Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients

Joo, LiJin; Zhang, Tongwu; Koka, Hela; Lee, Donghyuk; Shi, Jianxin; Lee, Priscilla; Wang, Difei; Wang, Rui; Chan, Wing-cheong; Law, Sze Hong; Tsoi, Yee-kei; Tse, Gary M.; Lai, Shui Wun; Wu, Çherry; Yang, Sheng-Hong; Chan, Emily Ying Yang; Wong, Samuel Yeung Shan; Wang, Mingyi; Song, Lei; Jones, Kristine; Zhu, Bin; Hutchinson, Amy; Hicks, Belynda; Prokunina‐Olsson, Ludmila; Chanock, Stephen J.; Tse, Lap Ah; Yang, Xiaohong R.

doi:10.1016/j.xhgg.2021.100076

Cited by 4 publications

(3 citation statements)

References 40 publications

(52 reference statements)

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“…Follow the SOURCE and UniGene databases for the ESTEST sequence content of the gene to initially estimate the relative expression of the gene in normal and tumor tissue. The gene is most expressed in normal tissues in SOURCE in the front glands and cervix [in tumor tissues = 1112/1192(93%), positives = 1123/1192(94%)] using chstak for multisequence comparison and the results of the species evolutionary tree [ 38 ]. This is shown in Figure 6 .…”

Section: Resultsmentioning

confidence: 99%

Bioinformatics Method Was Used to Analyze the Highly Expressed Gene FAM83A of Breast Cancer in Young Women

Tang

Wang

et al. 2022

Applied Bionics and Biomechanics

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Objectives. Preliminary analysis of breast cancer related to unknown functional gene FAM83A through bioinformatics knowledge to inform further experimental studies. Select high expression genes for breast cancer and use bioinformatics methods to predict the biological function of FAM83A. Methods. Genes with significant differences in expression between breast tumors and normal breast tissue libraries were selected from CGAP’s SAGE Digital Gene Expression Displayer (DGED) database. An unknown functional gene, FAM83A, which is highly expressed in breast cancer, was screened. We performed an analysis of the gene structure, subcellular localization, physicochemical properties of the encoding products, functional sites, protein structure, and functional domains. Results. Through SAGE DGED, a total of 185 genes with expression differences were found. The structure and function of FAM83A have ideal predictions, and it is generally determined that this gene encodes a nuclear protein with a nucleoprotein. The active site of PLDc and the functional domain of DUF1669 can be involved in signal transduction and gene expression regulation in tumorigenesis and metastasis. Digital gene representation of the Tumor Genome Project Data Library was used to select differentially expressed genes in breast cancer tissue and breast benign tumor tissue. Conclusion. Studies show that FAM83A is a potential research target associated with tumorigenesis and metastasis. Initial tests confirmed the expression of this gene. Lay a solid foundation for further research learning. FAM83A is a highly expressed gene in breast cancer and can serve as a target for studying molecular mechanisms in breast cancer.

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Section: Resultsmentioning

confidence: 99%

Bioinformatics Method Was Used to Analyze the Highly Expressed Gene FAM83A of Breast Cancer in Young Women

Tang

Wang

et al. 2022

Applied Bionics and Biomechanics

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“…3C ). SBS18 is an oxy-radical damage signature that was reported to be increased in Chinese patients with breast cancer ( 43 ).…”

Section: Resultsmentioning

confidence: 99%

Population-specific Mutation Patterns in Breast Tumors from African American, European American, and Kenyan Patients

Tang,

Zhang,

Byun

et al. 2023

Cancer Research Communications

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Women of African descent have the highest breast cancer mortality in the United States and are more likely than women from other population groups to develop an aggressive disease. It remains uncertain to what extent breast cancer in Africa is reminiscent of breast cancer in African American or European American patients. Here, we performed whole-exome sequencing of genomic DNA from 191 breast tumor and non-cancerous adjacent tissue pairs obtained from 97 African American, 69 European American, 2 Asian American, and 23 Kenyan patients. Our analysis of the sequencing data revealed an elevated tumor mutational burden in both Kenyan and African American patients, when compared with European American patients. TP53 mutations were most prevalent, particularly in African American patients, followed by PIK3CA mutations, which showed similar frequencies in European American, African American, and the Kenyan patients. Mutations targeting TBX3 were confined to European Americans and those targeting the FBXW7 tumor suppressor to African American patients whereas mutations in the ARID1A gene that are known to confer resistance to endocrine therapy were distinctively enriched among Kenyan patients. A Kyoto Encyclopedia of Genes and Genomes pathway analysis could link FBXW7 mutations to an increased mitochondrial oxidative phosphorylation capacity in tumors carrying these mutations. Finally, Catalogue of Somatic Mutations in Cancer (COSMIC) mutational signatures in tumors correlated with the occurrence of driver mutations, immune cell profiles, and neighborhood deprivation with associations ranging from being mostly modest to occasionally robust. To conclude, we found mutational profiles that were different between these patient groups. The differences concentrated among genes with low mutation frequencies in breast cancer. Significance: The study describes differences in tumor mutational profiles between African American, European American, and Kenyan breast cancer patients. It also investigates how these profiles may relate to the tumor immune environment and the neighborhood environment in which the patients had residence. Finally, it describes an overrepresentation of ARID1A gene mutations in breast tumors of the Kenyan patients.

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“…Methods for somatic mutation and copy number alteration (SCNA) analyses, based on WES/WGS data, were previously described in our previous HKBC genomic study [ 10 ]. WGS-based analyses such as mutational signature, telomere length, and homologous recombination deficiency (HRD) were described in detail in Zhang et al [ 11 ].…”

Section: Methodsmentioning

confidence: 99%

DNA methylation age in paired tumor and adjacent normal breast tissue in Chinese women with breast cancer

et al. 2023

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Background Few studies have examined epigenetic age acceleration (AA), the difference between DNA methylation (DNAm) predicted age and chronological age, in relation to somatic genomic features in paired cancer and normal tissue, with less work done in non-European populations. In this study, we aimed to examine DNAm age and its associations with breast cancer risk factors, subtypes, somatic genomic profiles including mutation and copy number alterations and other aging markers in breast tissue of Chinese breast cancer (BC) patients from Hong Kong. Methods We performed genome-wide DNA methylation profiling of 196 tumor and 188 paired adjacent normal tissue collected from Chinese BC patients in Hong Kong (HKBC) using Illumina MethylationEPIC array. The DNAm age was calculated using Horvath’s pan-tissue clock model. Somatic genomic features were based on data from RNA sequencing (RNASeq), whole-exome sequencing (WES), and whole-genome sequencing (WGS). Pearson’s correlation (r), Kruskal–Wallis test, and regression models were used to estimate associations of DNAm AA with somatic features and breast cancer risk factors. Results DNAm age showed a stronger correlation with chronological age in normal (Pearson r = 0.78, P < 2.2e−16) than in tumor tissue (Pearson r = 0.31, P = 7.8e−06). Although overall DNAm age or AA did not vary significantly by tissue within the same individual, luminal A tumors exhibited increased DNAm AA (P = 0.004) while HER2-enriched/basal-like tumors exhibited markedly lower DNAm AA (P = < .0001) compared with paired normal tissue. Consistent with the subtype association, tumor DNAm AA was positively correlated with ESR1 (Pearson r = 0.39, P = 6.3e−06) and PGR (Pearson r = 0.36, P = 2.4e−05) gene expression. In line with this, we found that increasing DNAm AA was associated with higher body mass index (P = 0.039) and earlier age at menarche (P = 0.035), factors that are related to cumulative exposure to estrogen. In contrast, variables indicating extensive genomic instability, such as TP53 somatic mutations, high tumor mutation/copy number alteration burden, and homologous repair deficiency were associated with lower DNAm AA. Conclusions Our findings provide additional insights into the complexity of breast tissue aging that is associated with the interaction of hormonal, genomic, and epigenetic mechanisms in an East Asian population.

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Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients

Cited by 4 publications

References 40 publications

Bioinformatics Method Was Used to Analyze the Highly Expressed Gene FAM83A of Breast Cancer in Young Women

Bioinformatics Method Was Used to Analyze the Highly Expressed Gene FAM83A of Breast Cancer in Young Women

Population-specific Mutation Patterns in Breast Tumors from African American, European American, and Kenyan Patients

DNA methylation age in paired tumor and adjacent normal breast tissue in Chinese women with breast cancer

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