02/06/2023]
Abstract
DEAD-box RNA helicases comprise a family within helicase superfamily 2 and make up the largest group of RNA helicases. They are a profoundly conserved family of RNA-binding proteins, carrying a generic Asp-Glu-Ala-Asp (D-E-A-D) motif that gives the family its name. Members of the DEAD-box family of RNA helicases are engaged in all facets of RNA metabolism from biogenesis to decay. DEAD-box proteins ordinarily function as constituents of enormous multi-protein complexes and it is believed that interactions with other components in the complexes might be answerable for the various capacities ascribed to these proteins. Therefore, their exact function is probably impacted by their interacting partners and to be profoundly context dependent. This may give a clarification to the occasionally inconsistent reports proposing that DEAD-box proteins have both pro- and anti-proliferative functions in cancer. There is emerging evidence that DEAD-box family of RNA helicases play pivotal functions in various cellular processes and in numerous cases have been embroiled in cellular proliferation and/or neoplastic transformation. In various malignancy types, DEAD-box RNA helicases have been reported to possess pro-proliferation or even oncogenic roles as well as anti-proliferative or tumor suppressor functions. Clarifying the exact function of DEAD-box helicases in cancer is probably intricate, and relies upon the cellular milieu and interacting factors. This review aims to summarize the current data on the numerous capacities that have been ascribed to DEAD-box RNA helicases. It also highlights their diverse actions upon malignant transformation in the various tumor types.
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Videira A, Beckedorff FC, daSilva LF, Verjovski-Almeida S. PVT1 signals an androgen-dependent transcriptional repression program in prostate cancer cells and a set of the repressed genes predicts high-risk tumors. Cell Commun Signal 2021; 19:5. [PMID: 33430890 PMCID: PMC7798249 DOI: 10.1186/s12964-020-00691-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 12/01/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Androgen receptor (AR) and polycomb repressive complex 2 (PRC2) are known to co-occupy the loci of genes that are downregulated by androgen-stimulus. Long intergenic non-coding RNA (lincRNA) PVT1 is an overexpressed oncogene that is associated with AR in LNCaP prostate cancer cells, and with PRC2 in HeLa and many other types of cancer cells. The possible involvement of PVT1 in mediating androgen-induced gene expression downregulation in prostate cancer has not been explored. METHODS LNCaP cell line was used. Native RNA-binding-protein immunoprecipitation with anti-AR or anti-EZH2 was followed by RT-qPCR with primers for PVT1. Knockdown of PVT1 with specific GapmeRs (or a control with scrambled GapmeR) was followed by differentially expressed genes (DEGs) determination with Agilent microarrays and with Significance Analysis of Microarrays statistical test. DEGs were tested as a tumor risk classifier with a machine learning Random Forest algorithm run with gene expression data from all TCGA-PRAD (prostate adenocarcinoma) tumors as input. ChIP-qPCR was performed for histone marks at the promoter of one DEG. RESULTS We show that PVT1 knockdown in androgen-stimulated LNCaP cells caused statistically significant expression upregulation/downregulation of hundreds of genes. Interestingly, PVT1 knockdown caused upregulation of 160 genes that were repressed by androgen, including a significantly enriched set of tumor suppressor genes, and among them FAS, NOV/CCN3, BMF, HRK, IFIT2, AJUBA, DRAIC and TNFRSF21. A 121-gene-set (out of the 160) was able to correctly predict the classification of all 293 intermediate- and high-risk TCGA-PRAD tumors, with a mean ROC area under the curve AUC = 0.89 ± 0.04, pointing to the relevance of these genes in cancer aggressiveness. Native RIP-qPCR in LNCaP showed that PVT1 was associated with EZH2, a component of PRC2. PVT1 knockdown followed by ChIP-qPCR showed significant epigenetic remodeling at the enhancer and promoter regions of tumor suppressor gene NOV, one of the androgen-repressed genes that were upregulated upon PVT1 silencing. CONCLUSIONS Overall, we provide first evidence that PVT1 was involved in signaling a genome-wide androgen-dependent transcriptional repressive program of tumor suppressor protein-coding genes in prostate cancer cells. Identification of transcriptional inhibition of tumor suppressor genes by PVT1 highlights the pathway to the investigation of mechanisms that lie behind the oncogenic role of PVT1 in cancer. Video Abstract.
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Affiliation(s)
- Alexandre Videira
- Laboratório de Expressão Gênica Em Eucariotos, Instituto Butantan, Av. Vital Brasil 1500, São Paulo, SP 05503-900 Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-900 Brazil
| | - Felipe C. Beckedorff
- Laboratório de Expressão Gênica Em Eucariotos, Instituto Butantan, Av. Vital Brasil 1500, São Paulo, SP 05503-900 Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-900 Brazil
- Present Address: Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - Lucas F. daSilva
- Laboratório de Expressão Gênica Em Eucariotos, Instituto Butantan, Av. Vital Brasil 1500, São Paulo, SP 05503-900 Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-900 Brazil
- Present Address: Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - Sergio Verjovski-Almeida
- Laboratório de Expressão Gênica Em Eucariotos, Instituto Butantan, Av. Vital Brasil 1500, São Paulo, SP 05503-900 Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-900 Brazil
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Yousefi M, Koopaie M, Karimi R, Kermani FM, Kolahdooz S, Shamshiri A. Effect of photodynamic therapy on expression of HRAS, NRAS and caspase 3 genes at mRNA levels, apoptosis of head and neck squamous cell carcinoma cell line. Photodiagnosis Photodyn Ther 2021; 33:102142. [PMID: 33307231 DOI: 10.1016/j.pdpdt.2020.102142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 11/14/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVES This study aimed to assess the effect of photodynamic therapy (PDT) on expression of CASP3, NRAS and HRAS genes at mRNA levels, and apoptosis of head and neck squamous cell carcinoma (HNSCC) cell line. MATERIALS AND METHODS In order to complete the present in vitro study, HNSCC cell line (NCBI C196 HN5) purchased from Pasteur Institute. Cells were divided into four groups; Group 1: photodynamic treatment (laser + methylene blue (MB) as photosensitizer), group 2: MB, group 3: laser (with 660 nm wavelength), and group 4: control (without any treatment). To determine the optimal concentration of MB, in a pilot study, toxicity of MB in different concentration was assessed using MTT assay. Cells in group 1, 2 and 3 was treated at optimal concentration of MB (1.6 μg/mL). Gene expression at mRNA levels was assessed after 24 h incubation, using real-time (qRT)-PCR. The expression of BAX and BCL2 genes at the mRNA levels was analyzed to evaluate apoptosis. 2-ΔΔCt values of BCL2, BAX, CASP3, NRAS, and HRAS in groups was analyzed using ANOVA. Tukey's HSD and Games Howell test was used to compare between two groups. RESULTS Over-expression of BAX (p < 0.001), CASP3 (p < 0.001) and down-regulation of BCL2 (p = 0.004), HRAS (p = 0.023) and NRAS (p = 0.045) were noted in group 1 (PDT), compared with the control group. Treatment by laser alone induce down-regulation of CASP3 (p < 0.05), BAX (p < 0.05), BCL2 (p > 0.05), HRAS (p > 0.05) and NRAS (p > 0.05). CONCLUSION PDT caused down-regulation of NRAS, HRAS and BCL2 and over-expression of CASP3 and BAX genes at mRNA levels in HNSCC cell line. The present study raises the possibility that the role of MB on BCL2 down-regulation and BAX and CASP3 over-expression was higher than laser alone while it seems that laser alone was more effective than MB in HRAS and NRAS down-regulation.
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Witek Ł, Janikowski T, Gabriel I, Bodzek P, Olejek A. Analysis of microRNA regulating cell cycle-related tumor suppressor genes in endometrial cancer patients. Hum Cell 2020; 34:564-569. [PMID: 33123872 PMCID: PMC7900021 DOI: 10.1007/s13577-020-00451-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/12/2020] [Indexed: 12/04/2022]
Abstract
Endometrial cancer remains the most common malignancy of the female genital system in developed countries. Tumor suppressor genes are responsible for controlling the cells fate in the cell cycle and preventing cancerogenesis. Gene expression affects cancer progression and is modulated by microRNAs defined as both tumor suppressors and oncogenes. These molecules indirectly regulate multiple processes like cell proliferation, differentiation and apoptosis. The aim of this study was to analyze miRNAs expression that can regulate the activity of tumor suppressor genes related to the cell cycle in patients with endometrioid endometrial cancer. The study group consisted of 12 samples that met the inclusion criteria from a total of 48 obtained. The 12 samples were used to analyze microRNA expression. Complementary miRNAs were identified using TargetScan Database and statistical analysis. MicroRNAs were determined for the tumor suppressor genes: CYR61, WT1, TSPYL5, HNRNPA0, BCL2L1 and BAK1. All the miRNAs were complementary to the described target genes based on TargetScan Database. There were five miRNAs differentially expressed that can regulate tumor suppressor genes related to the cell cycle. The distinguished miRNAs: mir-340-3p, mir-1236-5p, mir-874-3p, mir-873-5p.2 and mir-548-5p were differentially expressed in endometrial cancer in comparison to the control. Among the distinguished miRNAs, the most promising is mir-874-3p, which may have an important role in endometrial adenocarcinoma proliferation.
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Affiliation(s)
- Łukasz Witek
- Department of Gynecology, Obstetrics and Oncological Gynecology, Medical University of Silesia, Bytom, Poland
| | | | - Iwona Gabriel
- Department of Gynecology, Obstetrics and Oncological Gynecology, Medical University of Silesia, Bytom, Poland
| | - Piotr Bodzek
- Department of Gynecology, Obstetrics and Oncological Gynecology, Medical University of Silesia, Bytom, Poland
| | - Anita Olejek
- Department of Gynecology, Obstetrics and Oncological Gynecology, Medical University of Silesia, Bytom, Poland
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Liu YX, Li QZ, Cao YN, Zhang LQ. Identification of key genes and important histone modifications in hepatocellular carcinoma. Comput Struct Biotechnol J 2020; 18:2657-2669. [PMID: 33033585 PMCID: PMC7533298 DOI: 10.1016/j.csbj.2020.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/26/2020] [Accepted: 09/10/2020] [Indexed: 01/14/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer death in the world. It has been reported that HCC is closely related to the changes of histone modifications. However, finding histone modification patterns in key genes which related to HCC is still an important task. In our study, the patterns of 11 kinds of histone modifications in the promoter regions for the different types of genes were analyzed by hierarchical screening for hepatocyte (normal) cell line and HepG2 (tumor) cell line. The important histone modifications and their key modification regions in different types of genes were found. The results indicate that these important genes may play a pivotal role in the occurrence of HCC. By analyzing the differences of histone modifications and gene expression levels for these important genes between the two cell lines, we found that the signals of H3K4me3, H3K27ac, H3K9ac, and H3K4me2 in HCC are significantly stronger. The changed regions of important histone modifications in 17 key genes were also identified. For example, the H3K4me3 signals increased 150 times in regions (−1500, −500) bp and (0, 1000) bp of ARHGAP5 in tumor cell line than in normal cell line. Finally, a prognostic risk scoring model was constructed, and the effects of key genes on the prognosis of HCC were verified by the survival analysis. Our results may provide a more precise potential therapeutic targets for identifying key genes and histone modifications in HCC as new biomarkers.
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Key Words
- Biomarkers
- DHLEG, Different highly and lowly expressed genes
- Gene expression
- H2AFZ, H2A histone family member Z
- H3K27ac, Histone H3 acetylated at lysine 27
- H3K27me3, Histone H3 trimethylated at lysine 27
- H3K36me3, Histone H3 trimethylated at lysine 36
- H3K4me1, Histone H3 monomethylated at lysine 4
- H3K4me2, Histone H3 dimethylated at lysine 4
- H3K4me3, Histone H3 trimethylated at lysine 4
- H3K79me2, Histone H3 dimethylated at lysine 79
- H3K9ac, Histone H3 acetylated at lysine 9
- H3K9me3, Histone H3 trimethylated at lysine 9
- H4K20me1, Histone H4 monomethylated at lysine 20
- HCC, Hepatocellular carcinoma
- Histone modification signals
- NH, The genes are highly expressed in normal cell line but not in tumor cell line
- NH-TL, The genes are highly expressed in normal cell line and lowly expressed in tumor cell line
- NL, The genes are lowly expressed in normal cell line but not in tumor cell line
- NL-TH, The genes are lowly expressed in normal cell line and highly expressed in tumor cell line
- ONCO, Oncogenes
- Oncogenes
- TH, The genes are highly expressed in tumor cell line but not in normal cell line
- TL, The genes are lowly expressed in tumor cell line but not in normal cell line
- TSG, Tumor suppressor genes
- Tumor suppressor genes
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Affiliation(s)
- Yu-Xian Liu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.,The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China
| | - Yan-Ni Cao
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Lu-Qiang Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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Emam M, Machado JP, Antunes A. Evolutionary genomics of mammalian lung cancer genes reveals signatures of positive selection in APC, RB1 and TP53. Genomics 2020; 112:4722-31. [PMID: 32818633 DOI: 10.1016/j.ygeno.2020.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/14/2020] [Indexed: 11/21/2022]
Abstract
Lung cancer is the type of cancer causing most deaths in humans, with 234,030 new cases of lung cancer diagnosed in the United States in 2018. Recently, Tumor suppressor genes (TSGs) or the control of its pathway became promising drug targets for cancer therapy. A diverse group of TSGs is involved in progression and metastasis of lung cancer. Here, we surveyed nine highly significant mutated genes in 20 mammalian genomes to assess signatures of adaptive evolution using maximum likelihood approaches. We found that three genes (APC, RB1, and TP53) are under strong positive selection, influencing amino acids located in functionally important protein domains, such as three sites in APC found in the APC_N_CC domain, which is responsible for the binding to beta-catenin armadillo repeats that regulate beta-catenin level (beta-catenin is a transcription factor and its misregulation lead to malignant transformation of normal cells). Such sites substitutions mostly increase the stability of the domain. Moreover, substitution of some other sites found in important motifs, such as codon 47 (proline-directed kinase motif) in TP53, modify the phosphorylation activity of TP53 playing a key role in cancer risk. Our findings will open recommendation to drug targeting sites and will foster further research to understand better these proteins function.
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Abstract
We increasingly recognize the importance of alterations in DNA in the development of cancer. Beginning with the first somatic mutation identified in a urinary bladder carcinoma cell line, recombinant-DNA technology has led to an explosion of this field, bringing a wealth of data, yet to be fully analyzed. As the number of putative cancer genes has grown several groups have compiled lists of cancer genes with the Catalogue Of Somatic Mutations In Cancer, list as one of several highly regarded. With an interest in the distribution of cancer genes in human chromosomes and discerning whether some chromosomes predominated in cancer gene content, we undertook this review of their distribution in the modern-day human genome. We conclude that cancer genes are uniformly distributed across all human chromosomes having been accreted to the evolving human genome likely in a random fashion over the millennia.
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Affiliation(s)
- Bahar Laderian
- Columbia University Irving Medical Center, New York City, NY.
| | - Mengxi Zhou
- Columbia University Irving Medical Center, New York City, NY
| | - Tito Fojo
- Columbia University Irving Medical Center, New York City, NY; James J. Peters VA Medical Center, New York City, NY
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Santhekadur PK, Kumar DP. RISC assembly and post-transcriptional gene regulation in Hepatocellular Carcinoma. Genes Dis 2020; 7:199-204. [PMID: 32215289 PMCID: PMC7083748 DOI: 10.1016/j.gendis.2019.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/07/2019] [Accepted: 09/09/2019] [Indexed: 12/16/2022] Open
Abstract
RNA-induced silencing complex (RISC) is one of the basic eukaryotic cellular machinery which plays a pivotal role in post-transcriptional gene regulation. Discovery of miRNAs and their role in gene regulation have changed the course of modern biology. The method of gene silencing using small interfering RNAs and miRNAs has become major tool in molecular biology and genetic engineering. Hepatocellular Carcinoma (HCC) is a very common malignancy of liver in developing countries and due to various risk factors; the prevalence of this disease is rapidly increasing throughout the globe. There exists an imbalance in interplay between oncogenes and tumor suppressor genes and their regulation plays a major role in HCC growth, development and metastasis. The regulatory function of RISC and miRNAs make them a very important mediators of cancer signaling in HCC. Therefore, targeting the RISC complex for HCC therapy is the need of the time.
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Affiliation(s)
- Prasanna K. Santhekadur
- Corresponding author. Department of Biochemistry, Center of Excellence in Molecular Biology and Regenerative Medicine, JSS Medical College, JSS Academy of Higher Education and Research, Sri Shivarathreeshwara Nagar, Mysore 570015, Karnataka, India.
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Kanchan K, Iyer K, Yanek LR, Carcamo-Orive I, Taub MA, Malley C, Baldwin K, Becker LC, Broeckel U, Cheng L, Cowan C, D'Antonio M, Frazer KA, Quertermous T, Mostoslavsky G, Murphy G, Rabinovitch M, Rader DJ, Steinberg MH, Topol E, Yang W, Knowles JW, Jaquish CE, Ruczinski I, Mathias RA. Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program. Stem Cell Res 2020; 46:101803. [PMID: 32442913 PMCID: PMC7575060 DOI: 10.1016/j.scr.2020.101803] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/11/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022] Open
Abstract
Human induced pluripotent stem cell (hiPSC) lines have previously been generated through the NHLBI sponsored NextGen program at nine individual study sites. Here, we examined the structural integrity of 506 hiPSC lines as determined by copy number variations (CNVs). We observed that 149 hiPSC lines acquired 258 CNVs relative to donor DNA. We identified six recurrent regions of CNVs on chromosomes 1, 2, 3, 16 and 20 that overlapped with cancer associated genes. Furthermore, the genes mapping to regions of acquired CNVs show an enrichment in cancer related biological processes (IL6 production) and signaling cascades (JNK cascade & NFκB cascade). The genomic region of instability on chr20 (chr20q11.2) includes transcriptomic signatures for cancer associated genes such as ID1, BCL2L1, TPX2, PDRG1 and HCK. Of these HCK shows statistically significant differential expression between carrier and non-carrier hiPSC lines. Overall, while a low level of genomic instability was observed in the NextGen generated hiPSC lines, the observation of structural instability in regions with known cancer associated genes substantiates the importance of systematic evaluation of genetic variations in hiPSCs before using them as disease/research models.
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Affiliation(s)
- Kanika Kanchan
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kruthika Iyer
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lisa R Yanek
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ivan Carcamo-Orive
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public health, Johns Hopkins University, Baltimore, MD, USA
| | - Claire Malley
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kristin Baldwin
- Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Lewis C Becker
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ulrich Broeckel
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Linzhao Cheng
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Chad Cowan
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Thomas Quertermous
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Gustavo Mostoslavsky
- The Center for Regenerative Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - George Murphy
- The Center for Regenerative Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Marlene Rabinovitch
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Daniel J Rader
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martin H Steinberg
- Department of Medicine, Section of Hematology-Oncology, Boston University School of Medicine, Boston, MA, USA
| | - Eric Topol
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Wenli Yang
- Penn Center for Pulmonary Biology and Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joshua W Knowles
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public health, Johns Hopkins University, Baltimore, MD, USA
| | - Rasika A Mathias
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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Campanella NC, Silva EC, Dix G, de Lima Vazquez F, Escremim de Paula F, Berardinelli GN, Balancin M, Chammas R, Mendoza Lopez RV, Silveira HCS, Capelozzi VL, Reis RM. Mutational Profiling of Driver Tumor Suppressor and Oncogenic Genes in Brazilian Malignant Pleural Mesotheliomas. Pathobiology 2020; 87:208-216. [PMID: 32369821 DOI: 10.1159/000507373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/20/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Malignant pleural mesothelioma (MPM) is a highly lethal disease comprising a heterogeneous group of tumors with challenging to predict biological behavior. The diagnosis is complex, and the histologic classification includes 2 major subtypes of MPM: epithelioid (∼60% of cases) and sarcomatous (∼20%). Its identification depends upon pathological investigation supported by clinical and radiological evidence and more recently ancillary molecular testing. Treatment options are currently limited, with no known targeted therapies available. OBJECTIVES To elucidate the mutation profile of driver tumor suppressor and oncogenic genes in a cohort of Brazilian patients. METHODS We sequenced 16 driver genes in a series of 43 Brazilian malignant mesothelioma (MM) patients from 3 distinct Brazilian centers. Genomic DNA was extracted from formalin-fixed paraffin-embedded tumor tissue blocks, and the TERT promoter region was amplified by PCR followed by direct capillary sequencing. The Illumina TruSight Tumor 15 was used to evaluate 250 amplicons from 15 genes associated with solid tumors (AKT1, GNA11, NRAS, BRAF, GNAQ, PDGFRA, EGFR, KIT, PIK3CA, ERBB2, KRAS, RET, FOXL2, MET,and TP53). Library preparation with the TruSight Tumor 15 was performed before sequencing at the MiSeq platform. Data analysis was performed using Sophia DDM software. RESULTS Out of 43 MPM patients, 38 (88.4%) were epithelioid subtype and 5 (11.6%) were sarcomatoid histotype. Asbestos exposure was present in 15 (39.5%) patients with epithelioid MPM and 3 (60%) patients with sarcomatoid MPM. We found a TERT promoter mutation in 11.6% of MM, and the c.-146C>T mutation was the most common event. The next-generation sequencing was successful in 33 cases. A total of 18 samples showed at least 1 pathogenic, with a median of 1.8 variants, ranging from 1 to 6. The most mutated genes were TP53 and ERBB2 with 7 variants each, followed by NRAS BRAF, PI3KCA, EGFR and PDGFRA with 2 variants each. KIT, AKT1, and FOXL2 genes exhibited 1 variant each. Interestingly, 2 variants observed in the PDGFRA gene are classic imatinib-sensitive therapy. CONCLUSIONS We concluded that Brazilian MPM harbor mutation in classic tumor suppressor and oncogenic genes, which might help in the guidance of personalized treatment of MPM.
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Affiliation(s)
| | | | - Gustavo Dix
- Department of Surgery, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | - Marcelo Balancin
- Department of Pathology, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.,Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, São Paulo, Brazil
| | - Roger Chammas
- Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, São Paulo, Brazil
| | - Rossana V Mendoza Lopez
- Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, São Paulo, Brazil
| | | | - Vera Luiza Capelozzi
- Department of Pathology, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil, .,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal, .,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal,
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Zhao Y, Pan Y, Cheng C, Zheng D, Zhang Y, Gao Z, Fu F, Li H, Zheng S, Zhuge L, Mao H, Kuang M, Tao X, Peng Y, Hu H, Xiang J, Li Y, Sun Y, Chen H. EGFR-mutant lung adenocarcinoma harboring co-mutational tumor suppressor genes predicts poor prognosis. J Cancer Res Clin Oncol 2020; 146:1781-9. [PMID: 32361787 DOI: 10.1007/s00432-020-03237-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/24/2020] [Indexed: 12/30/2022]
Abstract
INTRODUCTION EGFR mutations occur most frequently in patients with lung adenocarcinoma in East Asia. However, the prognostic and therapeutic impact of co-mutational status of EGFR and tumor suppressor genes is not fully understood. This study aims to provide a deeper understanding of lung adenocarcinoma patients with co-mutation of EGFR and tumor suppressor genes. METHODS From November 2009 to May 2016, 675 patients with lung adenocarcinoma who underwent complete surgery were included in this study. Samples were collected and pathologically examined. Whole-exome sequencing was performed on 197 samples, while direct sequencing of major driver genes, including EGFR, KRAS, ERBB2 and BRAF and Ion-torrent targeted sequencing of tumor suppressor genes, including TP53, KEAP1, MGA, NF1, RB1, SMARCA4 and STK11, were performed on 478 samples. Tumor mutational burden was calculated and survival analyses were performed. RESULTS The frequency of EGFR and TP53 mutation was 409 (60.6%) and 215 (31.9%), respectively. Co-mutation of EGFR and TP53 occured in 151 patients (22.4%), while co-mutation of EGFR and at least one tumor suppressor gene occured in 184 patients (27.3%). Compared with patients with only EGFR mutations, patients with co-mutations of EGFR and TP53 had a higher tumor mutational burden (p = 0.007) and worse recurrence-free survival (p = 0.010), while patients with co-mutations of EGFR and at least one tumor suppressor gene had a higher tumor mutational burden (p = 0.007), worse recurrence-free survival (p = 0.016) and worse overall survival (p = 0.018). CONCLUSIONS Lung adenocarcinoma patients harboring EGFR and co-mutational tumor suppressor genes should be regarded as a unique subgroup.
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Abstract
Objective: The transformation in cells at genetic levels stimulatesthe proliferation of cancer. The current review highlights the role of miRNA in management of cancer by altering processes of body at cellular levels. Methods: A deep research on the literature available till date for miRNA in cancer was conducted using various medical sites like PubMed, MEDLINE from internet and data was collected. The articles were majorly preferred in English language. Results: The development of normal cells into cancerous cells is a multivalent procedure highlighting numerous responsible factors. During the progression of cancer, the role of oncogene and tumor suppressor genes outshines at different levels of tumorogenesis. Metastasis poses highest threat in cancer progression and fabricates obstacles to clinicians and researchers in preventing formation of tumor on secondary sites. The mesenchymal-epithelial transition (MET) and epithelial mesenchymal transition (EMT) induce dissemination and ultimately progression of cancer. Conclusion: A comprehensive knowledge of the altered genes and the mechanism by which they induce formation of tumor is essential as they contribute in proliferating cancer at various stages, aggravating clinical symptoms. Hence miRNAs can be efficiently employed as an emerging treatment therapy for cancer.
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Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Chanchal Kumar
- Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rashita Makkar
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Amit Gupta
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
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Son HJ, Choi EJ, Yoo NJ, Lee SH. Inactivating mutations of tumor suppressor genes KLOTHO and DTWD1 in colorectal cancers. Pathol Res Pract 2020; 216:152816. [PMID: 31924336 DOI: 10.1016/j.prp.2020.152816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/01/2020] [Indexed: 01/02/2023]
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Sanaei M, Kavoosi F, Esmi Z. The Effect of 5-Aza-2'-Deoxycytidine in Combination to and in Comparison with Vorinostat on DNA Methyltransferases, Histone Deacetylase 1, Glutathione S-Transferase 1 and Suppressor of Cytokine Signaling 1 Genes Expression, Cell Growth Inhibition and Apoptotic Induction in Hepatocellular LCL-PI 11 Cell Line. Int J Hematol Oncol Stem Cell Res 2020; 14:45-55. [PMID: 32337014 PMCID: PMC7167604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background: Aberrant methylation and histone deacetylation of tumor suppressor genes (TSGs) are the most epigenetic alterations involving in tumorigenesis. Overexpression of DNA methyltransferases (DNMTs) and histone deacetylase 1 (HDAC1) have been reported in several cancers. The reversion of hypermethylation and deacetylation by epi-drugs such as 5-aza-2'-deoxycytidine (5-AZA-CdR) and vorinostat (SAHA) can restore normal expression of TSGs. Previously, we reported that 5-AZA-CdR and valproic acid (VPA) can inhibit DNMT1 in hepatocellular carcinoma (HCC). The aim of this study was to investigate the effect of 5-AZA-CdR in combination to and in comparison with SAHA on DNMT1, DNMT3a, DNMT3b, histone deacetylase 1 (HDAC1), glutathione S-transferase 1 (GSTP1) and suppressor of cytokine signaling 1 (SOCS1) genes expression, cell growth inhibition and apoptotic induction in hepatocellular LCL-PI 11 cell line. Materials and Methods: The cells were treated with 5-AZA-CdR and SAHA and then MTT assay, cell apoptosis assay and Real-time quantitative RT-PCR (qRT-PCR) were done. Results: Both agents indicated significant inhibitory and apoptotic effect (P< 0.001). The apoptotic effect of SAHA was more than that of 5-Aza-CdR. The result of qRT-PCR indicated that 5-Aza-CdR decreased DNMT1, DNMT3a, DNMT3b and increased GSTP1and SOCS1 genes expression and SAHA decreased HDAC1 and increased GSTP1 and SOCS1 genes expression significantly. Maximal apoptosis and genes expression were seen with combined treatment. Conclusion: 5-AZA-CdR and SAHA down-regulated DNMT1, DNMT3a, DNMT3b, and HDAC1 and up-regulated GSTP1 and SOCS1 gene expression by which inhibited cell viability and induced apoptosis, suggesting that they could be used in the treatment of HCC.
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Affiliation(s)
- Masumeh Sanaei
- Research Center for Non-communicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Fraidoon Kavoosi
- Research Center for Non-communicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Zahra Esmi
- Research Committee Student, Jahrom University of Medical Sciences, Jahrom, Iran
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Abstract
Genetic testing should be offered to all women less than 40 years of age who are diagnosed with breast cancer, and patients with PABC are generally among them. However, there is no specific study about these cases, and whether genetic testing should be carried out during or after pregnancy is not known. Generally, testing before delivery should only be performed if positive results change management plans, such as undergoing fetal testing and choosing mastectomy instead of breast conserving surgery.
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Roberts J, Mehta R, Curran I, Raju J. Dietary acrylamide exposure in F344 rats and colon tumor-bearing nude nu/nu mice: Dataset of gene expression of cancer pathway targets and methylation status of tumor suppressor genes in colon mucosae and tumors. Data Brief 2019; 27:104763. [PMID: 31828184 PMCID: PMC6889650 DOI: 10.1016/j.dib.2019.104763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 11/29/2022] Open
Abstract
Dietary acrylamide, a thermally induced food contaminant, at a level (2 mg/kg diet) typifying higher occurrence in certain food products - is neither an independent carcinogen nor a tumor promoter in the colon. This is evidenced by our previous studies using the medium-term azoxymethane (AOM)-induced colon tumorigenesis assay in F344 rats and the human colon tumor xenograft model in athymic nude (nu/nu) mice (https://doi.org/10.1371/journal.pone.0073916) [1]. In addition, we found that acrylamide may act as a colon co-carcinogen in association with a known carcinogen (AOM) in F344 rats. Furthermore, exposure to acrylamide at 2 mg/kg in the diet was not associated with any toxicologically relevant changes in clinical biochemistry, hematology, and apical endpoints in healthy rats (exposed only to saline injections) (https://doi.org/10.1016/j.toxrep.2016.08.010) [2]. Here we report data from our previous investigation [1] on gene expression of cancer pathway targets as well as the methylation status of select tumor suppressor genes. Briefly, mRNA and DNA were extracted from (a) colon mucosae and tumors from F344 rats exposed to AOM or saline and (b) athymic nude (nu/nu) mice bearing human colon tumor xenografts, both exposed to dietary acrylamide at concentrations of 0 or 2 mg/kg diet for 20 and 4 weeks, respectively. RT2 Profiler PCR Cancer PathwayFinder Arrays (Qiagen) and EpiTect Methyl II DNA Restriction kits and PCR Assays (Qiagen) were used to detect cancer-relevant gene expression (84 genes representing 9 pathways) and the methylation status of the CpG islands associated with 22 tumor suppressor genes in colon mucosae, tumors and xenografts. Additionally, RT2 Profiler PCR Arrays (Qiagen) for cell cycle regulation, growth factors, inflammatory cytokines and receptors, and inflammatory response and autoimmunity were used to investigate the gene expression (84 genes in each array) of targets involved in these select cellular pathways in the colon mucosae from AOM-treated F344 rats.
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Affiliation(s)
- Jennifer Roberts
- Regulatory Toxicology Research Division, Bureau of Chemical Safety, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Rekha Mehta
- Regulatory Toxicology Research Division, Bureau of Chemical Safety, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Ivan Curran
- Regulatory Toxicology Research Division, Bureau of Chemical Safety, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Jayadev Raju
- Regulatory Toxicology Research Division, Bureau of Chemical Safety, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
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DiNatale RG, Gorelick AN, Makarov V, Blum KA, Silagy AW, Freeman B, Chowell D, Marcon J, Mano R, Sanchez A, Attalla K, Weng S, Voss M, Motzer RJ, Russo P, Coleman JA, Reuter VE, Chen YB, Chan TA, Reznik E, Tickoo SK, Hakimi AA. Putative Drivers of Aggressiveness in TCEB1-mutant Renal Cell Carcinoma: An Emerging Entity with Variable Clinical Course. Eur Urol Focus 2019; 7:381-389. [PMID: 31813809 DOI: 10.1016/j.euf.2019.11.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/06/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND TCEB1-mutant renal cell carcinoma (RCC) is a rare variant of RCC with clear-cell features. Owing to its unique morphological and molecular features it has recently been proposed as a separate entity. Initial series suggested an indolent, early-stage phenotype. Here we expand our clinical cohort and describe a more detailed genomic analysis looking for potential drivers of aggressiveness. DESIGN, SETTING, AND PARTICIPANTS We identified five new cases in our institutional sequencing cohort, four of whom were found to have high-stage disease (American Joint Committee on Cancer stage III/IV). Twelve previously reported cases were pooled for comparison purposes (Sato, The Cancer Genome Atlas, TRACERx Renal). OUTCOME MEASURES AND STATISTICAL ANALYSIS We used our previously validated pipeline to analyze somatic mutations and copy number alterations (CNAs) in seven tumor samples with available data and estimated the number of cancer cells bearing each somatic mutation. The oncogenic potential of mutations was assessed using OncoKB and two other algorithms. Mann-Whitney U tests were used to evaluate differences in genomic markers between stage groups. RESULTS AND LIMITATIONS All tumors showed biallelic inactivation of the TCEB1 gene according to a combination of somatic mutation and CNA analyses. Mutations were always found in residues involved in hydrophobic interactions with VHL. We found that high-stage tumors had additional oncogenic mutations (median 1, interquartile range [IQR] 1-1 vs 2, IQR 2-2; median difference 1, 95% confidence interval [CI] 1-1; p= 0.002) and showed whole-genome doubling events. They also seemed to have a higher burden of somatic CNAs (median fraction CNA genome 0.10, IQR 0.10-0.15 vs 0.63, IQR 0.58-0.68), however, this finding did not reach statistical significance (median difference 0.49, 95% CI 0.33-0.63; p=0.052). CONCLUSIONS TCEB1-mutant RCC can show variable behavior ranging from very indolent to aggressive. Specific molecular events leading to high genomic instability seem to be associated with aggressiveness. This study expands the clinical spectrum of TCEB1-mutant RCC. PATIENT SUMMARY We present four cases of aggressive TCEB1-mutant renal cell carcinoma, a rare type of kidney cancer. In-depth analysis of the genomes of these tumors revealed certain abnormalities that might explain this aggressive behavior.
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Affiliation(s)
- Renzo G DiNatale
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander N Gorelick
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vladimir Makarov
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kyle A Blum
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew W Silagy
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin Freeman
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diego Chowell
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julian Marcon
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roy Mano
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Sanchez
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kyrollis Attalla
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stanley Weng
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin Voss
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert J Motzer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul Russo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan A Coleman
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Victor E Reuter
- Pathology Department, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying-Bei Chen
- Pathology Department, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Satish K Tickoo
- Pathology Department, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - A Ari Hakimi
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Hershlag A, Peyser A, Bristow SL, Puig O, Pollock A, Niknazar M, Mills AA. The potential impact of tumor suppressor genes on human gametogenesis: a case-control study. J Assist Reprod Genet 2020; 37:341-6. [PMID: 31792669 DOI: 10.1007/s10815-019-01634-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/04/2019] [Indexed: 10/25/2022] Open
Abstract
PURPOSE To study the incidence of tumor suppressor gene (TSG) mutations in men and women with impaired gametogenesis. METHODS Gene association analyses were performed on blood samples in two distinct patient populations: males with idiopathic male infertility and females with unexplained diminished ovarian reserve (DOR). The male study group consisted of men with idiopathic azoospermia, oligozoospermia, asthenozoospermia, or teratozoospermia. Age-matched controls were men with normal semen analyses. The female study group consisted of women with unexplained DOR with anti-Müllerian hormone levels ≤ 1.1 ng/mL. Controls were age-matched women with normal ovarian reserve (> 1.1 ng/mL). RESULTS Fifty-seven male cases (mean age = 38.4; mean sperm count = 15.7 ± 12.1; mean motility = 38.2 ± 24.7) and 37 age-matched controls (mean age = 38.0; mean sperm count = 89.6 ± 37.5; mean motility = 56.2 ± 14.3) were compared. Variants observed in CHD5 were found to be enriched in the study group (p = 0.000107). The incidence of CHD5 mutation c.*3198_*3199insT in the 3'UTR (rs538186680) was significantly higher in cases compared to controls (p = 0.0255). 72 DOR cases (mean age = 38.7; mean AMH = 0.5 ± 0.3; mean FSH = 11.7 ± 12.5) and 48 age-matched controls (mean age = 37.6; mean AMH = 4.1 ± 3.0; mean FSH = 7.1 ± 2.2) were compared. Mutations in CHD5 (c.-140A>C), RB1 (c.1422-18delT, rs70651121), and TP53 (c.376-161A>G, rs75821853) were found at significantly higher frequencies in DOR cases compared to controls (p ≤ 0.05). In addition, 363 variants detected in the DOR patients were not present in the control group. CONCLUSION Unexplained impaired gametogenesis in both males and females may be associated with genetic variation in TSGs. TSGs, which play cardinal roles in cell-cycle control, might also be critical for normal spermatogenesis and oogenesis. If validated in larger prospective studies, it is possible that TSGs provide an etiological basis for some patients with impaired gametogenesis.
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Fatma Karaman E, Caglayan M, Sancar-Bas S, Ozal-Coskun C, Arda-Pirincci P, Ozden S. Global and region-specific post-transcriptional and post-translational modifications of bisphenol A in human prostate cancer cells. Environ Pollut 2019; 255:113318. [PMID: 31610501 DOI: 10.1016/j.envpol.2019.113318] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/10/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
Bisphenol A (BPA), as synthetic monomer used in the production of polycarbonate plastic and epoxy resins, has endocrine disruptor properties and high risk on human health. Epigenetic alterations could act an important role in BPA-induced toxicity, but its mechanism has not been fully understood. We investigated the effects of BPA on gene expression of chromatin modifying enzymes, promoter methylation of tumor suppressor genes and histone modifications in human prostate carcinoma cells (PC-3). IC50 value of BPA was determined as 217 and 190 μM in PC-3 cells by MTT and NRU tests, respectively. We revealed an increase in global levels of 5-methylcytocine and 5-hydroxymethylcytocine at 10 μM of BPA for 96 h. We observed a significant increase on promoter DNA methylation and decrease on gene expression of p16 gene while no change was observed for Cyclin D2 and Rassf1. Significant changes were observed in global histone modifications (H3K9ac, H3K9me3, H3K27me3, and H4K20me3) in PC-3 cells. According to these results, we investigated wide-range epigenetic modifications using PCR arrays. After 96 h BPA exposure, chromatin modifying enzymes including KDM5B and NSD1 were significantly downregulated. Also, promoter methylation of tumor suppressor genes including BCR, GSTP1, LOX, MGMT, NEUROG1, PDLIM4, PTGS2, PYCARD, TIMP3, TSC2 and ZMYDN10 altered significantly. ChIP results showed that H3K9ac, H3K9me3 and H3K27me3 modifications on p16 gene showed significant increases after 1 and 10 μM of BPA exposure. In conclusion, epigenetic signatures such as DNA methylation and histone modifications could be proposed as molecular biomarkers of BPA-induced prostate cancer progression.
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Affiliation(s)
- Ecem Fatma Karaman
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, 34116, Beyazit, Istanbul, Turkey
| | - Mine Caglayan
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, 34116, Beyazit, Istanbul, Turkey
| | - Serap Sancar-Bas
- Department of Biology, Faculty of Science, Istanbul University, 34134, Vezneciler, Istanbul, Turkey
| | - Cansu Ozal-Coskun
- Section of Biology, Institute of Graduate Studies in Sciences, Istanbul University, 34134, Vezneciler, Istanbul, Turkey
| | - Pelin Arda-Pirincci
- Department of Biology, Faculty of Science, Istanbul University, 34134, Vezneciler, Istanbul, Turkey
| | - Sibel Ozden
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, 34116, Beyazit, Istanbul, Turkey.
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S SK, Swamy SN, Premalatha CS, Pallavi VR, Gawari R. Aberrant Promoter Hypermethylation of RASSF1a and BRCA1 in Circulating Cell-Free Tumor DNA Serves as a Biomarker of Ovarian Carcinoma. Asian Pac J Cancer Prev 2019; 20:3001-3005. [PMID: 31653147 PMCID: PMC6982682 DOI: 10.31557/apjcp.2019.20.10.3001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Indexed: 12/04/2022] Open
Abstract
Objective: Ovarian cancer is one of the leading causes of cancer deaths in women. Ovarian cancer is diagnosed at the late stages and generally relapses within 12-14 months of cytoreductive surgery. This is attributed to lack of precise molecular detection methodologies to detect and track the disease. Epigenetic alteration such as aberrant promoter hypermethylation is an important early event that occurs during cancer development and progression. This study focuses on development of a minimally invasive methylation marker that could be used for detection and prognosis of ovarian cancer patients. Methods: Aberrant promoter hypermethylation of RASSF1a and BRCA1 was assessed in circulating DNA of 72 EOC patients using methylation-specific PCR. The findings were correlated with various clinicopathological parameters. Statistical analysis was done using the Fisher exact test and chi-square test. Results: The aberrant methylation patterns of RASSF1a and BRCA1 was identified to be present in the cancerous samples. A total of 31.9 % and 56.9% methylation was observed for RASSF1a and BRCA1 respectively. A striking 50% methylation of BRCA1 was identified in the benign sample cohort, which marks the significance of assessing the hypermethylation pattern to detect cancer at its early stages. Methylation of the two tumor suppressor genes was evident across various stages and grades of ovarian tumors suggesting that this could also help as a prognostic marker. Conclusion: The results of the current study hold significance since the hypermethylation patterns can be identified in the cell-free circulating tumor DNA from a small volume of blood plasma and is a simple and minimally-invasive method. Assessment of hypermethylation patterns of a panel of TSG along with the existing screening markers could aid in better diagnosis and management of the disease. It could also aid in designing specifically tailored treatment strategies to fight the disease.
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Affiliation(s)
- Sandeep Kumar S
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - Shalini N Swamy
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - C S Premalatha
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - V R Pallavi
- Department of Gynaeconcology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - Ramesh Gawari
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
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Khatami F, Larijani B, Heshmat R, Nasiri S, Saffar H, Shafiee G, Mossafa A, Tavangar SM. Promoter Methylation of Four Tumor Suppressor Genes in Human Papillary Thyroid Carcinoma. Iran J Pathol 2019; 14:290-298. [PMID: 31754358 PMCID: PMC6824767 DOI: 10.30699/ijp.2019.94401.1922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 07/27/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND & OBJECTIVE Papillary thyroid cancer (PTC) is considered to be the most common type of thyroid malignancies. Epigenetic alteration, in which the chromatin conformation and gene expression change without changing the sequence of DNA, can occur in some tumor suppressor genes and oncogenes. Methylation is the most common type of epigenetic alterations that can be an excellent indicator of PTC invasive behavior. METHODS In this research, we determined the promoter methylation status of four tumor suppressor genes (SLC5A8, RASSF1, MGMT, and DNMT1) and compared the results of 55 PTC cases with 40 goiter patients. For methylation, we used the methylation-sensitive high resolution melting (MS-HRM) assay technique. The resulting graphs of each run were compared with those of 0%, 50%, and 100% methylated controls. RESULTS Our data showed that the promoter methylation of SLC5A8, Ras association domain family member 1(RASSF1), and MGMT were significantly different between PTC tissue and goiter with P-value less than 0.05. The most significant differences were observed in RASSF1; 77.2% of hyper-methylated PTC patients versus 15.6% hyper-methylated goiter samples (P<0.001). CONCLUSION RASSF1 promoter methylation can be a PTC genetic marker. RASSF1 promoter methylation is under the impact of the methyltransferase genes (DNMT1 and MGMT), protein expression, and promoter methylation.
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Affiliation(s)
- Fatemeh Khatami
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramin Heshmat
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirzad Nasiri
- Department of Surgery, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
| | - Hiva Saffar
- Department of Pathology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Gita Shafiee
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Azam Mossafa
- Department of Surgery, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
| | - Seyed Mohammad Tavangar
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Department of Pathology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Mollashahi B, Aghamaleki FS, Movafagh A. The Roles of miRNAs in Medulloblastoma: A Systematic Review. J Cancer Prev 2019; 24:79-90. [PMID: 31360688 PMCID: PMC6619858 DOI: 10.15430/jcp.2019.24.2.79] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/27/2019] [Accepted: 05/13/2019] [Indexed: 01/10/2023] Open
Abstract
Medulloblastoma is considered one of the most threatening malignant brain tumors with an extremely high mortality rate in children. In the medulloblastoma, there are several genes and mutations found to work in an unregulated manner that works together to push the cells into a cancerous state. With the discovery of non-coding RNAs such as microRNAs (miRNAs), it has been shown that a different layer of gene regulations may be disrupted which would cause cancer. This fact led scientists to put their focus on the role of miRNAs in cancer. A mature miRNA contains a seed sequence which gives the miRNA to identify and attach to the interest mRNA; this attachment may lead degradation of mRNA or suppress of translation of the mRNA. The expression of miRNAs in medulloblastoma shows that some of these non-coding RNAs are overexpressed (OncomiRs) which help cells to proliferate and keep their stemness features. On the other hand, there are other forms of these miRNAs which normally inhibit cell proliferation and promote cell differentiation (tumor suppressor). These are down-regulated during cancer progression. In this systematic review, we attempted to gather several important studies on miRNAs’ role in medulloblastoma tumors and the importance of these non-coding RNAs in the future study of cancer.
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Affiliation(s)
- Behrouz Mollashahi
- Department of Cellular-Molecular Biology, Faculty of Biological Sciences and Technologies, Shahid Beheshti University, Tehran, Iran
| | - Fateme Shaabanpour Aghamaleki
- Department of Cellular-Molecular Biology, Faculty of Biological Sciences and Technologies, Shahid Beheshti University, Tehran, Iran
| | - Abolfazl Movafagh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Bouras E, Karakioulaki M, Bougioukas KI, Aivaliotis M, Tzimagiorgis G, Chourdakis M. Gene promoter methylation and cancer: An umbrella review. Gene 2019; 710:333-340. [PMID: 31202904 DOI: 10.1016/j.gene.2019.06.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 12/11/2022]
Abstract
Gene promoter methylation is a common epigenetic event, taking place in the early phase of tumorigenesis, which has a great potential as a diagnostic and prognostic cancer biomarker. In this umbrella review, we provide an overview on the association between gene-promoter methylation of protein-coding genes and cancer risk based on currently available meta-analyses data on gene promoter methylation. We searched MEDLINE via PubMed and the Cochrane Database of Systematic Reviews for meta-analyses that examine the association between gene-promoter methylation and cancer, published until January 2019 in English. We used AMSTAR to assess the quality of the included studies and applied a set of pre-specified criteria to evaluate the magnitude of each association. We provide a comprehensive overview of 80 unique combinations between 22 different genes and 18 cancer outcomes, all of which indicated a positive association between promoter hypermethylation and cancer. In total, the 70 meta-analyses produced significant results under a random-effects model with odds ratios that ranged from 1.94 to 26.60, with the summary effect being in favor of the unmethylated group in all cases. Three of the strong evidence associations involve RASSF1 methylation on bladder cancer risk (OR = 18.46; 95% CI: 12.69-26.85; I2 = 0%), MGMT methylation on NSCLC (OR = 4.25; 95% CI: 2.83-6.38; I2 = 22.4%) and RARB methylation on prostate cancer (OR = 6.87; 95% CI: 4.68-10.08; I2 = 0%). Meta-analyses showed a moderate quality, AMSTAR score ranging from 4 to 9 (Mdn = 8; IQR: 7.0 to 8.0). As primary studies and meta-analyses on the subject accumulate, more genetic loci may be found to be highly associated with specific cancer types and hence the biomarker sets will become wider.
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Affiliation(s)
- Emmanouil Bouras
- Laboratory of Hygiene, Social & Preventive Medicine and Medical Statistics, Department of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Greece
| | - Meropi Karakioulaki
- Laboratory of Hygiene, Social & Preventive Medicine and Medical Statistics, Department of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Greece
| | - Konstantinos I Bougioukas
- Laboratory of Hygiene, Social & Preventive Medicine and Medical Statistics, Department of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Greece
| | - Michalis Aivaliotis
- Laboratory of Biochemistry, Department of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece; Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece; Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Georgios Tzimagiorgis
- Laboratory of Biochemistry, Department of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Greece; Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece; Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Michael Chourdakis
- Laboratory of Hygiene, Social & Preventive Medicine and Medical Statistics, Department of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Greece.
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Deng W, Lu YF. Methylation of tumor suppressor genes and risk factors of colorectal cancer. Shijie Huaren Xiaohua Zazhi 2018; 26:2088-2095. [DOI: 10.11569/wcjd.v26.i36.2088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although the diagnostic methods and treatment options are continuously optimized, the incidence and mortality of colorectal cancer (CRC) are still rising. Therefore, "preventive treatment of disease" is the key to solving this problem. In recent years, hypermethylation of promoter CpG islands (CGIs) in tumor suppressor genes has been a hot research topic because it is reversible and early events in the development of CRC, and affects drug resistance, disease treatment, and patient prognosis. CRC risk factors such as poor dietary choice, lack of physical activity, excessive drinking, and unhealthy weight can regulate promoter CGI hypermethylation, which will help develop new methylation-related cancer prevention strategies. This article mainly introduces the significance and regulatory mechanism of methylation of tumor suppressor genes and its relationship with risk factors in CRC.
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Affiliation(s)
- Wei Deng
- Department of Gastroenterology, the Affiliated Hospital of Qinghai University, Xining 810000, Qinghai Province, China
| | - Yong-Fu Lu
- Department of Gastroenterology, the Affiliated Hospital of Qinghai University, Xining 810000, Qinghai Province, China
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50
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Subat S, Mogushi K, Yasen M, Kohda T, Ishikawa Y, Tanaka H. Identification of genes and pathways, including the CXCL2 axis, altered by DNA methylation in hepatocellular carcinoma. J Cancer Res Clin Oncol 2018; 145:675-684. [PMID: 30564899 DOI: 10.1007/s00432-018-2824-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/12/2018] [Indexed: 12/12/2022]
Abstract
PURPOSE Recent genetic studies have suggested that tumor suppressor genes are often silenced during carcinogenesis via epigenetic modification caused by methylation of promoter CpG islands. Here, we characterized genes inactivated by DNA methylation in human hepatocellular carcinoma (HCC) to identify the genes and pathways involved in DNA methylation in hepatocellular carcinoma. METHODS Eight HCC-derived cell lines were treated with a DNA demethylating agent, 5-aza-2'-deoxycytidine. Additionally, 100 pairs of primary HCC and adjacent non-cancerous tissues as well as 15 normal liver tissues were analyzed by comprehensive gene expression analysis using microarrays. Moreover, gene set enrichment analysis identified the major molecular pathways associated with DNA methylation. Validation of gene expression and DNA methylation status was performed by real-time PCR after bisulfite modification. RESULTS We showed that CXCL2, an immune-related chemokine, expression was significantly downregulated in tumor tissues and also significantly upregulated by DAC treatment in cell lines. Furthermore, we observed a statistically significant difference in methylation status between normal liver tissues and tumor tissues (P < 0.05). In addition, tumors with higher CXCL2 expression included significantly more numbers of multiple tumors than the lower expression group. CONCLUSIONS We identified CXCL2, an immune-related chemokine, decreased in hepatocellular carcinoma and the regulation mechanism may be controlled by methylation. Further studies should be warranted to examine if and to what extent the gene is actually suppressed by methylation and if there is a possibility that the CXCL2 axis plays a role for diagnosis and treatment of hepatocellular carcinoma.
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Affiliation(s)
- Sophia Subat
- Department of Systems Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Epigenetics, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
- Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ward, Tokyo, 135-8550, Japan
| | - Kaoru Mogushi
- Department of Systems Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Mahmut Yasen
- Department of Systems Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
- Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ward, Tokyo, 135-8550, Japan
- Department of Surgery, Xinjiang Medical University Affiliated Tumor Hospital, Urumqi, Xinjiang Uyghur Autonomous Region, China
| | - Takashi Kohda
- Department of Epigenetics, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuichi Ishikawa
- Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ward, Tokyo, 135-8550, Japan.
| | - Hiroshi Tanaka
- Department of Systems Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
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