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Ascension AM, Arauzo-Bravo MJ. BigMPI4py: Python Module for Parallelization of Big Data Objects Discloses Germ Layer Specific DNA Demethylation Motifs. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1507-1522. [PMID: 33301409 DOI: 10.1109/tcbb.2020.3043979] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Parallelization in Python integrates Message Passing Interface via the mpi4py module. Since mpi4py does not support parallelization of objects greater than 231 bytes, we developed BigMPI4py, a Python module that wraps mpi4py, supporting object sizes beyond this boundary. BigMPI4py automatically determines the optimal object distribution strategy, and uses vectorized methods, achieving higher parallelization efficiency. BigMPI4py facilitates the implementation of Python for Big Data applications in multicore workstations and High Performance Computer systems. We use BigMPI4py to speed-up the search for germ line specific de novo DNA methylated/unmethylated motifs from the 59 whole genome bisulfite sequencing DNA methylation samples from 27 human tissues of the ENCODE project. We developed a parallel implementation of the Kruskall-Wallis test to find CpGs with differential methylation across germ layers. The parallel evaluation of the significance of 55 million CpG achieved a 22x speedup with 25 cores allowing us an efficient identification of a set of hypermethylated genes in ectoderm and mesoderm-related tissues, and another set in endoderm-related tissues and finally, the discovery of germ layer specific DNA demethylation motifs. Our results point out that DNA methylation signal provide a higher degree of information for the demethylated state than for the methylated state. BigMPI4py is available at https://https://www.arauzolab.org/tools/bigmpi4py and https://gitlab.com/alexmascension/bigmpi4py and the Jupyter Notebook with WGBS analysis at https://gitlab.com/alexmascension/wgbs-analysis.
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Domingues GAB, Kizys MML, Janovsky CCPS, de Barros Maciel RM, Dias-da-Silva MR, Martins JRM, Camacho CP, Cunha LL. The impact of the genetic background in a patient with papillary thyroid cancer and familial adenomatous polyposis. ARCHIVES OF ENDOCRINOLOGY AND METABOLISM 2022; 66:112-117. [PMID: 35263052 PMCID: PMC9991026 DOI: 10.20945/2359-3997000000439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Thyroid cancer is the most common endocrine malignancy, and papillary thyroid carcinoma (PTC) is the main subtype. The cribriform morular variant is a histological phenotype of PTC characterized by its relationship with familial adenomatous polyposis (FAP). Description of the case: We report the genetic assessment of a 20-year-old female patient diagnosed with a cribriform-morular variant of PTC and FAP. We aimed to assess the genetic background of the reported patient, looking for variants that would help us explain the predisposition to tumorigenesis. Genomic DNA was extracted from peripheral blood lymphocytes, and whole exome sequencing was performed. We applied an overrepresentation and gene-set enrichment analysis to look for an accumulation of effects of variants in multiple genes at the genome. We found an overrepresentation of single nucleotide variants (SNVs) in extracellular matrix interactions and cell adhesion genes. Underrepresentation of SNVs in genes related to the regulation of autophagy and cell cycle control was also observed. We hypothesize that the package of alterations of our patient may help to explain why she presented colonic manifestations and thyroid cancer. Our findings suggest that multiple variants with minor impact, when considered together, may be helpful to characterize one particular clinical condition.
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Affiliation(s)
| | - Marina Malta Letro Kizys
- Laboratório de Endocrinologia Molecular e Translacional, Divisão de Endocrinologia, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | | | - Rui Monteiro de Barros Maciel
- Laboratório de Endocrinologia Molecular e Translacional, Divisão de Endocrinologia, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - Magnus Régios Dias-da-Silva
- Laboratório de Endocrinologia Molecular e Translacional, Divisão de Endocrinologia, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - João Roberto Maciel Martins
- Laboratório de Endocrinologia Molecular e Translacional, Divisão de Endocrinologia, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - Cleber Pinto Camacho
- Laboratório de Endocrinologia Molecular e Translacional, Divisão de Endocrinologia, Universidade Federal de São Paulo, São Paulo, SP, Brasil.,Laboratório de Inovação Molecular e Biotecnologia, Divisão de Pós-Graduação Médica, Universidade Nove de Julho, São Paulo, SP, Brasil
| | - Lucas Leite Cunha
- Laboratório de Endocrinologia Molecular e Translacional, Divisão de Endocrinologia, Universidade Federal de São Paulo, São Paulo, SP, Brasil,
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A network-based approach to identify key genes between follicular thyroid cancer and follicular thyroid adenoma. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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The Associations of Genetic Variants in E-cadherin Gene With Clinical Outcome of Epithelial Ovarian Cancer. Int J Gynecol Cancer 2016; 26:1601-1607. [DOI: 10.1097/igc.0000000000000829] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
ObjectiveThe E-cadherin protein plays major roles in tumor progression, invasion, and metastasis. Polymorphisms located in the E-cadherin gene (CDH1) may contribute to increased risks of specific cancers. In this study, we evaluated the associations between genetic variants inCDH1and the clinical outcomes of patients with epithelial ovarian cancer (EOC).Materials and MethodsWe assessed the−160C/Aand−347G/GApolymorphisms in the promoter region, as well as the3′-UTR +54C/Tpolymorphism of E-cadherin, in 257 patients with EOC by ligase detection reaction–polymerase chain reaction.ResultsMultivariate analysis showed that patients with EOC with theCDH1 −347GA/GAgenotype had shorter progression-free survival and overall survival (hazard ratio [HR], 2.16; 95% confidence interval [CI], 1.06–4.40 and HR, 2.06; 95% CI, 1.01–4.19, respectively) compared to those carrying the G/G genotype. Likewise, the patients with theCDH1 −160A/Agenotype had a shorter progression-free survival than those with the C/C genotype (HR, 4.12; 95% CI, 1.43–111.88). No significant association was detected between theCDH1 3′-UTR +54C/Tpolymorphism and survival of the patients with EOC.ConclusionsTheCDH1 −347GA/GAand−160A/Agenotypes may be prognostic markers that can help to identify patients at increased risk of invasive/metastatic cancer in northern China.
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Donmez C, Konac E, Aydogan BT, Bilen CY. Might E-cadherin promoter polymorphisms of rs16260 and rs5030625 associate with the risk of nephrolithiasis? SPRINGERPLUS 2016; 5:1673. [PMID: 27733975 PMCID: PMC5040654 DOI: 10.1186/s40064-016-3363-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/22/2016] [Indexed: 12/30/2022]
Abstract
Purpose To study whether −160 C > A (rs16260) and −347 G > GA (rs5030625) single nucleotide polymorphisms of the regulatory region (rSNPs) of CDH1 gene modulate the risk of nephrolithiasis. Methods Genomic DNA of 101 patients with calcium oxalate nephrolithiasis and 114 healthy controls were screened for both polymorphisms, using polymerase chain reaction-restriction fragments length polymorphism method (PCR-RLFP). Haplotype frequencies were also analyzed. To determine the association of rSNPs of CDH1 gene with the clinicopathological features of nephrolithiasis, nearly all possible etiological factors were documented. These factors were family history, gender, age, body mass index, liquid consumption, eating habits, tea–coffee and meat (oxalate rich) consumption, adequate physical activity, and all serum and urine levels—the serum levels of Na, K, Cl, phosphate, Ca, Mg, uric acid, albumin, blood urea nitrogen (BUN), creatinine and serum parathyroid hormone (PTH) as well as 24 h urine excretions of creatinine, Na, K, Cl, phosphate, Ca, Mg, citrate, oxalate, uric acid, albumin and BUN. Results Significant differences were found between rs16260 and the risk of nephrolithiasis. Patients having CA genotype of rs16260 CDH1 polymorphism were associated with an almost trifold increased risk for developing kidney stone than those with the AA genotype (95 % CI 1.08–7.28, OR 2.8, P = 0.033). We also found that non-A allele carriers (CC) had significantly higher nephrolithiasis risk associated with the clinicopathological characteristics including serum calcium (P = 0.027) and 24 h urinary magnesium level (P = 0.042). Moreover, we did find a directly proportional relationship between the CA genotype and serum calcium levels (P = 0.041). There was no significant difference between patients and controls in terms of the distribution of rs5030625 genotypes and alleles (P > 0.05). Likewise, no associations between the rs16260 and rs5030625 haplotypes and susceptibility to kidney stone were observed (P > 0.05). Conclusion Regulatory variants of rs16260 of the CDH1 gene may confer susceptibility to nephrolithiasis. This may have important implications for understanding the pathophysiological mechanisms of the disease and suggesting novel targets for drug treatment.
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Affiliation(s)
- Cigdem Donmez
- Department of Medical Biology and Genetics, Faculty of Medicine, Gazi University, Besevler, 06510 Ankara, Turkey
| | - Ece Konac
- Department of Medical Biology and Genetics, Faculty of Medicine, Gazi University, Besevler, 06510 Ankara, Turkey
| | - Batuhan T Aydogan
- Department of Urology, Faculty of Medicine, Hacettepe University, Sıhhiye, 06100 Ankara, Turkey
| | - Cenk Y Bilen
- Department of Urology, Faculty of Medicine, Hacettepe University, Sıhhiye, 06100 Ankara, Turkey
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Figlioli G, Elisei R, Romei C, Melaiu O, Cipollini M, Bambi F, Chen B, Köhler A, Cristaudo A, Hemminki K, Gemignani F, Försti A, Landi S. A Comprehensive Meta-analysis of Case-Control Association Studies to Evaluate Polymorphisms Associated with the Risk of Differentiated Thyroid Carcinoma. Cancer Epidemiol Biomarkers Prev 2016; 25:700-13. [PMID: 26843521 DOI: 10.1158/1055-9965.epi-15-0652] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/23/2016] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Linkage analyses and association studies suggested that inherited genetic variations play a role in the development of differentiated thyroid carcinoma (DTC). METHODS We combined the results from a genome-wide association study (GWAS) performed by our group and from published studies on DTC. With a first approach, we evaluated whether a SNP published as associated with the risk of DTC could replicate in our GWAS (using FDR as adjustment for multiple comparisons). With the second approach, meta-analyses were performed between literature and GWAS when both sources suggested an association, increasing the statistical power of the analysis. RESULTS rs1799814 (CYP1A1), rs1121980 (FTO), and 3 SNPs within 9q22 (rs965513, rs7048394, and rs894673) replicated the associations described in the literature. In addition, the meta-analyses between literature and GWAS revealed 10 more SNPs within 9q22, six within FTO, two within SOD1, and single variations within HUS1, WDR3, UGT2B7, ALOX12, TICAM1, ATG16L1, HDAC4, PIK3CA, SULF1, IL11RA, VEGFA, and 1p31.3, 2q35, 8p12, and 14q13. CONCLUSION This analysis confirmed several published risk loci that could be involved in DTC predisposition. IMPACT These findings provide evidence for the role of germline variants in DTC etiology and are consistent with a polygenic model of the disease. Cancer Epidemiol Biomarkers Prev; 25(4); 700-13. ©2016 AACR.
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Affiliation(s)
- Gisella Figlioli
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. Department of Biology, University of Pisa, Pisa, Italy
| | - Rossella Elisei
- Department of Endocrinology and Metabolism, University of Pisa, Pisa, Italy
| | - Cristina Romei
- Department of Endocrinology and Metabolism, University of Pisa, Pisa, Italy
| | | | | | - Franco Bambi
- Blood Centre, Azienda Ospedaliero Universitaria A. Meyer, Firenze, Italy
| | - Bowang Chen
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aleksandra Köhler
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. II Medizinische Klinik, Gastrologie, Onkologie und Palliativmedizin, St.Agnes-Hospital Bocholt, Bocholt, Germany
| | - Alfonso Cristaudo
- Department of Endocrinology and Metabolism, University of Pisa, Pisa, Italy
| | - Kari Hemminki
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden
| | | | - Asta Försti
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden.
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy.
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Lin Y, Yuan J, Wang L, Wang L, Ma Y, Wang Y, Chen J, Zhao H. Correlation between SNPs in CDH1 and gastric cancer in Chinese population. Open Med (Wars) 2014; 10:57-62. [PMID: 28352678 PMCID: PMC5152961 DOI: 10.1515/med-2015-0007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 08/28/2014] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Many recent studies revealed that the single nucleotide polymorphisms have considerable effects on the susceptibility of cancer, such as prostate cancer, lung cancer and gastric cancer. The E-cadherin, a calcium-dependent transmembrane glycoprotein encoded by CDH1 gene, is critical for epithelial construction, intercellular adhesion and cell migration. Some associations have been reported between single nucleotide polymorphisms and gastric cancer in the Chinese population. OBJECTIVE To investigate whether the single nucleotide polymorphism in CDH1 gene is associated with the susceptibility of gastric cancer in the Chinese population. MATERIAL AND METHODS The genotypes of 5 known single nucleotide polymorphisms (rs33935154, rs121964871, rs121964874, rs121964875, rs121964876) were determined in 359 gastric cancer patients and 368 healthy controls. High resolution melting curve detection and sequencing analysis were used in the present study. RESULTS There is a statistical significance in the rs121964871 C>G polymorphism between gastric cancer patients and healthy controls (OR=1.769, 95%CI: 1.051-2.976). Elderly male individuals (>50 years of age) carrying this risk factor may be more susceptible to gastric cancer. CONCLUSIONS The results indicated that the rs121964871 C>G polymorphism is associated with the susceptibility of gastric cancer in the Chinese population, with some age and sex-dependent tendencies observed.
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Affiliation(s)
- Yijin Lin
- Danyang People's Hospital of Jiangsu Province, Danyang, China, Danyang Hospital affiliated to Nantong University, Danyang, Jiangsu 212300, China
| | - Jintao Yuan
- Danyang People's Hospital of Jiangsu Province, Danyang, China, Danyang Hospital affiliated to Nantong University, Danyang, Jiangsu 212300, China
| | - Lihui Wang
- Danyang People's Hospital of Jiangsu Province, Danyang, China, Danyang Hospital affiliated to Nantong University, Danyang, Jiangsu 212300, China
| | - Lan Wang
- Danyang Blood Center of Jiangsu Province, Danyang, Jiangsu 212300, China
| | - Yunjia Ma
- Danyang People's Hospital of Jiangsu Province, Danyang, China, Danyang Hospital affiliated to Nantong University, Danyang, Jiangsu 212300, China
| | - Yuhua Wang
- Danyang People's Hospital of Jiangsu Province, Danyang, China, Danyang Hospital affiliated to Nantong University, Danyang, Jiangsu 212300, China
| | - Jianhong Chen
- Danyang People's Hospital of Jiangsu Province, Danyang, China, Danyang Hospital affiliated to Nantong University, Danyang, Jiangsu 212300, China
| | - Hong Zhao
- Danyang People's Hospital of Jiangsu Province, Danyang, China, Danyang Hospital affiliated to Nantong University, Danyang, Jiangsu 212300, China
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Ban JY, Kim MK, Park SW, Kwon KH. Interleukin-1 beta polymorphisms are associated with lymph node metastasis in Korean patients with papillary thyroid carcinoma. Immunol Invest 2013; 41:888-905. [PMID: 23215728 DOI: 10.3109/08820139.2012.724751] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we investigated whether single nucleotide polymorphisms (SNPs) of the interleukin-1 beta (IL-1B) were associated with papillary thyroid carcinoma (PTC). We also assessed the relationships between IL-1B SNPs and the clinicopathologic characteristics of PTC patients. Ninety-three PTC patients and 324 controls were recruited. The patients with PTC were dichotomized and compared with respect to the clinicopathologic characteristics of PTC. Seven SNPs in the IL-1B gene were selected and genotyped using direct sequencing. Four SNPs (rs1143627, rs3136558, rs1143633, and rs1143643) in the IL-1B gene were significantly associated with PTC (p < 0.05). In clinicopathologic features, 3 SNPs (rs1143630, rs1143633, and rs1143643) showed a strong relationship with lymph node metastasis of PTC. The genotype and allele frequencies of rs1143630 and rs1143643 remained significantly associated with lymph node metastasis after Bonferroni correction for multiple testing. In haplotype analysis, two linkage disequilibrium blocks (block 1 consisted of rs1143627, rs3917356, and rs1143630; block 2 consisted of rs1143633 and rs1143643) also revealed significant associations with lymph node metastasis. Our results suggest that IL-1B polymorphisms may be associated with the risk of PTC in the Korean population. Especially, IL-1B polymorphisms might be a predictive factor for lymph node metastasis of PTC patients.
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Affiliation(s)
- Ju Yeon Ban
- Department of Pharmacology, School of Dentistry, Dankook University, Cheonan, Republic of Korea
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Kurtulmus N, Duren M, Ince U, Cengiz Yakicier M, Peker O, Aydın O, Altiok E, Giray S, Azizlerli H. BRAF(V600E) mutation in Turkish patients with papillary thyroid cancer: strong correlation with indicators of tumor aggressiveness. Endocrine 2012; 42:404-10. [PMID: 22426956 DOI: 10.1007/s12020-012-9651-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 02/29/2012] [Indexed: 12/24/2022]
Abstract
Papillary thyroid cancer (PTC) constitutes more than 90% of the thyroid cancers. MAP kinase/ERK pathway plays an important role in the development of several cancers. BRAF which is a member of Raf-kinase family activates this way. BRAF gene activating mutations lead to neoplastic transformation in thyroid follicle cells. In PTC, this mutation itself is a poor prognostic sign independent of other clinicopathological characteristics. We evaluated BRAF(V600E) mutation and clinical-pathological characteristics in Turkish population with PTC. We assessed 109 patients with PTC (88 female, 21 male). The average age was 38.7 ± 9.9 (17-71). BRAF(V600E) mutation was detected using polymerase chain reaction and fluorescent melting curve analysis. The results show that BRAF(V600E) mutation rate was found in 39.45% of our patients. We observed that BRAF(V600E) mutation was significantly higher in men, in tumors larger than 1 cm in size, and in patients with classical PTC. Moreover, statistically significant correlations of BRAF(V600E) with indicators of tumor aggressiveness such as thyroid capsular invasion, multifocality, lymph node metastasis, and extrathyroidal spread were found. Patient groups below and over the age of 45 did not differ in mutation frequency. Patients with micro-PTC were evaluated separately, it was found that BRAF(V600E) mutation was more frequent in the classic type and that lymph node metastasis rate significantly increased when the mutation was present. We concluded that BRAF(V600E) was correlated with indicators of tumor aggressiveness in our study population. This fact is taken into consideration in treatment and follow-up of our patients with PTC and positive BRAF(V600E) mutation.
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Affiliation(s)
- Neslihan Kurtulmus
- Department of Endocrinology, Acibadem Maslak Hospital, Buyukdere Cad. No: 40, Maslak, Istanbul, Turkey.
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Contribution of the -160C/A polymorphism in the E-cadherin promoter to cancer risk: a meta-analysis of 47 case-control studies. PLoS One 2012; 7:e40219. [PMID: 22792244 PMCID: PMC3390351 DOI: 10.1371/journal.pone.0040219] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/02/2012] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The -160C/A polymorphism (rs16260) of E-cadherin, a tumor repressor gene, has been shown to be a tumor susceptibility allele for various types of cancers. Because the significance of this polymorphism to cancer risk has been recognized, there are increasing studies investigating -160C/A in different types of cancers and ethnic populations. However, there is still uncertainty about the level of risk for a variety of cancers. METHODS To resolve the controversial question raised by these studies as of March 2012 and provide more statistical power for detecting the significance of -160C/A, we performed a meta-analysis of 47 case-control studies in 16 types of cancers (18,194 cases and 20,207 controls). A meta-regression model and subgroup analysis were employed to identify the source of heterogeneity. Publication bias was evaluated, and sensitivity analysis and cumulative evidence assessment were also performed. RESULTS Using fixed- and random-effects models, the -160AA homozygote was more susceptible to urothelial cancer compared with the -160CA heterozygote. Additionally, the -160A allele is an ethnicity-dependent risk factor for prostate and colorectal cancers. Carriers of the -160A allele in Asians and Europeans were more susceptible to prostate cancer, whereas their North American counterparts seemed tolerant. The -160AA homozygote plays a protective role for Europeans who develop colorectal cancer. The stability of these observations was confirmed by a one-way sensitivity analysis. However, the cumulative evidence for all cancer types was considered 'weak' using the Venice guidelines. CONCLUSIONS A meta-analysis indicated that the -160A allele of E-cadherin provides a higher risk for the development of prostate and urothelial cancers and a protective role for colorectal cancer in an ethnicity-dependent manner.
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