Genetic variants in SMARC genes are associated with DNA damage levels in Chinese population

Immunotherapy, prognostic, and tumor biomarker based on pancancer analysis, SMARCD3

BACKGROUND

SMARCD3 has recently been shown to be an important gene affecting cancer, playing an important role in medulloblastoma and pancreatic ductal adenocarcinoma. Therefore, we conducted this research to investigate the potential involvement of SMARCD3 across cancers and to offer recommendations for future studies.

METHODS

Utilizing information on 33 malignancies in the UCSC Xena database, SMARCD3 expression and its prognostic value were assessed. The tumor microenvironment was evaluated with the "CIBERSORT" and "ESTIMATE" algorithms. SMARCD3 and immune-related genes were analyzed using the TISIDB website. The pathways related to the target genes were examined using GSEA. MSI (microsatellite instability), TMB (tumor mutational burden), and immunotherapy analysis were used to evaluate the impact of target genes on the response to immunotherapy.

RESULTS

There is heterogeneity in terms of the expression and prognostic value of SMARCD3 among various cancers, but it is a risk factor for many cancers including uterine corpus endometrial cancer (UCEC), renal clear cell carcinoma (KIRC), and gastric adenocarcinoma (STAD). GSEA revealed that SMARCD3 is related to chromatin remodeling and transcriptional activation, lipid metabolism, and the activities of various immune cells. The TMB and MSI analyses suggested that SMARCD3 affects the immune response efficiency of KIRC, LUAD and STAD. Immunotherapy analysis suggested that SMARCD3 may be a potential immunotherapy target. RT-qPCR demonstrated the variation in SMARCD3 expression in KIRC, LUAD, and STAD.

CONCLUSION

Our study revealed that SMARCD3 affects the prognosis and immunotherapy response of some tumors, providing a direction for further research on this gene.

The Comet Assay as a Tool in Human Biomonitoring Studies of Environmental and Occupational Exposure to Chemicals-A Systematic Scoping Review

Biomonitoring of human populations exposed to chemical substances that can act as potential mutagens or carcinogens, may enable the detection of damage and early disease prevention. In recent years, the comet assay has become an important tool for assessing DNA damage, both in environmental and occupational exposure contexts. To evidence the role of the comet assay in human biomonitoring, we have analysed original research studies of environmental or occupational exposure that used the comet assay in their assessments, following the PRISMA-ScR method (preferred reporting items for systematic reviews and meta-analyses extension for scoping reviews). Groups of chemicals were designated according to a broad classification, and the results obtained from over 300 original studies (n = 123 on air pollutants, n = 14 on anaesthetics, n = 18 on antineoplastic drugs, n = 57 on heavy metals, n = 59 on pesticides, and n = 49 on solvents) showed overall higher values of DNA strand breaks in the exposed subjects in comparison with the unexposed. In summary, our systematic scoping review strengthens the relevance of the use of the comet assay in assessing DNA damage in human biomonitoring studies.

Case Report: Long-Term Survival of a Pediatric Patient With an Intra-Abdominal Undifferentiated Carcinoma of Unknown Primary

An 8-year and 10-month-old boy presented following 2 weeks of abdominal pain, vomiting, constipation, and rectal pain. A diffuse lower-abdominal mass was felt upon palpation, with radiological findings confirming the presence of a large, multilobulated intraperitoneal mass with mesenteric lymphadenopathy and hepatic metastatic disease. A biopsy of the mass revealed anatomical pathological findings consistent with a diagnosis of intra-abdominal undifferentiated carcinoma of unknown primary (CUP). The patient was treated with six cycles of carboplatin and gemcitabine prior to surgery. Following incomplete resection of the tumor, four further cycles were administered resulting in resolution of the pelvic mass, but progression in the right and left lobes of the liver. Therapy was accordingly adjusted, with administration of six cycles of ifosfamide and doxorubicin followed by 1 year of metronomic vinorelbine and cyclophosphamide maintenance therapy. The patient remains in remission 7 years from completion of therapy. Whole exome sequencing revealed missense mutations in the DNA-repair and chromatin-remodeling genes FANCM and SMARCD2, and a tumor-derived cell line revealed a complex karyotype suggesting chromosomal instability. CUP is an extremely rare diagnosis in the pediatric population, previously reported during adolescence. This report provides detailed characterization of CUP in a young child and in the absence of defined therapeutic guidelines for pediatric CUP, the successful treatment strategy described should be considered for similar cases.

Genetic predisposition for multiple myeloma

Multiple myeloma (MM) is the second most common blood malignancy. Epidemiological family studies going back to the 1920s have provided evidence for familial aggregation, suggesting a subset of cases have an inherited genetic background. Recently, studies aimed at explaining this phenomenon have begun to provide direct evidence for genetic predisposition to MM. Genome-wide association studies have identified common risk alleles at 24 independent loci. Sequencing studies of familial cases and kindreds have begun to identify promising candidate genes where variants with strong effects on MM risk might reside. Finally, functional studies are starting to give insight into how identified risk alleles promote the development of MM. Here, we review recent findings in MM predisposition field, and highlight open questions and future directions.

Genetic variants in nuclear DNA along with environmental factors modify mitochondrial DNA copy number: a population-based exome-wide association study

Background

Mitochondrial DNA (mtDNA) copy number has been found associated with multiple diseases, including cancers, diabetes and so on. Both environmental and genetic factors could affect the copy number of mtDNA. However, limited study was available about the relationship between genetic variants and mtDNA copy number. What’s more, most of previous studies considered only environmental or genetic factors. Therefore, it’s necessary to explore the genetic effects on mtDNA copy number with the consideration of PM_2.5 exposure and smoking.

Results

A multi-center population-based study was performed with 301 subjects from Zhuhai, Wuhan and Tianjin. Personal 24-h PM_2.5 exposure levels, smoking and mtDNA copy number were evaluated. The Illumina Human Exome BeadChip, which contained 241,305 single nucleotide variants, was used for genotyping. The association analysis was conducted in each city and meta-analysis was adopted to combine the overall effect among three cities. Seven SNPs showed significant association with mtDNA copy number with P value less than 1.00E-04 after meta-analysis. The following joint analysis of our identified SNPs showed a significant allele-dosage association between the number of variants and mtDNA copy number (P = 5.02 × 10^− 17). Further, 11 genes were identified associated with mtDNA copy number using gene-based analysis with a P value less than 0.01.

Conclusion

This study was the first attempt to evaluate the genetic effects on mtDNA copy number with the consideration of personal PM_2.5 exposure level. Our findings could provide more evidences that genetic variants played important roles in modulating the copy number of mtDNA.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5142-7) contains supplementary material, which is available to authorized users.

Genetic variants in autophagy associated genes are associated with DNA damage levels in Chinese population

Autophagy associated genes (ATGs) played an important role in the repair process of DNA damage and decreased autophagy may weaken the repair process and aggravate DNA damage. Based on this, we hypothesized that DNA damage levels might be modified by genetic variants in autophagy associated genes. In order to validate our hypothesis, 307 subjects were recruited from three different cities (Zhuhai, Wuhan and Tianjin) in China. Demographic data, individual 24-h PM_2.5 exposure and peripheral blood DNA damage levels were also detected. Seven potentially functional polymorphisms in four essential autophagy associated genes (ATG5, ATG7, ATG8 and ATG13) were screened to evaluate the relationship between the polymorphisms of autophagy associated genes and DNA damage levels. This association was assessed by using multivariable linear regression model, age, sex, smoke and PM_2.5 exposure levels were adjusted in each city. We found that rs12599322 in ATG8 (A>G, β=0.263, 95% CI: 0.108-0.419, P=8.98×10^-4) and rs7484002 in ATG13 (A>G, β=0.396, 95% CI: 0.085-0.708, P=0.013) were significantly associated with higher DNA damage levels. Furthermore, functional annotations showed that both rs12599322 and rs7484002 located at transcription factor binding sites (TFBS), indicating that they could regulate the expression of related genes through TF regulation. Following allelic trend analysis revealed that the DNA damage levels were significantly aggravated with the increasing number of risk variants in autophagy associated genes (P for trend: 8.09×10^-5). Our findings suggested that the polymorphisms in ATGs may influence DNA damage levels in one of the Chinese population.

Genetic variants in multisynthetase complex genes are associated with DNA damage levels in Chinese populations

Aminoacyl-tRNA synthetases (ARSs) and ARS-interacting multi-functional proteins (AIMPs) form a multisynthetase complex (MSC) and play an important role in the process of DNA damage repair. We hypothesized that genetic variants in key ARSs and AIMPs might regulate the DNA damage response. Therefore, we systematically screened 23 potentially functional polymorphisms in MSC genes and evaluated the association between the genetic variants and DNA damage levels in 307 subjects from three cities in southern, central and northern China (Zhuhai, Wuhan and Tianjin, respectively). We examined personal 24-h PM2.5 exposure levels and DNA damage levels in peripheral blood lymphocytes for each subject. We found that the variant allele of rs12199241 in AIMP3 was significantly associated with DNA damage levels (β=0.343, 95%CI: 0.133-0.554, P=0.001). Meanwhile, the results of rs5030754 in EPRS and rs3784929 in KARS indicated their suggestive roles in DNA damage processes (β=0.331, 95%CI: 0.062-0.599, P=0.016 for rs5030754; β=0.192, 95%CI: 0.016-0.368, P=0.033 for rs3784929, respectively). After multiple testing, rs12199241 was still significantly associated with DNA damage levels. Combined analysis of these three polymorphisms showed a significant allele-dosage association between the number of risk alleles and higher DNA damage levels (Ptrend<0.001). These findings indicate that genetic variants in MSC genes may account for PM2.5-modulated DNA damage levels in Chinese populations.