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Al-Asadi S, Mansour H, Ataimish AJ, Al-Kahachi R, Rampurawala J. MicroRNAs Regulate Tumorigenesis by Downregulating SOCS3 Expression: An In silico Approach. Bioinform Biol Insights 2023; 17:11779322231193535. [PMID: 37701630 PMCID: PMC10493049 DOI: 10.1177/11779322231193535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 07/24/2023] [Indexed: 09/14/2023] Open
Abstract
Tumor microenvironment is characterized by the occurrence of significant changes due to disrupted signaling pathways that affect a broad spectrum of cellular activities such as proliferation, differentiation, signaling, invasiveness, migration, and apoptosis. Similarly, a downregulated suppressor of cytokine signaling 3 (SOCS3) promotes increased JAK/STAT function due to aberrant cytokine signaling, which results in increased cell proliferation, differentiation, and migration. Multiple carcinomas including breast cancer, prostate cancer, hepatocellular carcinoma, pancreatic cancer, and colorectal cancer involve the disruption of SOCS3 expression due to microRNA overexpression. MicroRNAs are small, conserved, and non-coding RNA molecules that regulate gene expression through post-transcriptional inhibition and mRNA destabilization. The aim of this study was to identify putative microRNAs that interact with SOCS3 and downregulate its expression. In this study, miRWalk, TargetScan, and miRDB were used to identify microRNAs that interact with SOCS3, whereas RNA22 was utilized to identify the binding sites of 238 significant microRNAs. The tertiary structures of shortlisted microRNAs and SOCS3 regions were predicted through MC Sym and RNAComposer, respectively. For molecular docking, HDOCK was used, which predicted 80 microRNA-messengerRNA complexes and the interactions of the top 5 shortlisted complexes were assessed. The complexes were shortlisted on the basis of least binding affinity score and maximum confidence score. This study identifies the interactions of known (miR-203a-5p) and novel (miR-6756-5p, miR-6732-5p, miR-1203, miR-6887-5p) microRNAs with SOCS3 regions due to their maximum interactions. Identifying the interactions of these microRNAs with SOCS3 will significantly advance the understanding of oncomiRs (miRNAs that are associated with cancer development) in tumor development due to their influence on SOCS3 expression. These insights will assist in future studies to understand the significance of miRNA-SOCS3-associated tumor development and progression.
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Affiliation(s)
- Sura Al-Asadi
- College of Health and Medical Techniques, Middle Technical University, Baghdad, Iraq
| | - Hiba Mansour
- College of Health and Medical Techniques, Middle Technical University, Baghdad, Iraq
| | | | - Rusul Al-Kahachi
- Department of Scholarships and Cultural Relationship, Republic of Iraq Ministry of Higher Education and Scientific Research, Baghdad, Iraq
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Timilsina M, Fey D, Buosi S, Janik A, Costabello L, Carcereny E, Abreu DR, Cobo M, Castro RL, Bernabé R, Minervini P, Torrente M, Provencio M, Nováček V. Synergy between imputed genetic pathway and clinical information for predicting recurrence in early stage non-small cell lung cancer. J Biomed Inform 2023; 144:104424. [PMID: 37352900 DOI: 10.1016/j.jbi.2023.104424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 06/25/2023]
Abstract
OBJECTIVE Lung cancer exhibits unpredictable recurrence in low-stage tumors and variable responses to different therapeutic interventions. Predicting relapse in early-stage lung cancer can facilitate precision medicine and improve patient survivability. While existing machine learning models rely on clinical data, incorporating genomic information could enhance their efficiency. This study aims to impute and integrate specific types of genomic data with clinical data to improve the accuracy of machine learning models for predicting relapse in early-stage, non-small cell lung cancer patients. METHODS The study utilized a publicly available TCGA lung cancer cohort and imputed genetic pathway scores into the Spanish Lung Cancer Group (SLCG) data, specifically in 1348 early-stage patients. Initially, tumor recurrence was predicted without imputed pathway scores. Subsequently, the SLCG data were augmented with pathway scores imputed from TCGA. The integrative approach aimed to enhance relapse risk prediction performance. RESULTS The integrative approach achieved improved relapse risk prediction with the following evaluation metrics: an area under the precision-recall curve (PR-AUC) score of 0.75, an area under the ROC (ROC-AUC) score of 0.80, an F1 score of 0.61, and a Precision of 0.80. The prediction explanation model SHAP (SHapley Additive exPlanations) was employed to explain the machine learning model's predictions. CONCLUSION We conclude that our explainable predictive model is a promising tool for oncologists that addresses an unmet clinical need of post-treatment patient stratification based on the relapse risk while also improving the predictive power by incorporating proxy genomic data not available for specific patients.
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Affiliation(s)
- Mohan Timilsina
- Data Science Institute, Insight Centre for Data Analytics, University of Galway, Ireland.
| | - Dirk Fey
- Systems Biology Ireland, University College Dublin, Ireland.
| | - Samuele Buosi
- Data Science Institute, Insight Centre for Data Analytics, University of Galway, Ireland.
| | | | | | - Enric Carcereny
- Catalan Institute of Oncology, Hospital Universitari Germans Trias i Pujol, B-ARGO, IGTP, Badalona, Spain.
| | | | - Manuel Cobo
- Medical Oncology Intercenter Unit. Regional and Virgen de la Victoria University Hospitals. IBIMA. Málaga., Spain.
| | | | - Reyes Bernabé
- Hospital Universitario Virgen del Rocio, Sevilla, Spain.
| | | | - Maria Torrente
- Medical Oncology Department, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain.
| | - Mariano Provencio
- Medical Oncology Department, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain.
| | - Vít Nováček
- Data Science Institute, Insight Centre for Data Analytics, University of Galway, Ireland; Faculty of Informatics, Masaryk University Brno, Czech Republic; Masaryk Memorial Cancer Institute, Brno, Czech Republic.
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Wang F, Moon W, Letsou W, Sapkota Y, Wang Z, Im C, Baedke JL, Robison L, Yasui Y. Genome-Wide Analysis of Rare Haplotypes Associated with Breast Cancer Risk. Cancer Res 2023; 83:332-345. [PMID: 36354368 PMCID: PMC9852031 DOI: 10.1158/0008-5472.can-22-1888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/09/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022]
Abstract
Numerous common genetic variants have been linked to breast cancer risk, but they only partially explain the total breast cancer heritability. Inference from Nordic population-based twin data indicates rare high-risk loci as the chief determinant of breast cancer risk. Here, we use haplotypes, rather than single variants, to identify rare high-risk loci for breast cancer. With computationally phased genotypes from 181,034 white British women in the UK Biobank, a genome-wide haplotype-breast cancer association analysis was conducted using sliding windows of 5 to 500 consecutive array-genotyped variants. In the discovery stage, haplotype-breast cancer associations were evaluated retrospectively in the prestudy-enrollment data including 5,487 breast cancer cases. Breast cancer hazard ratios (HR) for additive haplotypic effects were estimated using Cox regression. The replication analysis included a prospective cohort of women free of breast cancer at enrollment, of whom 3,524 later developed breast cancer. This two-stage analysis detected 13 rare loci (frequency <1%), each associated with an appreciable breast cancer-risk increase (discovery: HRs = 2.84-6.10, P < 5 × 10-8; replication: HRs = 2.08-5.61, P < 0.01). In contrast, the variants that formed these rare haplotypes individually exhibited much smaller effects. Functional annotation revealed extensive cis-regulatory DNA elements in breast cancer-related cells underlying the replicated rare haplotypes. Using phased, imputed genotypes from 30,064 cases and 25,282 controls in the DRIVE OncoArray case-control study, 6 of the 13 rare-loci associations were found generalizable (odds ratio estimates: 1.48-7.67, P < 0.05). This study demonstrates the complementary advantage of utilizing rare haplotypes to capture novel risk loci and suggests the potential for the discovery of more genetic elements contributing to cancer heritability as large data sets of germline whole-genome sequencing become available. SIGNIFICANCE A genome-wide two-stage haplotype analysis identifies rare haplotypes associated with breast cancer risk and suggests that the rare risk haplotypes represent long-range interactions with regulatory consequences influencing cancer risk.
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Affiliation(s)
- Fan Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Wonjong Moon
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - William Letsou
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Cindy Im
- School of Public Health, University of Alberta, Edmonton, Alberta T6G 1C9, Canada
| | - Jessica L. Baedke
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Leslie Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
- School of Public Health, University of Alberta, Edmonton, Alberta T6G 1C9, Canada
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Fashina A, Busch T, Young M, Adamson O, Awotoye W, Alade A, Adeleke C, Hassan M, Oladayo AM, Gowans LJJ, Eshete M, Naicker T, Olotu J, Adeyemo WL, Butali A. Investigating the relationship between cancer and orofacial clefts using GWAS significant loci for cancers: A case-control and case-triad study. FRONTIERS IN ORAL HEALTH 2022; 3:915361. [PMID: 35990505 PMCID: PMC9388935 DOI: 10.3389/froh.2022.915361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundSeveral population-based case-control studies have reported concurrent presentation of cancer and congenital malformations. Many associations have been made between oral clefting and cancers, though some of these results are conflicting. Some studies have reported an increased risk of cancer among 1st-degree relatives of cleft cases and vice versa, and also an excess risk of cancers of the breast, lung, and brain among those with oral clefts. This study aimed to determine if the genetic polymorphisms found in some cancers are also associated with orofacial cleft in an African cohort.MethodsThe study was a case-control and case-triad study in which cases were 400 individuals clinically diagnosed with non-syndromic cleft lip and/or palate (CL/P), while controls were 450 individuals without CL/P. Samples were obtained from three African countries while DNA extraction, PCR, and genotyping were carried out at the University of Iowa, US. Eleven SNPs in genes coding for SWI/SNF subunits and 13 GWAS significant SNPs for cancers associated with orofacial cleft were selected. Case-control analysis, transmission disequilibrium test (TDT), and DFAM to combine the parent-offspring trio data and unrelated case/control data in a single analysis were carried out using PLINK.ResultsFor the case-control analyses that included all the clefts and for the CLP subtype, none of the SNPs were statistically significant. Statistically increased risk for the following SNPs rs34775372 (p = 0.02; OR = 1.54, CI:1.07–2.22), rs55658222 (p = 0.009; OR = 2.64, CI:1.28–5.45) and rs72728755 (p = 0.02; OR=2.27, CI:1.17–4.45) was observed with the CL only sub-group. None of these were significant after Bonferoni correction. In the TDT analyses, a significantly reduced risk with rs10941679 (p = 0.003; OR = 0.43, CI:0.24–0.75) was observed and this was significant after Bonferroni correction. The rs10941679 was also significant (p = 0.003) in the DFAM analyses as well even after Bonferroni correction.ConclusionThe results from this study represent an important starting point for understanding the concurrent presentation of some cancers in orofacial clefts, and cancer risks in cleft patients. The associations observed warrant further investigation in a larger cohort and will set the stage for a more mechanistic approach toward understanding the risk for cancers in families with clefts.
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Affiliation(s)
- Azeez Fashina
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
- *Correspondence: Azeez Fashina
| | - Tamara Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Mary Young
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Olawale Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Waheed Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Chinyere Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Mohaned Hassan
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Abimbola M. Oladayo
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Lord J. J. Gowans
- Komfo Anokye Teaching Hospital, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen Eshete
- Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Thirona Naicker
- School of Clinical Medicine, KwaZulu-Natal University, Durban, South Africa
| | - Joy Olotu
- Department of Anatomy, University of Port Harcourt, Port Harcourt, Nigeria
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
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Lee H, Lee HW, Park EJ, Kang J, Baik SH. Clinicopathologic Characteristics and Survival of Patients With Double Primary Malignancies: Breast and Colorectal Cancer. Ann Coloproctol 2021; 38:197-206. [PMID: 34657410 PMCID: PMC9263303 DOI: 10.3393/ac.2021.00640.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/26/2021] [Indexed: 11/15/2022] Open
Abstract
Purpose This study aimed to investigate the clinicopathologic features and survival in patients with both breast cancer (BrC) and colorectal cancer (CRC). Methods Between 1996 and 2019, patients who were diagnosed with both BrC and CRC were evaluated retrospectively. Patients with distant metastasis, palliative resection, and previous cancer histories except for BrCs or CRCs were excluded. Altogether, 105 patients were divided into the B=C group (n=21), B-first group (n=40), and C-first group (n=44) according to the definition of synchronous and metachronous cancers. The clinicopathologic features and overall survival were evaluated. Results TNM stages and histologic types were comparable among the 3 groups (P=0.434). The interval of diagnosis was 67.1±40.4 and 59.3±47.2 months in the B- and C-first groups, respectively. The incidence of adjuvant chemotherapy in the B-first group was 57.5%, which was higher than the B=C and C-first groups (P<0.001). The estrogen receptor, progesterone receptor, Ki-67, and HER-2 molecular markers were not significantly different among the groups. The overall survival of the B-first group showed lower survival rates than the C-first group (P=0.039). In the logistic regression, HER-2 status (hazard ratio [HR], 11.9; P=0.032) and lymph node metastasis of CRC (HR, 5.8; P=0.036) were prognostic factors affecting overall survival. Conclusion B-first group had poorer survival outcomes than the C-first group in patients with the metachronous BrC and CRC. HER2 positivity and CRC lymph node metastasis may be prognostic factors that affect overall survival in these patients. The findings support that a colorectal cancer screening program should be included during BrC surveillance.
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Affiliation(s)
- Hyundo Lee
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Hae Won Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Eun Jung Park
- Division of Colon and Rectal Surgery, Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jeonghyun Kang
- Division of Colon and Rectal Surgery, Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Hyuk Baik
- Division of Colon and Rectal Surgery, Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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Cumova A, Vymetalkova V, Opattova A, Bouskova V, Pardini B, Kopeckova K, Kozevnikovova R, Lickova K, Ambrus M, Vodickova L, Naccarati A, Soucek P, Vodicka P. Genetic variations in 3´UTRs of SMUG1 and NEIL2 genes modulate breast cancer risk, survival and therapy response. Mutagenesis 2021; 36:269-279. [PMID: 34097065 DOI: 10.1093/mutage/geab017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/06/2021] [Indexed: 12/12/2022] Open
Abstract
Breast cancer (BC) is the most frequent malignancy in women accounting for approximately 2 million new cases worldwide annually. Several genetic, epigenetic and environmental factors are known to be involved in BC development and progression, including alterations in post-transcriptional gene regulation mediated by microRNAs (miRNAs). Single nucleotide polymorphisms (SNPs) located in miRNA binding sites (miRSNPs) in 3'-untranslated (UTR) regions of target genes may affect miRNA-binding affinity and consequently modulate gene expression. We have previously reported a significant association of miRSNPs in the SMUG1 and NEIL2 genes with overall survival in colorectal cancer patients. SMUG1 and NEIL2 are DNA glycosylases involved in base excision DNA repair (BER). Assuming that certain genetic traits are common for solid tumours, we have investigated wherever variations in SMUG1 and NEIL2 genes display an association with BC risk, prognosis, and therapy response in a group of 673 BC patients and 675 healthy female controls. Patients with TC genotype of NEIL2 rs6997097 and receiving only hormonal therapy displayed markedly shorter overall survival (OS) (HR=4.15, 95% CI=1.7-10.16, P= 0.002) and disease-free survival (DFS) (HR=2.56, 95% CI=1.5-5.7, P= 0.02). Our results suggest that regulation of base excision repair glycosylases operated by miRNAs may modulate the prognosis of hormonally treated BC.
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Affiliation(s)
- Andrea Cumova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Alena Opattova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Bouskova
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Barbara Pardini
- IIGM Italian Institute for Genomic Medicine, Candiolo, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Katerina Kopeckova
- Department of Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | | | - Katerina Lickova
- Radiotherapy and Oncology Department, Third Faculty of Medicine, Charles University and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Miloslav Ambrus
- Radiotherapy and Oncology Department, Third Faculty of Medicine, Charles University and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Alessio Naccarati
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,IIGM Italian Institute for Genomic Medicine, Candiolo, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Pavel Soucek
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
| | - Pavel Vodicka
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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