Genetic factors associated with cancer racial disparity – an integrative study across twenty‐one cancer types

Yan, Li; Pang, Xiaodong; Cui, Zihan; Zhou, Yidong; Mao, Feng; Yang, Lin; Zhang, Xiaohui; Shen, Songjie; Zhu, Peixin; Zhao, Tingting; Sun, Qiang; Zhang, Jinfeng

doi:10.1002/1878-0261.12799

Cited by 11 publications

(12 citation statements)

References 61 publications

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“…As the principal polyphenol isolated from turmeric, curcumin exhibits many pharmacological effects such as anti‐inflammatory, antioxidant, antiapoptotic, and so on. [ 1,2 ] Furthermore, curcumin is also able to restrain the growth of various cancer cell lines in vitro, especially in lung cancer. [ 3‐5 ] However, low stability and bioavailability of curcumin limit its practical clinical application.…”

Section: Introductionmentioning

confidence: 99%

Antiproliferative effect and autophagy induction of curcumin derivative ZYX02‐Na on the human lung cancer cells A549

Zhou

Guo

Liu

et al. 2020

J Biochem & Molecular Tox

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At present, a large number of curcumin derivatives had been produced and identified aiming to replace the curcumin in view of its low bioavailability and stability. Here, a novel curcumin derivative ZYX02-Na was first used to reduce the cell viability of human non-small cell lung cells A549, which was confirmed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Flow cytometry and Western blot analysis showed that ZYX02-Na could lead to cell cycle arrest in G0/G1 phase, which demonstrated that ZYX02-Na inhibited the proliferation of A549 cells. Furthermore, the AMPK/mTOR/4E-BP1 signaling pathway was activated in ZYX02-Na-treated A549 cells. Besides, wounding healing and transwell experiments showed that ZYX02-Na could also inhibited the migration ability of A549 cells. Moreover, we also found that ZYX02-Na could induce autophagy of A549 cells by acridine orange staining, GFP-LC3 subcellular localization observation and Western blotting analysis, respectively. In short, our current studies indicated that ZYX02-Na possessed the antiproliferation effect and autophagy induction on A549 cells, while in vivo anticancer study of ZYX02-Na needs to be done in future.

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Section: Introductionmentioning

confidence: 99%

Antiproliferative effect and autophagy induction of curcumin derivative ZYX02‐Na on the human lung cancer cells A549

Zhou

Guo

Liu

et al. 2020

J Biochem & Molecular Tox

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“…The breakpoints were located at 8q13.3 and 15q26.2 and, and the Chromosome 8 breakpoint separates exons 2 and 3 of XKR9 . This gene is a cell membrane bound protein and a member of the Kell Blood Group complex subunit-related gene family [51]. Based on a National Library of Medicine Pubmed literature search during the submission of this manuscript, there were no articles describing functional studies of this gene.…”

Section: Resultsmentioning

confidence: 99%

“…Based on a National Library of Medicine Pubmed literature search during the submission of this manuscript, there were no articles describing functional studies of this gene. One recent article reported that XKR9 gene expression in cancer was associated with decreased overall survival [51]. In this report, Li et al used the TCGA genomic data from 21 cancer types and identified differential expressed genes in tumors originating from different ethnicities.…”

Section: Chromosome 8 Translocation In An Msi Crcmentioning

confidence: 99%

Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8

Shin

Greer

Hopmans

et al. 2020

Preprint

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Colorectal carcinomas (CRCs) which have lost DNA mismatch repair display hypermutability evident in a molecular phenotype called microsatellite instability (MSI). These mismatch repair deficient tumors are thought to lack widespread genomic instability features, such as copy number changes and rearrangements. To identify MSI for clinical diagnosis, current molecular testing looks for changes in mononucleotide or dinucleotide repeats. However, microsatellites have other types of sequence tandem repeats such as tri- and tetranucleotide motifs. These additional classes of microsatellites are generally not examined for MSI but are known to be unstable in a phenotype known as elevated microsatellite alterations at selected tetranucleotide repeats, or EMAST. We developed a sequencing approach that provides ultra-high coverage (>2500X) of microsatellite targets and cancer genes for profiling genomic instability. We assessed the diverse repeat motifs across 200 microsatellites. Our approach provides highly sensitive detection of MSI with high specificity, evaluates copy number alterations with high accuracy, delineates chromosomal instability (CIN) classification and deconvolutes subclonal architecture. By examining both MSI and CIN, we discovered mutations and copy number alterations that defined mixed genomic instability states of CIN and MSI, which are normally considered exclusive. An increase in copy number of chromosome arm 8q was prevalent among MSI tumors. Moreover, we identified an inter-chromosomal translocation event from a CRC with co-occurrence of MSI. Subclonal analysis demonstrated that mutations which are typically considered to be exclusive in MSI, shows mutual occurrence in MSI tumors with more sensitive characterization. Our approach revealed that MSH3 mutations are a potential source of mixed genomic instability features. Overall, our study demonstrates that some colorectal cancers have features of both microsatellite and chromosomal instability. This result may have implications for immunotherapy treatment.

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“…We used several different types of data obtained from TCGA: RNA-seq, protein expression, DNA methylation, and microRNA-seq, which have been used in our previous studies (Stewart, Luks, Roycik, Sang and Zhang 2013, Li, et al 2017, Shi, et al 2017, Li, et al 2020.…”

Section: Genomics and Epigenomics Data From The Cancer Genome Atlas (mentioning

confidence: 99%

Biological Network Inference with GRASP: A Bayesian Network Structure Learning Method Using Adaptive Sequential Monte Carlo

Yu¹,

Cui

Sui

et al. 2021

Preprint

Self Cite

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Bayesian networks (BNs) provide a probabilistic, graphical framework for modeling high-dimensional joint distributions with complex correlation structures. BNs have wide applications in many disciplines, including biology, social science, finance and biomedical science. Despite extensive studies in the past, network structure learning from data is still a challenging open question in BN research. In this study, we present a sequential Monte Carlo (SMC)-based three-stage approach, GRowth-based Approach with Staged Pruning (GRASP). A double filtering strategy was first used for discovering the overall skeleton of the target BN. To search for the optimal network structures we designed an adaptive SMC (adSMC) algorithm to increase the quality and diversity of sampled networks which were further improved by a third stage to reclaim edges missed in the skeleton discovery step. GRASP gave very satisfactory results when tested on benchmark networks. Finally, BN structure learning using multiple types of genomics data illustrates GRASP’s potential in discovering novel biological relationships in integrative genomic studies.

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Genetic factors associated with cancer racial disparity – an integrative study across twenty‐one cancer types

Cited by 11 publications

References 61 publications

Antiproliferative effect and autophagy induction of curcumin derivative ZYX02‐Na on the human lung cancer cells A549

Antiproliferative effect and autophagy induction of curcumin derivative ZYX02‐Na on the human lung cancer cells A549

Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8

Biological Network Inference with GRASP: A Bayesian Network Structure Learning Method Using Adaptive Sequential Monte Carlo

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