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Sarkar P, Malik S, Banerjee A, Datta C, Pal DK, Ghosh A, Saha A. Differential Microbial Signature Associated With Benign Prostatic Hyperplasia and Prostate Cancer. Front Cell Infect Microbiol 2022; 12:894777. [PMID: 35865814 PMCID: PMC9294280 DOI: 10.3389/fcimb.2022.894777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Apart from other risk factors, chronic inflammation is also associated with the onset of Prostate Cancer (PCa), wherein pathogen infection and tissue microbiome dysbiosis are known to play a major role in both inflammatory response and cancer development. However, except for a few studies, the link between microbes and PCa remained poorly understood. To explore the potential microbiome signature associated with PCa in Indian patients, we investigated differential compositions of commensal bacteria among patients with benign prostatic hyperplasia (BPH) and PCa using 16S rRNA amplicon sequencing followed by qPCR analyses using two distinct primer sets. Using two independent cohorts, we show that Prevotella copri, Cupriavidus campinensis, and Propionibacterium acnes represent the three most abundant bacteria in diseased prostate lesions. LEfSe analyses identified that while Cupriavidus taiwanensis and Methylobacterium organophilum are distinctly elevated in PCa samples, Kocuria palustris and Cellvibrio mixtus are significantly enriched in BPH samples. Furthermore, we identify that a number of human tumor viruses, including Epstein-Barr virus (EBV) and hepatitis B virus (HBV), along with two high-risk human papillomaviruses - HPV-16 and HPV-18, are significantly associated with the PCa development and strongly correlated with PCa bacterial signature. The study may thus offer to develop a framework for exploiting this microbial signature for early diagnosis and prognosis of PCa development.
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Affiliation(s)
- Purandar Sarkar
- School of Biotechnology, Presidency University, New Town, Kolkata, India
| | - Samaresh Malik
- School of Biotechnology, Presidency University, New Town, Kolkata, India
| | - Anwesha Banerjee
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Chhanda Datta
- Department of Pathology, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Dilip Kumar Pal
- Department of Urology, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Amlan Ghosh
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Abhik Saha
- School of Biotechnology, Presidency University, New Town, Kolkata, India
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2
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Contreras-Romero C, Pérez-Yépez EA, Martinez-Gutierrez AD, Campos-Parra A, Zentella-Dehesa A, Jacobo-Herrera N, López-Camarillo C, Corredor-Alonso G, Martínez-Coronel J, Rodríguez-Dorantes M, de León DC, Pérez-Plasencia C. Gene Promoter-Methylation Signature as Biomarker to Predict Cisplatin-Radiotherapy Sensitivity in Locally Advanced Cervical Cancer. Front Oncol 2022; 12:773438. [PMID: 35359376 PMCID: PMC8963763 DOI: 10.3389/fonc.2022.773438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
Despite efforts to promote health policies focused on screening and early detection, cervical cancer continues to be one of the leading causes of mortality in women; in 2020, estimated 30,000 deaths in Latin America were reported for this type of tumor. While the therapies used to treat cervical cancer have excellent results in tumors identified in early stages, those women who are diagnosed in locally advanced and advanced stages show survival rates at 5 years of <50%. Molecular patterns associated with clinical response have been studied in patients who present resistance to treatment; none of them have reached clinical practice. It is therefore necessary to continue analyzing molecular patterns that allow us to identify patients at risk of developing resistance to conventional therapy. In this study, we analyzed the global methylation profile of 22 patients diagnosed with locally advanced cervical cancer and validated the genomic results in an independent cohort of 70 patients. We showed that BRD9 promoter region methylation and CTU1 demethylation were associated with a higher overall survival (p = 0.06) and progression-free survival (p = 0.0001), whereas DOCK8 demethylation was associated with therapy-resistant patients and a lower overall survival and progression-free survival (p = 0.025 and p = 0.0001, respectively). Our results suggest that methylation of promoter regions in specific genes may provide molecular markers associated with response to treatment in cancer; further investigation is needed.
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Affiliation(s)
| | - Eloy-Andrés Pérez-Yépez
- Laboratorio de Genómica, Insituto Nacional de Cancerología, Ciudad de México, Mexico.,Cátedra CONACYT, Dirección de cátedras, Consejo Nacional de Ciencia y Tecnología (CONACYT), Mexico City, Mexico
| | | | - Alma Campos-Parra
- Laboratorio de Genómica, Insituto Nacional de Cancerología, Ciudad de México, Mexico
| | - Alejandro Zentella-Dehesa
- Programa Institucional de Cáncer de Mama, Dpto Medicina Genómica y Toxicología Ambiental, IIB, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Nadia Jacobo-Herrera
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Ciudad de México, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Mexico City, Mexico
| | | | | | | | - David Cantu de León
- Laboratorio de Genómica, Insituto Nacional de Cancerología, Ciudad de México, Mexico
| | - Carlos Pérez-Plasencia
- Laboratorio de Genómica, Insituto Nacional de Cancerología, Ciudad de México, Mexico.,Laboratorio de Genómica, Unidad de Biomedicina, FES-Iztacala, UNAM, Tlalnepantla, Mexico
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3
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Strelnikov VV, Kuznetsova EB, Tanas AS, Rudenko VV, Kalinkin AI, Poddubskaya EV, Kekeeva TV, Chesnokova GG, Trotsenko ID, Larin SS, Kutsev SI, Zaletaev DV, Nemtsova MV, Simonova OA. Abnormal promoter DNA hypermethylation of the integrin, nidogen, and dystroglycan genes in breast cancer. Sci Rep 2021; 11:2264. [PMID: 33500458 PMCID: PMC7838398 DOI: 10.1038/s41598-021-81851-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/12/2021] [Indexed: 12/18/2022] Open
Abstract
Cell transmembrane receptors and extracellular matrix components play a pivotal role in regulating cell activity and providing for the concerted integration of cells in the tissue structures. We have assessed DNA methylation in the promoter regions of eight integrin genes, two nidogen genes, and the dystroglycan gene in normal breast tissues and breast carcinomas (BC). The protein products of these genes interact with the basement membrane proteins LAMA1, LAMA2, and LAMB1; abnormal hypermethylation of the LAMA1, LAMA2, and LAMB1 promoters in BC has been described in our previous publications. In the present study, the frequencies of abnormal promoter hypermethylation in BC were 13% for ITGA1, 31% for ITGA4, 4% for ITGA7, 39% for ITGA9, 38% for NID1, and 41% for NID2. ITGA2, ITGA3, ITGA6, ITGB1, and DAG1 promoters were nonmethylated in normal and BC samples. ITGA4, ITGA9, and NID1 promoter hypermethylation was associated with the HER2 positive tumors, and promoter hypermethylation of ITGA1, ITGA9, NID1 and NID2 was associated with a genome-wide CpG island hypermethylated BC subtype. Given that ITGA4 is not expressed in normal breast, one might suggest that its abnormal promoter hypermethylation in cancer is non-functional and is thus merely a passenger epimutation. Yet, this assumption is not supported by our finding that it is not associated with a hypermethylated BC subtype. ITGA4 acquires expression in a subset of breast carcinomas, and methylation of its promoter may be preventive against expression in some tumors. Strong association of abnormal ITGA4 hypermethylation with the HER2 positive tumors (p = 0.0025) suggests that simultaneous presence of both HER2 and integrin α4 receptors is not beneficial for tumor cells. This may imply HER2 and integrin α4 signaling pathways interactions that are yet to be discovered.
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Affiliation(s)
- Vladimir V Strelnikov
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia.
| | - Ekaterina B Kuznetsova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya St 8-2, 119991, Moscow, Russia
| | - Alexander S Tanas
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Viktoria V Rudenko
- Molecular Genetic Diagnostics Laboratory 2, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Alexey I Kalinkin
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Elena V Poddubskaya
- Clinic of Personalized Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya St 8-2, 119991, Moscow, Russia.,VitaMed LLC, Seslavinskaya St 10, 121309, Moscow, Russia
| | - Tatiana V Kekeeva
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Galina G Chesnokova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Ivan D Trotsenko
- Institute of Medicine, Peoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya St 6, 117198, Moscow, Russia
| | - Sergey S Larin
- Molecular Immunology Laboratory, Federal Scientific Clinical Centre of Pediatric Hematology Oncology Immunology Named After Dmitry Rogachev, Samory Mashela St 1, 117997, Moscow, Russia.,Gene Therapy Laboratory, Institute of Gene Biology, Vavilova St 34/5, 119334, Moscow, Russia
| | - Sergey I Kutsev
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
| | - Dmitry V Zaletaev
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya St 8-2, 119991, Moscow, Russia
| | - Marina V Nemtsova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya St 8-2, 119991, Moscow, Russia
| | - Olga A Simonova
- Molecular Genetic Diagnostics Laboratory 2, Research Centre for Medical Genetics, Moskvorechie St 1, 115522, Moscow, Russia
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Tumor suppressor properties of the small C-terminal domain phosphatases in non-small cell lung cancer. Biosci Rep 2020; 39:221348. [PMID: 31774910 PMCID: PMC6911153 DOI: 10.1042/bsr20193094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/17/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023] Open
Abstract
Non-Small Cell Lung Cancer (NSCLC) is responsible for the majority of deaths caused by cancer. Small C-terminal domain (CTD) phosphatases (SCP), CTDSP1, CTDSP2 and CTDSPL (CTDSPs) belong to SCP/CTDSP subfamily and are involved in many vital cellular processes and tumorigenesis. High similarity of their structures suggests similar functions. However their role in NSCLC remains insufficiently understood. For the first time we revealed the suppressor function of CTDSPs leading to a significant growth slowdown and senescence of A549 lung adenocarcinoma (ADC) cells in vitro. Their tumor-suppressive activity can be realized through increasing the proportion of the active form of Rb protein dephosphorylated at Ser807/811, Ser780, and Ser795 (P<0.05) thereby negatively regulating cancer cell proliferation. Moreover, we observed that a frequent (84%, 39/46) and highly concordant (Spearman's rank correlation coefficient (rs) = 0.53-0.62, P≤0.01) down-regulation of CTDSPs and RB1 is characteristic of primary NSCLC samples (n=46). A clear difference in their mRNA levels was found between lung ADCs with and without lymph node metastases, but not in squamous cell carcinomas (SCCs) (P≤0.05). Based on The Cancer Genome Atlas (TCGA) data and the results obtained using the CrossHub tool, we suggest that the well-known oncogenic cluster miR-96/182/183 could be a common expression regulator of CTDSPs. Indeed, according to our qPCR, the expression of CTDSPs negatively correlates with these miRs, but positively correlates with their intronic miR-26a/b. Our results reflect functional association of CTDSP1, CTDSP2, and CTDSPL, expand knowledge about their suppressor properties through Rb dephosphorylation and provide new insights into the regulation of NSCLC growth.
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Dasgupta H, Islam S, Alam N, Roy A, Roychoudhury S, Panda CK. Hypomethylation of mismatch repair genes MLH1 and MSH2 is associated with chemotolerance of breast carcinoma: Clinical significance. J Surg Oncol 2018; 119:88-100. [PMID: 30481381 DOI: 10.1002/jso.25304] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/31/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND OBJECTIVES The aim of the study was to understand the importance of mismatch repair genes MLH1 and MSH2 in chemotolerance and prognosis of breast carcinoma (BC). METHODS First, the alterations (deletion/methylation/expression) of MLH1 and MSH2 were analyzed in 45 neoadjuvant chemotherapy (NACT)-treated and 133 pretherapeutic BC samples. The chemotolerant BC cells were characterized by treating two BC cell lines MCF-7 and MDA MB 231 with two anthracycline antitumor antibiotics, doxorubicin and nogalamycin. RESULTS The deletion frequencies were 32% to 38% in MLH1/MSH2 genes and promoter methylation frequencies were 49% to 62% in MLH1 and 41% to 51% in MSH2 in both NACT-treated and pretherapeutic samples. The overall alteration of MLH1 and MSH2 was 58% to 71% in the samples. Reduced messenger RNA (mRNA) and protein expression were found in both the genes and it showed concordance with the molecular alterations. NACT-treated patients showed better prognosis. The chemotherapeutic drug induced increased mRNA/protein expression of the genes in BC cell lines was due to their promoter hypomethylation, as analyzed by quantitative methylation assay. This phenomenon was also evident in NACT-treated BC samples. CONCLUSION MLH1/MSH2 genes play a critical role in the development of BC. Hypomethylation of MLH1/MSH2 genes might be important in chemotolerance of the disease.
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Affiliation(s)
- Hemantika Dasgupta
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
| | - Saimul Islam
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
| | - Neyaz Alam
- Department of Surgical Oncology, Chittaranjan National Cancer Institute, Kolkata, India
| | - Anup Roy
- Department of Pathology, Nil Ratan Sircar Medical College and Hospital, Kolkata, India
| | - Susanta Roychoudhury
- Research Divison, Saroj Gupta Cancer Center and Research Institute, Kolkata, India
| | - Chinmay Kumar Panda
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
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6
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Pal D, Sur S, Roy R, Mandal S, Kumar Panda C. Epigallocatechin gallate in combination with eugenol or amarogentin shows synergistic chemotherapeutic potential in cervical cancer cell line. J Cell Physiol 2018; 234:825-836. [PMID: 30078217 DOI: 10.1002/jcp.26900] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/13/2018] [Indexed: 01/07/2023]
Abstract
In this study, antitumor activity of epigallocatechin gallate (EGCG; major component of green tea polyphenol), eugenol (active component of clove), and amarogentin (active component of chirata plant) either alone or in combination were evaluated in Hela cell line. It was evident that EGCG with eugenol-amrogentin could highly inhibit the cellular proliferation and colony formation than individual treatments. Induction of apoptosis was also higher after treatment with EGCG in combination with eugenol-amrogentin than individual compound treatments. The antiproliferative effect of these compounds was due to downregulation of cyclinD1 and upregulation of cell cycle inhibitors LIMD1, RBSP3, and p16 at G1/S phase of cell cycle. Treatment of these compounds could induce promoter hypomethylation of LimD1 and P16 genes as a result of reduced expression of DNA methyltransferase 1 (DNMT1). Thus, our study indicated the better chemotherapeutic effect of EGCG in combination with eugenol-amarogentin in Hela cell line. The chemotherapeutic effect might be due to the epigenetic modification particularly DNA hypomethylation through downregulation of DNMT1.
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Affiliation(s)
- Debolina Pal
- Department of Oncogene Regulation, Chittarangan National Cancer Institute, Kolkata, India
| | - Subhayan Sur
- Department of Oncogene Regulation, Chittarangan National Cancer Institute, Kolkata, India
| | - Rituparna Roy
- Department of Oncogene Regulation, Chittarangan National Cancer Institute, Kolkata, India
| | - Suvra Mandal
- Department of Chemistry, National Research Institute for Ayurvedic Drug Development, Kolkata, India
| | - Chinmay Kumar Panda
- Department of Oncogene Regulation, Chittarangan National Cancer Institute, Kolkata, India
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Control of PD-L1 expression by miR-140/142/340/383 and oncogenic activation of the OCT4-miR-18a pathway in cervical cancer. Oncogene 2018; 37:5257-5268. [PMID: 29855617 PMCID: PMC6160397 DOI: 10.1038/s41388-018-0347-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 03/20/2018] [Accepted: 05/01/2018] [Indexed: 12/16/2022]
Abstract
PD-L1, a key inhibitory immune receptor, has crucial functions in cancer immune evasion, but whether PD-L1 promotes the malignant properties of cervical cancer (CC) cells and the mechanism by which PD-L1 is regulated in CC remains unclear. We report that PD-L1 is overexpressed in CC, and shRNA-mediated PD-L1 depletion suppresses the proliferation, invasion, and tumorigenesis of CC cells. Loss of miR-140/142/340/383 contributes to PD-L1 upregulation. miR-18a enhances PD-L1 levels by targeting PTEN, WNK2 (ERK1/2 pathway inhibitor), and SOX6 (Wnt/β-catenin pathway inhibitor and p53 pathway activator) to activate the PI3K/AKT, MEK/ERK, and Wnt/β-catenin pathways and inhibit the p53 pathway, and miR-18a also directly suppresses the expression of the tumor suppressors BTG3 and RBSP3 (CTDSPL). miR-18a overexpression in CC cells is triggered by OCT4 overexpression. Our data implicate PD-L1 as a novel oncoprotein and indicate that miR-140/142/340/383 and miR-18a are key upstream regulators of PD-L1 and potential targets for CC treatment.
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Sarkar S, Alam N, Mandal SS, Chatterjee K, Ghosh S, Roychoudhury S, Panda CK. Differential transmission of the molecular signature of RBSP3, LIMD1 and CDC25A in basal/ parabasal versus spinous of normal epithelium during head and neck tumorigenesis: A mechanistic study. PLoS One 2018; 13:e0195937. [PMID: 29672635 PMCID: PMC5909606 DOI: 10.1371/journal.pone.0195937] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/03/2018] [Indexed: 12/16/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a global disease and mortality burden, necessitating the elucidation of its molecular progression for effective disease management. The study aims to understand the molecular profile of three candidate cell cycle regulatory genes, RBSP3, LIMD1 and CDC25A in the basal/ parabasal versus spinous layer of normal oral epithelium and during head and neck tumorigenesis. Immunohistochemical expression and promoter methylation was used to determine the molecular signature in normal oral epithelium. The mechanism of alteration transmission of this profile during tumorigenesis was then explored through additional deletion and mutation in HPV/ tobacco etiological groups, followed byclinico-pathological correlation. In basal/parabasal layer, the molecular signature of the genes was low protein expression/ high promoter methylation of RBSP3, high expression/ low methylation of LIMD1 and high expression of CDC25A. Dysplastic epithelium maintained the signature of RBSP3 through high methylation/ additional deletion with loss of the signatures of LIMD1 and CDC25A via deletion/ additional methylation. Similarly, maintenance and / or loss of signature in invasive tumors was by recurrent deletion/ methylation. Thus, differential patterns of alteration of the genes might be pre-requisite for the development of dysplastic and invasive lesions. Etiological factors played a key role in promoting genetic alterations and determining prognosis. Tobacco negative HNSCC patients had significantly lower alterations of LIMD1 and CDC25A, along with better survival among tobacco negative/ HPV positive patients. Our data suggests the necessity for perturbation of normal molecular profile of RBSP3, LIMD1 and CDC25A in conjunction with etiological factors for head and neck tumorigenesis, implying their diagnostic and prognostic significance.
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Affiliation(s)
- Shreya Sarkar
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
| | - Neyaz Alam
- Department of Surgical Oncology, Chittaranjan National Cancer Institute, Kolkata, India
| | - Syam Sundar Mandal
- Department of Epidemiology and Biostatistics, Chittaranjan National Cancer Institute, Kolkata, India
| | - Kabita Chatterjee
- Department of Oral and Maxillofacial Pathology, Buddha Institute of Dental Sciences and Hospital, Patna, India
| | - Supratim Ghosh
- Department of Oral and Maxillofacial Pathology, Burdwan Dental College and Hospital, Burdwan, India
| | - Susanta Roychoudhury
- Basic Research, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Chinmay Kumar Panda
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
- * E-mail:
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Skrypkina I, Tsyba L, Onyshchenko K, Morderer D, Kashparova O, Nikolaienko O, Panasenko G, Vozianov S, Romanenko A, Rynditch A. Concentration and Methylation of Cell-Free DNA from Blood Plasma as Diagnostic Markers of Renal Cancer. DISEASE MARKERS 2016; 2016:3693096. [PMID: 27725787 PMCID: PMC5048037 DOI: 10.1155/2016/3693096] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 12/13/2022]
Abstract
The critical point for successful treatment of cancer is diagnosis at early stages of tumor development. Cancer cell-specific methylated DNA has been found in the blood of cancer patients, indicating that cell-free DNA (cfDNA) circulating in the blood is a convenient tumor-associated DNA marker. Therefore methylated cfDNA can be used as a minimally invasive diagnostic marker. We analysed the concentration of plasma cfDNA and methylation of six tumor suppressor genes in samples of 27 patients with renal cancer and 15 healthy donors as controls. The cfDNA concentrations in samples from cancer patients and healthy donors was measured using two different methods, the SYBR Green I fluorescence test and quantitative real-time PCR. Both methods revealed a statistically significant increase of cfDNA concentrations in cancer patients. Hypermethylation on cfDNA was detected for the LRRC3B (74.1%), APC (51.9%), FHIT (55.6%), and RASSF1 (62.9%) genes in patients with renal cancer. Promoter methylation of VHL and ITGA9 genes was not found on cfDNA. Our results confirmed that the cfDNA level and methylation of CpG islands of RASSF1A, FHIT, and APC genes in blood plasma can be used as noninvasive diagnostic markers of cancer.
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Affiliation(s)
- Inessa Skrypkina
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Liudmyla Tsyba
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Kateryna Onyshchenko
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Dmytro Morderer
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Olena Kashparova
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Oleksii Nikolaienko
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Grigory Panasenko
- Department of Molecular Oncogenetics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Sergii Vozianov
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Alina Romanenko
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Alla Rynditch
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
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Association of P16-RBSP3 inactivation with phosphorylated RB1 overexpression in basal-parabasal layers of normal cervix unchanged during CACX development. Biochem J 2016; 473:3221-36. [PMID: 27458253 DOI: 10.1042/bcj20160323] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 07/25/2016] [Indexed: 12/21/2022]
Abstract
To understand the molecular mechanism of RB1 phosphorylation in basal-parabasal layers of normal cervix and during cervical cancer (CACX) development, we analyzed the alterations (expression/methylation/deletion/mutation) of RB1/phosphorylated RB1 (p-RB1) (ser807/811 and ser567) and two RB1 phosphorylation inhibitors, P16 and RBSP3, in disease-free normal cervical epithelium (n = 9), adjacent normal cervical epithelium of tumors (n = 70), cervical intraepithelial neoplasia (CIN; n = 28), CACX (n = 102) samples and two CACX cell lines. Immunohistochemical analysis revealed high/medium expression of RB1/p-RB1 (ser807/811 and ser567) and low expression of P16 and RBSP3 in proliferating basal-parabasal layers of majority of normal cervical epitheliums, irrespective of HPV16 infection. Interestingly, 35-52% samples showed high/medium expression of P16 in basal-parabasal layers of normal and had significant association with deleterious non-synonimous SNPs of P16. Methylation of P16 and RBSP3 in basal-parabasal layers of normal cervix (32 and 62%, respectively) showed concordance with their respective expressions in basal-parabasal layers. The methylation frequency of P16 and RBSP3 in basal-parabasal layers of normal did not change significantly in CIN and CACX. The deletion frequency of P16 and RB1 increased significantly with CACX progression. While, deletion of RBSP3 was high in CIN and comparable during CACX progression. P16 showed scattered and infrequent mutation in CACX. The alteration of P16 and RBSP3 was synergistic and showed association with overexpression of p-RB1 in tumors and associated with poor prognosis of patients. Thus, our data suggest that overexpression of p-RB1 in basal-parabasal layers of normal cervical epithelium was due to methylation/low functional-linked non-synonimous SNPs of P16 and RBSP3. This pattern was maintained during cervical carcinogenesis by additional deletion/mutation.
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11
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Nawaz I, Hu LF, Du ZM, Moumad K, Ignatyev I, Pavlova TV, Kashuba V, Almgren M, Zabarovsky ER, Ernberg I. Integrin α9 gene promoter is hypermethylated and downregulated in nasopharyngeal carcinoma. Oncotarget 2015; 6:31493-507. [PMID: 26372814 PMCID: PMC4741620 DOI: 10.18632/oncotarget.5154] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 08/27/2015] [Indexed: 02/07/2023] Open
Abstract
Epigenetic silencing of tumor suppressor genes (TSGs) by promoter methylation can be an early event in the multi-step process of carcinogenesis. Human chromosome 3 contains clusters of TSGs involved in many cancer types including nasopharyngeal carcinoma (NPC), the most common cancer in Southern China. Among ten candidate TSGs identified in chromosome 3 using NotI microarray, ITGA9 and WNT7A could be validated. 5'-aza-2' deoxycytidine treatment restored the expression of ITGA9 and WNT7A in two NPC cell lines. Immunostaining showed strong expression of these genes in the membrane and cytoplasm of adjacent control nasopharyngeal epithelium cells, while they were weakly expressed in NPC tumor cells. The ITGA9 promoter showed marked differentially methylation between tumor and control tissue, whereas no differentially methylation could be detected for the WNT7A promoter. The expression level of ITGA9 in NPC tumors was downregulated 4.9-fold, compared to the expression in control. ITGA9 methylation was detected by methylation specific PCR (MSP) in 56% of EBV positive NPC-cases with 100% specificity. Taken together, this suggests that ITGA9 might be a TSG in NPC that is involved in tumor cell biology. The possibility of using ITGA9 methylation as a marker for early detection of NPC should further be explored.
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Affiliation(s)
- Imran Nawaz
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology, Faculty of Life Sciences, University of Balochistan, Quetta, Pakistan
| | - Li-Fu Hu
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Zi-Ming Du
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- State Key Laboratory of Oncology in South China, and Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Khalid Moumad
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Oncovirology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Ilya Ignatyev
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tatiana V. Pavlova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vladimir Kashuba
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Malin Almgren
- Department Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Centre for Molecular Medicine, Stockholm, Sweden
| | - Eugene R. Zabarovsky
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical & Experimental Medicine, Division of Cell Biology, Linköping University, Linköping, Sweden
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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Maiti GP, Mondal P, Mukherjee N, Ghosh A, Ghosh S, Dey S, Chakrabarty J, Roy A, Biswas J, Roychoudhury S, Panda CK. Overexpression of EGFR in head and neck squamous cell carcinoma is associated with inactivation of SH3GL2 and CDC25A genes. PLoS One 2013; 8:e63440. [PMID: 23675485 PMCID: PMC3651136 DOI: 10.1371/journal.pone.0063440] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 04/04/2013] [Indexed: 12/03/2022] Open
Abstract
The aim of this study is to understand the mechanism of EGFR overexpression in head and neck squamous cell carcinoma (HNSCC). For this reason, expression/mutation of EGFR were analyzed in 30 dysplastic head and neck lesions and 148 HNSCC samples of Indian patients along with 3 HNSCC cell lines. In addition, deletion/methylation/mutation/expression of SH3GL2 (associated with EGFR degradation) and CDC25A (associated with dephosphorylation of EGFR) were analyzed in the same set of samples. Our study revealed high frequency of EGFR overexpression (66–84%), low frequency of gene amplification (10–32.5%) and absence of functional mutation in the dysplastic lesions and HNSCC samples. No correlation was found between protein overexpression and mRNA expression/gene amplification status of EGFR. On the other hand, frequent alterations (deletion/methylation) of SH3GL2 (63–77%) and CDC25A (37–64%) were seen in the dysplastic and HNSCC samples. Two novel single nucleotide polymorphism (SNPs) were found in the promoter region of SH3GL2. Reduced expression of these genes showed concordance with their alterations. Overexpression of EGFR and p-EGFR were significantly associated with reduced expression and alterations of SH3GL2 and CDC25A respectively. In-vitro demethylation experiment by 5-aza-2′-deoxycytidine (5-aza-dC) showed upregulation of SH3GL2 and CDC25A and downregulation of EGFR expression in Hep2 cell line. Poor patient outcome was predicted in the cases with alterations of SH3GL2 and CDC25A in presence of human papilloma virus (HPV) infection. Also, low SH3GL2 and high EGFR expression was a predictor of poor patient survival. Thus, our data suggests that overexpression of EGFR due to its reduced degradation and dephosphorylation is needed for development of HNSCC.
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Affiliation(s)
- Guru Prasad Maiti
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
| | - Pinaki Mondal
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Nupur Mukherjee
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
| | - Amlan Ghosh
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
- Department of Zoology, Presidency University, Kolkata, India
| | - Susmita Ghosh
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Sanjib Dey
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jayanta Chakrabarty
- Department of Surgical Oncology, Chittaranjan National Cancer Institute, Kolkata, India
| | - Anup Roy
- North Bengal Medical College, Sushruta Nagar,Darjeeling, West Bengal, India
| | - Jaydip Biswas
- Department of Surgical Oncology, Chittaranjan National Cancer Institute, Kolkata, India
| | - Susanta Roychoudhury
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Chinmay Kumar Panda
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
- * E-mail:
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13
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Senchenko VN, Kisseljova NP, Ivanova TA, Dmitriev AA, Krasnov GS, Kudryavtseva AV, Panasenko GV, Tsitrin EB, Lerman MI, Kisseljov FL, Kashuba VI, Zabarovsky ER. Novel tumor suppressor candidates on chromosome 3 revealed by NotI-microarrays in cervical cancer. Epigenetics 2013; 8:409-20. [PMID: 23478628 DOI: 10.4161/epi.24233] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Genetic and epigenetic alterations in cervical carcinomas were investigated using NotI-microarrays containing 180 cloned sequences flanking all NotI-sites associated with genes on chromosome 3. In total, 48 paired normal/tumor DNA samples, specifically enriched in NotI-sites, were hybridized to NotI-microarrays. Thirty genes, including tumor suppressors or candidates (for example, VHL, RBSP3/CTDSPL, ITGA9, LRRC3B, ALDH1L1, EPHB1) and genes previously unknown as cancer-associated (ABHD5, C3orf77, PRL32, LOC285375, FGD5 and others), showed methylation/deletion in 21-44% of tumors. The genes were more frequently altered in squamous cell carcinomas (SCC) than in adenocarcinomas (ADC, p<0.01). A set of seven potential markers (LRRN1, PRICKLE2, VHL, BHLHE40, RBSP3, CGGBP1 and SOX14) is promising for discrimination of ADC and SCC. Alterations of more than 20 genes simultaneously were revealed in 23% of SCC. Bisulfite sequencing analysis confirmed methylation as a frequent event in SCC. High down-regulation frequency was shown for RBSP3, ITGA9, VILL, APRG1/C3orf35 and RASSF1 (isoform A) genes (3p21.3 locus) in SCC. Both frequency and extent of RASSF1A and RBSP3 mRNA level decrease were more pronounced in tumors with lymph node metastases compared with non-metastatic ones (p ≤ 0.05). We confirmed by bisulfite sequencing that RASSF1 promoter methylation was a rare event in SCC and, for the first time, demonstrated RASSF1A down-regulation at both the mRNA and protein levels without promoter methylation in tumors of this histological type. Thus, our data revealed novel tumor suppressor candidates located on chromosome 3 and a frequent loss of epigenetic stability of 3p21.3 locus in combination with down-regulation of genes in cervical cancer.
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Affiliation(s)
- Vera N Senchenko
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia
| | - Natalia P Kisseljova
- N.N. Blokhin Russian Cancer Research Center; Russian Academy of Medical Sciences; Moscow, Russia
| | - Tatyana A Ivanova
- N.N. Blokhin Russian Cancer Research Center; Russian Academy of Medical Sciences; Moscow, Russia; Karolinska Institute; Department of Microbiology, Tumour and Cell Biology; Stockholm, Sweden
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia; I.I.Mechnikov Scientific Research Institute of Vaccines and Sera; Russian Academy of Medical Sciences; Moscow, Russia
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia
| | - Grigory V Panasenko
- Institute of Molecular Biology and Genetics; Ukrainian Academy of Sciences; Kiev, Ukraine
| | - Evgeny B Tsitrin
- Koltzov Institute of Developmental Biology; Russian Academy of Sciences; Moscow, Russia
| | | | - Fyodor L Kisseljov
- N.N. Blokhin Russian Cancer Research Center; Russian Academy of Medical Sciences; Moscow, Russia
| | - Vladimir I Kashuba
- Institute of Molecular Biology and Genetics; Ukrainian Academy of Sciences; Kiev, Ukraine
| | - Eugene R Zabarovsky
- Karolinska Institute; Department of Microbiology, Tumour and Cell Biology; Stockholm, Sweden
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14
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NotI microarrays: novel epigenetic markers for early detection and prognosis of high grade serous ovarian cancer. Int J Mol Sci 2012. [PMID: 23202957 PMCID: PMC3497331 DOI: 10.3390/ijms131013352] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chromosome 3-specific NotI microarray (NMA) containing 180 clones with 188 genes was used in the study to analyze 18 high grade serous ovarian cancer (HGSOC) samples and 7 benign ovarian tumors. We aimed to find novel methylation-dependent biomarkers for early detection and prognosis of HGSOC. Thirty five NotI markers showed frequency of methylation/deletion more or equal to 17%. To check the results of NMA hybridizations several samples for four genes (LRRC3B, THRB, ITGA9 and RBSP3 (CTDSPL)) were bisulfite sequenced and confirmed the results of NMA hybridization. A set of eight biomarkers: NKIRAS1/RPL15, THRB, RBPS3 (CTDSPL), IQSEC1, NBEAL2, ZIC4, LOC285205 and FOXP1, was identified as the most prominent set capable to detect both early and late stages of ovarian cancer. Sensitivity of this set is equal to (72 ± 11)% and specificity (94 ± 5)%. Early stages represented the most complicated cases for detection. To distinguish between Stages I + II and Stages III + IV of ovarian cancer the most perspective set of biomarkers would include LOC285205, CGGBP1, EPHB1 and NKIRAS1/RPL15. The sensitivity of the set is equal to (80 ± 13)% and the specificity is (88 ± 12)%. Using this technique we plan to validate this panel with new epithelial ovarian cancer samples and add markers from other chromosomes.
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15
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Mostovich LA, Prudnikova TY, Kondratov AG, Loginova D, Vavilov PV, Rykova VI, Sidorov SV, Pavlova TV, Kashuba VI, Zabarovsky ER, Grigorieva EV. Integrin alpha9 (ITGA9) expression and epigenetic silencing in human breast tumors. Cell Adh Migr 2012; 5:395-401. [PMID: 21975548 DOI: 10.4161/cam.5.5.17949] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Integrin alpha9 (ITGA9) is one of the less studied integrin subunits that facilitates accelerated cell migration and regulates diverse biological functions such as angiogenesis, lymphangiogenesis, cancer cell proliferation and migration. In this work, integrin alpha9 expression and its epigenetic regulation in normal human breast tissue, primary breast tumors and breast cancer cell line MCF7 were studied. It was shown that integrin alpha9 is expressed in normal human breast tissue. In breast cancer, ITGA9 expression was downregulated or lost in 44% of tumors while another 45% of tumors showed normal or increased ITGA9 expression level (possible aberrations in the ITGA9 mRNA structure were supposed in 11% of tumors). Methylation of ITGA9 CpG-island located in the first intron of the gene was shown in 90% of the breast tumors with the decreased ITGA9 expression while no methylation at 5'-untranslated region of ITGA9 was observed. 5-aza-dC treatment restored integrin alpha9 expression in ITGA9-negative MCF7 breast carcinoma cells, Trichostatin A treatment did not influenced it but a combined treatment of the cells with 5-aza-dC/Trichostatin A doubled the ITGA9 activation. The obtained results suggest CpG methylation as a major mechanism of integrin alpha9 inactivation in breast cancer with a possible involvement of other yet unidentified molecular pathways.
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16
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Mazumder Indra D, Mitra S, Roy A, Mondal RK, Basu PS, Roychoudhury S, Chakravarty R, Panda CK. Alterations of ATM and CADM1 in chromosomal 11q22.3-23.2 region are associated with the development of invasive cervical carcinoma. Hum Genet 2011; 130:735-48. [PMID: 21643982 DOI: 10.1007/s00439-011-1015-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 05/22/2011] [Indexed: 12/29/2022]
Abstract
To understand the importance of chr11q22.3-23.2 region in the development of cervical cancer, we have studied the genetic and epigenetic alterations of the candidate genes ATM, PPP2R1B, SDHD and CADM1 in cervical intraepithelial neoplasia (CIN) and cervical carcinoma (CACX) samples. Our study revealed low expression and high alterations (methylation/deletion) (55-59%) of ATM and CADM1 genes along with poor patient outcome. The alterations of ATM and CADM1 are associated with the progression of tumor from CIN to Stage I/II, thus implying their role in early invasiveness. The two genes, PPP2R1B and SDHD, lying in between ATM and CADM1, have low frequency of alterations, and majority of the alterations are in CACX samples, indicating that their alterations might be associated with disease progression. Expressions (mRNA/protein) of the genes showed concordance with their molecular alterations. Significant co-alteration of ATM and CADM1 points to their synergic action for the development of CACX. Mutation is, however, a rare phenomenon for inactivation of ATM. Association between the alteration of ATM and CHEK1 and poor survival of the patients having co-alterations of ATM and CHEK1 points to the DNA damage response pathway disruption in development of CACX. Thus, our data suggest that inactivation of ATM-CHEK1-associated DNA damage response pathway and CADM1-associated signaling network might have an important role in the development of CACX.
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Affiliation(s)
- Dipanjana Mazumder Indra
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata 700026, India
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Senchenko VN, Anedchenko EA, Kondratieva TT, Krasnov GS, Dmitriev AA, Zabarovska VI, Pavlova TV, Kashuba VI, Lerman MI, Zabarovsky ER. Simultaneous down-regulation of tumor suppressor genes RBSP3/CTDSPL, NPRL2/G21 and RASSF1A in primary non-small cell lung cancer. BMC Cancer 2010; 10:75. [PMID: 20193080 PMCID: PMC2841140 DOI: 10.1186/1471-2407-10-75] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 03/01/2010] [Indexed: 11/16/2022] Open
Abstract
Background The short arm of human chromosome 3 is involved in the development of many cancers including lung cancer. Three bona fide lung cancer tumor suppressor genes namely RBSP3 (AP20 region),NPRL2 and RASSF1A (LUCA region) were identified in the 3p21.3 region. We have shown previously that homozygous deletions in AP20 and LUCA sub-regions often occurred in the same tumor (P < 10-6). Methods We estimated the quantity of RBSP3, NPRL2, RASSF1A, GAPDH, RPN1 mRNA and RBSP3 DNA copy number in 59 primary non-small cell lung cancers, including 41 squamous cell and 18 adenocarcinomas by real-time reverse transcription-polymerase chain reaction based on TaqMan technology and relative quantification. Results We evaluated the relationship between mRNA level and clinicopathologic characteristics in non-small cell lung cancer. A significant expression decrease (≥2) was found for all three genes early in tumor development: in 85% of cases for RBSP3; 73% for NPRL2 and 67% for RASSF1A (P < 0.001), more strongly pronounced in squamous cell than in adenocarcinomas. Strong suppression of both, NPRL2 and RBSP3 was seen in 100% of cases already at Stage I of squamous cell carcinomas. Deregulation of RASSF1A correlated with tumor progression of squamous cell (P = 0.196) and adenocarcinomas (P < 0.05). Most likely, genetic and epigenetic mechanisms might be responsible for transcriptional inactivation of RBSP3 in non-small cell lung cancers as promoter methylation of RBSP3 according to NotI microarrays data was detected in 80% of squamous cell and in 38% of adenocarcinomas. With NotI microarrays we tested how often LUCA (NPRL2, RASSF1A) and AP20 (RBSP3) regions were deleted or methylated in the same tumor sample and found that this occured in 39% of all studied samples (P < 0.05). Conclusion Our data support the hypothesis that these TSG are involved in tumorigenesis of NSCLC. Both genetic and epigenetic mechanisms contribute to down-regulation of these three genes representing two tumor suppressor clusters in 3p21.3. Most importantly expression of RBSP3, NPRL2 and RASSF1A was simultaneously decreased in the same sample of primary NSCLC: in 39% of cases all these three genes showed reduced expression (P < 0.05).
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Affiliation(s)
- Vera N Senchenko
- Laboratory of Structural and Functional Genomics, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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