Inherited variants in genes somatically mutated in thyroid cancer

Campo, C; Köhler, Aleksandra; Figlioli, Gisella; Elisei, Rossella; Romei, Cristina; Cipollini, Monica; Bambi, Franco; Hemminki, Kari; Gemignani, Federica; Landi, Stefano; Försti, Asta

doi:10.1371/journal.pone.0174995

Cited by 7 publications

(5 citation statements)

References 44 publications

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“…Of note is the missense SNP rs459552 in APC whose minor allele 'T' (MAF, 0.2019/24418-ExAC, NCBI-dbSNP Short Genetic Variations) was present in all the CR-CSC lines. However, the association of APC rs459552 with cancer remains unclear [37,38].…”

Section: Genetic Characterization Of Cr-csc Linesmentioning

confidence: 99%

DNA Methylation of Shelf, Shore and Open Sea CpG Positions Distinguish High Microsatellite Instability from Low or Stable Microsatellite Status Colon Cancer Stem Cells

et al. 2019

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Aim: To investigate the genome-wide methylation of genetically characterized colorectal cancer stem cell (CR-CSC) lines. Materials & methods: Eight CR-CSC lines were isolated from primary colorectal cancer (CRC) tissues, cultured and characterized for aneuploidy, mutational status of CRC-related genes and microsatellite instability (MSI). Genome-wide DNA methylation was assessed by MethylationEPIC microarray. Results: We describe a distinctive methylation pattern that is maintained following in vivo passages in immune-compromised mice. We identified an epigenetic CR-CSC signature associated with MSI. We noticed that the preponderance of the differentially methylated positions do not reside at CpG islands, but spread to shelf and open sea regions. Conclusion: Given that CRCs with MSI-high status have a lower metastatic potential, the identification of a MSI-related methylation signature could provide new insights and possible targets into metastatic CRC.

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Section: Genetic Characterization Of Cr-csc Linesmentioning

confidence: 99%

DNA Methylation of Shelf, Shore and Open Sea CpG Positions Distinguish High Microsatellite Instability from Low or Stable Microsatellite Status Colon Cancer Stem Cells

et al. 2019

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“…The deleteriousness of the amino acid changes were predicted using SIFT () and PolyPhen-2 (). Genotyping was performed using the previously published protocol [17].…”

Section: Methodsmentioning

confidence: 99%

Association of NLRP1 Coding Polymorphism with Lung Function and Serum IL-1β Concentration in Patients Diagnosed with Chronic Obstructive Pulmonary Disease (COPD)

Ozretić

Filho

Catalano

et al. 2019

Genes

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Chronic obstructive pulmonary disease (COPD) is a chronic disease characterized by a progressive decline in lung function due to airflow limitation, mainly related to IL-1β-induced inflammation. We have hypothesized that single nucleotide polymorphisms (SNPs) in NLRP genes, coding for key regulators of IL-1β, are associated with pathogenesis and clinical phenotypes of COPD. We recruited 704 COPD individuals and 1238 healthy controls for this study. Twenty non-synonymous SNPs in 10 different NLRP genes were genotyped. Genetic associations were estimated using logistic regression, adjusting for age, gender, and smoking history. The impact of genotypes on patients’ overall survival was analyzed with the Kaplan–Meier method with the log-rank test. Serum IL-1β concentration was determined by high sensitivity assay and expression analysis was done by RT-PCR. Decreased lung function, measured by a forced expiratory volume in 1 s (FEV1% predicted), was significantly associated with the minor allele genotypes (AT + TT) of NLRP1 rs12150220 (p = 0.0002). The same rs12150220 genotypes exhibited a higher level of serum IL-1β compared to the AA genotype (p = 0.027) in COPD patients. NLRP8 rs306481 minor allele genotypes (AG + AA) were more common in the Global Initiative for Chronic Obstructive Lung Disease (GOLD) definition of group A (p = 0.0083). Polymorphisms in NLRP1 (rs12150220; OR = 0.55, p = 0.03) and NLRP4 (rs12462372; OR = 0.36, p = 0.03) were only nominally associated with COPD risk. In conclusion, coding polymorphisms in NLRP1 rs12150220 show an association with COPD disease severity, indicating that the fine-tuning of the NLRP1 inflammasome could be important in maintaining lung tissue integrity and treating the chronic inflammation of airways.

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“…The onset and progression of caner are often triggered by genome-wide accumulated structural abnormalities, especially by dysregulated oncogenes variation. Many genomic variations have been found in thyroid cancer, including point mutation, SV, gene fusion and other complex genomic variation [7][8][9], which were reported to be correlated with genomic instability and patient clinical traits [10][11][12][13].…”

Section: Genomic Structural Variation In Thyroid Cancermentioning

confidence: 99%

Structural Variation Detection of Adolescent Thyroid Cancer Using Optical Mapping

Yang

Liao

et al. 2022

Preprint

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Structural variation (SV) is a fundamental genetic cause for cancer, with demonstrated correlation to disease progression and treatment response. Traditional sequencing method cannot provide full genomic landscape especially large-scale and complex structural variation. To overcome these limitations, we adopted a combined sequencing approaches, including optical mapping, single molecular sequencing and short reads shotgun sequencing, to evaluate the SV in thyroid cancer. Different numbers, length and types of structural variation, with genes affected by SV were scrutinized. Integrating these results could showed comprehensive scenario for thyroid cancer in a genomic view. We demonstrate that integrated approaches could provide a powerful tool for capturing a higher level of genomic SV, creating new interpretation of sequencing data of particular relevance to human cancer.

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Inherited variants in genes somatically mutated in thyroid cancer

Cited by 7 publications

References 44 publications

DNA Methylation of Shelf, Shore and Open Sea CpG Positions Distinguish High Microsatellite Instability from Low or Stable Microsatellite Status Colon Cancer Stem Cells

DNA Methylation of Shelf, Shore and Open Sea CpG Positions Distinguish High Microsatellite Instability from Low or Stable Microsatellite Status Colon Cancer Stem Cells

Association of NLRP1 Coding Polymorphism with Lung Function and Serum IL-1β Concentration in Patients Diagnosed with Chronic Obstructive Pulmonary Disease (COPD)

Structural Variation Detection of Adolescent Thyroid Cancer Using Optical Mapping

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