Etiological roles of core promoter variation in triple-negative breast cancer

Huang, Teng; Zhang, Yingbo; Wang, Sanming

doi:10.1016/j.gendis.2022.01.003

Cited by 3 publications

(5 citation statements)

References 47 publications

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“…Promoter activity holds paramount significance in cancer subtyping as it governs the timing and expression levels of genes by interacting with transcription factors, thus dictating gene activity. Promoters have been demonstrated to play pivotal pathological roles in diverse cancers, such as BRCA 50 and bladder cancer. 51 Additionally, the 5′ UTR plays a pivotal role in modulating gene expression levels, and previous studies indicate that the DNA sequence of the 5′ UTR encompasses numerous cis -regulatory elements that engage with transcription factors.…”

Section: Resultsmentioning

confidence: 99%

Subtype-WGME enables whole-genome-wide multi-omics cancer subtyping

Yang,

Zhao,

et al. 2024

Cell Reports Methods

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Section: Resultsmentioning

confidence: 99%

Subtype-WGME enables whole-genome-wide multi-omics cancer subtyping

Yang,

Zhao,

et al. 2024

Cell Reports Methods

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“…Data from extensive genomic study in TNBC showed that the genomic abnormality in TNBC is highly diverse between the patients with different ethnic backgrounds, reflecting the influences of different genetic backgrounds in TNBC etiology [ 18 , 19 , 21 , 59 , 60 ]. Our study in the Chinese TNBC cohort revealed that core promoter mutation is commonly present in TNBC [ 13 ]. It is necessary to determine whether the core promoter mutation in TNBC follows the pattern of genetic mutation in another part of the TNBC genome, such as the coding region, or is more universally present in TNBC but not affected by ethnic background.…”

Section: Discussionmentioning

confidence: 99%

“…Using the normal polymorphism data as the control, we further investigated the core promoter mutation in the Chinese TNBC cohort and the Spanish bladder cancer cohort. We observed that the core promoter region is highly mutable in cancer in a cancer type-specific manner [ 13 ]. In the current study, we further investigated the issue of ethnic background for core promoter mutation in the same type of cancer, TNBC.…”

Section: Discussionmentioning

confidence: 99%

“…The results revealed a highly polymorphic nature of core promoter in the human population highlighting the importance of the core promoter variation in human evolution adaptation. To understand the potential pathogenic impact of the core promoter mutation, we characterized the core promoter mutations in breast cancer and bladder cancer [ 12 , 13 ]. The results showed the wide presence of germline and somatic core promoter mutations in both breast cancer and bladder cancer, suggesting that core promoter mutations could play etiological roles in oncogenesis in different types of cancer.…”

Section: Introductionmentioning

confidence: 99%

“…Gene expression in TNBC is also very different from other types of breast cancer [ 17–19 ]. In our previous study, we systematically analyzed core promoter mutation in Chinese TNBC patients and identified germline and somatic mutations in thousands of genes [ 13 ]. In the current study, we analyzed TNBC patients from Thailand to address the question of whether core promoter mutation in the same type of cancer could be ethnic-specific or universally present regardless of the ethnic background.…”

Section: Introductionmentioning

confidence: 99%

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Core promoter in TNBC is highly mutated with rich ethnic signature

Huang¹,

Zhang²,

Zhao³

et al. 2022

Briefings in Functional Genomics

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The core promoter plays an essential role in regulating transcription initiation by controlling the interaction between transcriptional factors and sequence motifs in the core promoter. Although mutation in core promoter sequences is expected to cause abnormal gene expression leading to pathogenic consequences, limited supporting evidence showed the involvement of core promoter mutation in diseases. Our previous study showed that the core promoter is highly polymorphic in worldwide human ethnic populations in reflecting human history and adaptation. Our recent characterization of the core promoter in triple-negative breast cancer (TNBC), a subtype of breast cancer, in a Chinese TNBC cohort revealed the wide presence of core promoter mutation in TNBC. In the current study, we analyzed the core promoter in a Thai TNBC cohort. We also observed rich core promoter mutation in the Thai TNBC patients. We compared the core promoter mutations between Chinese and Thai TNBC cohorts. We observed substantial differences of core promoter mutation in TNBC between the two cohorts, as reflected by the mutation spectrum, mutation-effected gene and functional category, and altered gene expression. Our study confirmed that the core promoter in TNBC is highly mutable, and is highly ethnic-specific.

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Adaptive Sparse Multi-Block PLS Discriminant Analysis: An Integrative Method for Identifying Key Biomarkers from Multi-Omics Data

Zhang

Datta

2023

Genes

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With the growing use of high-throughput technologies, multi-omics data containing various types of high-dimensional omics data is increasingly being generated to explore the association between the molecular mechanism of the host and diseases. In this study, we present an adaptive sparse multi-block partial least square discriminant analysis (asmbPLS-DA), an extension of our previous work, asmbPLS. This integrative approach identifies the most relevant features across different types of omics data while discriminating multiple disease outcome groups. We used simulation data with various scenarios and a real dataset from the TCGA project to demonstrate that asmbPLS-DA can identify key biomarkers from each type of omics data with better biological relevance than existing competitive methods. Moreover, asmbPLS-DA showed comparable performance in the classification of subjects in terms of disease status or phenotypes using integrated multi-omics molecular profiles, especially when combined with other classification algorithms, such as linear discriminant analysis and random forest. We have made the R package called asmbPLS that implements this method publicly available on GitHub. Overall, asmbPLS-DA achieved competitive performance in terms of feature selection and classification. We believe that asmbPLS-DA can be a valuable tool for multi-omics research.

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Etiological roles of core promoter variation in triple-negative breast cancer

Cited by 3 publications

References 47 publications

Subtype-WGME enables whole-genome-wide multi-omics cancer subtyping

Subtype-WGME enables whole-genome-wide multi-omics cancer subtyping

Core promoter in TNBC is highly mutated with rich ethnic signature

Adaptive Sparse Multi-Block PLS Discriminant Analysis: An Integrative Method for Identifying Key Biomarkers from Multi-Omics Data

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