Polymorphisms of PRLHR and HSPA12A and risk of gastric and colorectal cancer in the Chinese Han population

Genome-wide association study identified candidate genes for egg production traits in the Longyan Shan-ma duck

Egg production is an important economic trait in layer ducks and understanding the genetics basis is important for their breeding. In this study, a genome-wide association study (GWAS) for egg production traits in 303 female Longyan Shan-ma ducks was performed based on a genotyping-by-sequencing strategy. Sixty-two single nucleotide polymorphisms (SNPs) associated with egg weight traits were identified (P < 9.48 × 10-5), including 8 SNPs at 5% linkage disequilibrium (LD)-based Bonferroni-corrected genome-wide significance level (P < 4.74 × 10-6). One hundred and nineteen SNPs were associated with egg number traits (P < 9.48 × 10-5), including 13 SNPs with 5% LD-based Bonferroni-corrected genome-wide significance (P < 4.74 × 10-6). These SNPs annotated 146 target genes which contained known candidate genes for egg production traits, such as prolactin and prolactin releasing hormone receptor. This study identified that these associated genes were significantly enriched in egg production-related pathways (P < 0.05), such as the oxytocin signaling, MAPK signaling, and calcium signaling pathways. It was notable that 18 genes were differentially expressed in ovarian tissues between higher and lower egg production in Shan-ma ducks. The identified potential candidate genes and pathways provide insight into the genetic basis underlying the egg production trait of layer ducks.

Development and validation of ferroptosis-related lncRNA signature and immune-related gene signature for predicting the prognosis of cutaneous melanoma patients

Ferroptosis, a form of cell death caused by iron-dependent peroxidation of lipids, plays an important role in cancer. Recent studies have shown that long noncoding RNAs (lncRNAs) are involved in the regulation of ferroptosis in tumor cells and are also closely related to tumor immunity. Immune cell infiltration in the tumor microenvironment affects the prognosis and clinical outcome of immunotherapy in melanoma patients, and immune cell classification may be able to accurately predict the prognosis of melanoma patients. However, the prognostic value of ferroptosis-related lncRNAs (FRLs) in melanoma has not been thoroughly explored, and it is difficult to define the immune characteristics of melanoma. We used The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) database, and the FerrDb database to identify FRLs. FRLs with prognostic value were evaluated in an experimental cohort utilizing univariate, LASSO (least absolute shrinkage and selection operator) and multivariate Cox regression, followed by in vitro assays evaluating the expression levels and the biological functions of three candidate FRLs. Kaplan-Meier (K-M) and receiver operating characteristic (ROC) curve analyses were used to assess the validity of the risk model, and the drug sensitivity of FRLs was examined by drug sensitivity analysis. The differentially expressed genes between the high- and low-risk groups in the risk model were enriched in the immune pathway, and we further found immune gene signatures (IRGs) that could predict the prognosis of melanoma patients through a series of methods including single-sample Gene Set Enrichment Analysis (ssGSEA). Finally, two GEO cohorts were used to validate the predictive accuracy and reliability of these two signature models. Our findings suggest that FRLs and IRGs have the potential to predict the prognosis of patients with cutaneous melanoma.

PRLHR Immune Genes Associated With Tumor Mutation Burden can be Used as Prognostic Markers in Patients With Gliomas

Tumor mutation burden (TMB) is a useful biomarker for predicting the prognosis and efficacy of immune checkpoint inhibitor (ICIs). In this study, we aimed to explore the prognostic value of TMB and TMB-related PRLHR immune genes as prognostic markers in patients with gliomas. We downloaded MAF files, RNA-seq data, and clinical information from the Cancer Genome Atlas (TCGA) database. The TMB of glioma was calculated and its correlation with clinical features and prognosis was analyzed. We found that TMB was statistically correlated with the grade and age of patients with gliomas. Kaplan-Meier curve analysis showed that low TMB was associated with better clinical outcome in patients with gliomas. Additionally, a predictive model based on five HUB genes (FABP5, VEGFA, SAA1, ADM, and PRLHR) was constructed to predict OS in patients with gliomas. Receiver operating characteristic curve analysis shows that the model is reliable in predicting the risk of survival and prognosis. Immune microenvironment analysis revealed a correlation between TMB and infiltrating immune cells. The clinical-related immune gene, PRLHR, can be used as an independent prognostic factor for patients with brain glioma, and it is negatively correlated with the grade of glioma and age of patients with glioma. We found that the higher the tumor grade and the older the age, the lower the PRLHR expression, which was verified by CGGA database and independent experimental data. These results suggest that PRLHR may be a tumor suppressor for the progression of glioma and might provide a new therapeutic target for the treatment and improvement of survival rate in patients with glioma.

Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids

Human physiology is regulated by endogenous signalling compounds, including fatty acid amides (FAAs), chemical mimics of which are made by bacteria. The molecules produced by human-associated microbes are difficult to identify because they may only be made in a local niche or they require a substrate sourced from the host, diet or other microbes. We identified a set of uncharacterized gene clusters in metagenomics data from the human gut microbiome. These clusters were discovered to make FAAs by fusing exogenous fatty acids with amines. Using an in vitro assay, we tested their ability to incorporate 25 fatty acids and 53 amines known to be present in the human gut, from which the production of six FAAs was deduced (oleoyl dopamine, oleoyl tyramine, lauroyl tryptamine, oleoyl aminovaleric acid, α-linolenoyl phenylethylamine and caproyl tryptamine). These molecules were screened against panels of human G-protein-coupled receptors to deduce their putative human targets. Lauroyl tryptamine is found to be an antagonist to the immunomodulatory receptor EBI2 against its native oxysterol ligand (0.98 μM half-maximal inhibitory concentration), is produced in culture by Eubacterium rectale and is present in human faecal samples. FAAs produced by Clostridia may serve as a mechanism to modulate their host by mimicking human signalling molecules.

Assessment of ADCY9 polymorphisms and colorectal cancer risk in the Chinese Han population

BACKGROUND

Recently, ADCY9 has been found to be highly expressed in colon cancer, and high ADCY9 expressionis a poor prognostic factor of colon cancer. However, no study has reported on the relationship between single nucleotide polymorphisms (SNPs) of ADCY9 and colorectal cancer risk in the Chinese Han population.

METHODS

To evaluate the association between four ADCY9 SNPs and colorectal cancer risk, we performed a case-control study including 511 colorectal cancer patients and 511 healthy controls. SNPs were genotyped using the Agena MassARRAY platform (Agena Bioscience, San Diego, CA, USA). The distributions of alleles and genotypes frequencies between the case and control groups were compared using chi-squared. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by logistic regression adjusted for age and gender to assess the association between SNPs and colorectal cancer risk.

RESULTS

The overall analysis found that rs2230742 was associated with an increased risk of colorectal cancer (AA versus GG: OR = 3.54, 95% CI = 1.16-10.86, p = 0.027; recessive model: OR = 3.55, 95% CI = 1.16-10.85, p = 0.027). Stratification analysis showed that rs2230742 was associated with an increased rectal cancer risk; rs11076810 was associated with a reduced colorectal cancer risk for age > 59 years. No association was observed between other two SNPs and colorectal cancer risk.

CONCLUSIONS

Our findings suggest that ADCY9 polymorphisms (rs2230742 and rs11076810) have an effect on colorectal cancer risk in the Chinese Han population. Future association and functional studies are required to confirm our findings and explore the mechanism of ADCY2 in colorectal cancer.

Development and Validation of a Tumor Mutation Burden-Related Immune Prognostic Model for Lower-Grade Glioma

Tumor mutation burden (TMB) is a useful biomarker to predict prognosis and the efficacy of immune checkpoint inhibitors (ICIs). In this study, we aimed to explore the prognostic value of TMB and the potential association between TMB and immune infiltration in lower-grade gliomas (LGGs). Somatic mutation and RNA-sequencing (RNA-seq) data were downloaded from the Cancer Genome Atlas (TCGA) database. TMB was calculated and patients were divided into high- and low-TMB groups. After performing differential analysis between high- and low-risk groups, we identified six hub TMB and immune-related genes that were correlated with overall survival in LGGs. Then, Gene Set Enrichment Analysis was performed to screen significantly enriched GO terms between the two groups. Moreover, an immune-related risk score system was developed by LASSO Cox analysis based on the six hub genes and was validated with the Chinese Glioma Genome Atlas dataset. Using the TIMER database, we further systematically analyzed the relationships between mutants of the six hub genes and immune infiltration levels, as well as the relationships between the immune-related risk score system and the immune microenvironment in LGGs. The results showed that TMB was negatively correlated with OS and high TMB might inhibit immune infiltration in LGGs. Furthermore, the risk score system could effectively stratify patients into low- and high-risk groups in both the training and validation datasets. Multivariate Cox analysis demonstrated that TMB was not an independent prognostic factor, but the risk score was. Higher infiltration of immune cells (B cells, CD4⁺ T cells, CD8⁺ T cells, neutrophils, macrophages, and dendritic cells) and higher levels of immune checkpoints (PD-1, CTLA-4, LAG-3, and TIM-3) were found in patients in the high-risk group. Finally, a novel nomogram model was constructed and evaluated to estimate the overall survival of LGG patients. In summary, our study provided new insights into immune infiltration in the tumor microenvironment and immunotherapies for LGGs.

Association between polymorphisms of MIR17HG and risk of colorectal cancer in the Chinese Han population

Background

Colorectal cancer is the third most common cancer worldwide. Recently, an increasing number of evidences suggest that genetic susceptibility plays an important role in the occurrence of colorectal cancer. This study aimed to better understand the influence of MIR17HG polymorphisms on colorectal cancer susceptibility in the Chinese Han population.

Methods

We recruited 514 patients with colorectal cancer and 510 healthy controls to investigate the association between polymorphisms of MIR17HG and risk of colorectal cancer in the Chinese Han population. Genotyping was performed with the Agena MassARRAY platform. We used the χ² test to compare the distributions of single nucleotide polymorphisms (SNPs) allele and genotypes frequencies between cases and controls. Odds ratios and 95% confidence intervals were calculated by logistic regression analysis to evaluate the association under genetic models. Linkage disequilibrium between the five SNPs was assessed using the Haploview software.

Results

Overall analysis found that rs7336610 and rs1428 and haplotype CTAGA were significantly associated with increased risk of colorectal cancer. However, we found rs7318578 was associated with a decreased risk of colorectal cancer in the dominant model. Stratification analysis showed that rs7336610, rs7318578, and rs1428 were also associated with rectal cancer risk. Gender stratification analysis found that rs7336610, rs7318578, rs17735387, and rs1428 were significantly associated with colorectal cancer risk in males.

Conclusion

In conclusion, this study indicated that the polymorphisms of MIR17HG were associated with colorectal cancer risk. Therefore, our findings may provide new insights into the development of colorectal cancer. Further association and functional studies are of great importance to confirm these results and to define the potential biological mechanism of colorectal cancer.

IL1A polymorphisms is a risk factor for colorectal cancer in Chinese Han population: a case control study

BACKGROUND

Colorectal cancer (CRC) is one of the most common cancers worldwide, and genetic variations exert distinct roles in its pathogenesis. Single nucleotide polymorphisms (SNPs) in interleukin 1 alpha (IL1A) were reported to be correlated to the susceptibility of diverse cancers. The aim of this study was to assess the association of IL1A SNPs with the risk of colorectal cancer in a Chinese Han population.

METHODS

To evaluate the correlation between IL1A polymorphisms and CRC risk, Agena MassARRAY platform was used for genotype determination among 248 CRC patients and 463 controls. The relationships between IL1A variants and CRC susceptibility were examined by logistic regression analysis. Stratified analysis was conducted for the association detection in males and females. Haplotype construction and analysis were applied to evaluate the potential relationship between the genetic block and the risk of CRC. SNP functional exploration was performed with available bioinformatics datasets.

RESULTS

After adjusting for age and gender, the "AA" genotype of rs2856838 exhibited a risk association with colorectal cancer in the recessive model (adjusted OR = 1.98, 95% CI: 1.05-3.72, p = 0.036). With stratified analysis, the recessive models of rs3783550 (OR = 2.17, 95% CI: 1.03-4.60, p = 0.043), rs2856838 (OR = 2.58, 95% CI: 1.13-5.87, p = 0.024), rs1609682 (OR = 2.20, 95% CI: 1.04-4.65, p = 0.040), and rs3783521 (OR = 2.13, 95% CI: 1.01-4.49, p = 0.048) revealed significant relationships between these variants and an increased CRC risk only in females. Bioinformatics analysis also revealed the putative functions of the selected SNPs.

CONCLUSIONS

This study demonstrated that rs2856838 could influence the susceptibility to CRC in Chinese Han population from northwest China. IL1A variants rs3783550, rs2856838, rs1609682, and rs3783521 were associated with CRC risk only in females.

Association between IL-1 gene polymorphisms and tuberculosis susceptibility in the Chinese Tibetan population

Interleukin-1 (IL-1) gene is known to be implicated in tuberculosis (TB). The present case-control study was designed to investigate whether IL-1 polymorphisms associated with TB susceptibility in a Chinese Tibetan cohort. 300 Tibetan tuberculosis patients and 300 healthy controls were recruited for 12 single-nucleotide polymorphisms (SNPs) genotyping of IL-1 gene via Sequenom MassARRAY analysis. The odds ratio (OR) and 95% confidence interval (CI) were analyzed by unconditional logistic regression to evaluate the effect of polymorphisms on the risk of tuberculosis. Among genotyped SNPs, a significant high risk between TB and SNP rs3783550 G/T, rs3783546 G/C, rs2856838 A/G, rs1609682 G/T, rs3783521 A/G genotype within IL-1α as well as rs1143623 G/G genotype within IL-1β was found based on multiple model analysis. In addition, IL-1α SNPs mapped in a 10 kb LD block with D'>0.98, suggesting that a significant linkage disequilibrium presence among these SNPs, and "TCATG" haplotype of IL-1α SNPs with a 1.47-fold risk for TB was observed (P = 0.007). In conclusion, our data shed new light on how IL-1 SNPs may contribute to tuberculosis susceptibility in the Chinese Tibetan population.

Comprehensive transcriptomic analysis of heat shock proteins in the molecular subtypes of human breast cancer

BACKGROUND

Heat Shock Proteins (HSPs), a family of genes with key roles in proteostasis, have been extensively associated with cancer behaviour. However, the HSP family is quite large and many of its members have not been investigated in breast cancer (BRCA), particularly in relation with the current molecular BRCA classification. In this work, we performed a comprehensive transcriptomic study of the HSP gene family in BRCA patients from both The Cancer Genome Atlas (TCGA) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohorts discriminating the BRCA intrinsic molecular subtypes.

METHODS

We examined gene expression levels of 1097 BRCA tissue samples retrieved from TCGA and 1981 samples of METABRIC, focusing mainly on the HSP family (95 genes). Data were stratified according to the PAM50 gene expression (Luminal A, Luminal B, HER2, Basal, and Normal-like). Transcriptomic analyses include several statistical approaches: differential gene expression, hierarchical clustering and survival analysis.

RESULTS

Of the 20,531 analysed genes we found that in BRCA almost 30% presented deregulated expression (19% upregulated and 10% downregulated), while of the HSP family 25% appeared deregulated (14% upregulated and 11% downregulated) (|fold change| > 2 comparing BRCA with normal breast tissues). The study revealed the existence of shared HSP genes deregulated in all subtypes of BRCA while other HSPs were deregulated in specific subtypes. Many members of the Chaperonin subfamily were found upregulated while three members (BBS10, BBS12 and CCTB6) were found downregulated. HSPC subfamily had moderate increments of transcripts levels. Various genes of the HSP70 subfamily were upregulated; meanwhile, HSPA12A and HSPA12B appeared strongly downregulated. The strongest downregulation was observed in several HSPB members except for HSPB1. DNAJ members showed heterogeneous expression pattern. We found that 23 HSP genes correlated with overall survival and three HSP-based transcriptional profiles with impact on disease outcome were recognized.

CONCLUSIONS

We identified shared and specific HSP genes deregulated in BRCA subtypes. This study allowed the recognition of HSP genes not previously associated with BRCA and/or any cancer type, and the identification of three clinically relevant clusters based on HSPs expression patterns with influence on overall survival.

Combination analysis of NOS3, ABCB1 and IL23R polymorphisms with alcohol-induced osteonecrosis of the femoral head risk in Chinese males

Background

Common variants of multiple genes played a crucial role in osteonecrosis of the femoral head (ONFH) onset which was proved by many previous reports. We hypothesized that polymorphisms in NOS3, ABCB1 and IL23R were related to individual differences in alcohol sensitivity and the development of alcohol-induced ONFH.

Methods

In this case-control study, we evaluated 8 SNPs in three genes in the Chinese Han population including 355 male cases and 355 healthy male controls. These SNPs were genotyped by Sequenom MassARRAY RS1000. To identify their relationship with alcohol-induced ONFH susceptibility using χ² test and genetic model analysis.

Results

We found an association with alcohol-induced ONFH susceptibility for 4 SNPs (rs743506, rs3918184, rs13233308 and rs6693831) in three genes after adjusted by age. The genotype “G/A” of rs743506 in NOS3 gene acts as a risk factor in genotype (P = 0.003), dominant (P = 0.048), recessive (P = 0.005) and additive model(P = 0.006); The genotype “T/C” of rs3918184 in NOS3 gene acts as a risk factor in genotype (P = 0.012) and recessive model (P = 0.009); The genotype “T/C” of rs13233308 in ABCB1 gene acts as a risk factor in genotype (P = 0.038) and additive model(P = 0.041); The genotype “T/C” of rs6693831 in IL23R gene acts as a protective factor in genotype model (P = 0.046).

Conclusions

This study provides evidence for three alcohol-induced ONFH susceptibility genes (NOS3, ABCB1 and IL23R) in Chinese males and polymorphisms of them may be associated with alcohol-induced ONFH risk.

Association of genetic polymorphisms with laryngeal carcinoma prognosis in a Chinese population

We analyzed the effects of single-nucleotide polymorphisms (SNPs) on laryngeal carcinoma (LC) risk and overall survival (OS) in 170 Chinese male LC patients followed for 10 years. After assessment of clinical characteristics (age, laryngectomy, neck dissection, tumor differentiation, TNM status), the patients were genotyped for 24 SNPs associated with risk in multiple cancers. LC risk was assessed using log-rank test and Cox proportional hazard models. The median OS time was 48 months. By the follow-up deadline, OS was 41.2%. Kaplan-Meier analysis indicated 1-, 3-, and 5-year survival rates to be 84.7%, 57.2%, and 47.1%, respectively. Five LC clinicopathological characteristics, namely total laryngectomy (TL), low differentiation (LD), T3-T4, N1-N2, and clinical stage III-IV were associated with worse OS (HR: 2.35, p < 0.001; HR: 2.39, p = 0.02; HR: 2.17, p < 0.001; HR: 2.39, p < 0.001; and HR: 3.29, p < 0.001, respectively). Univariate cox regression analysis indicated that four SNPs were associated (p < 0.05) with LC OS in the codominant genetic model compared to patients with the homozygous wild-type genotype: rs10088262 G/A (HR = 1.57), rs1665650 A/G (HR = 0.65); rs3802842 C/C (HR = 2.18), and rs59336 T/A and T/T (HR = 0.61 and 2.61, respectively).

Inherited pancreatic cancer

Pancreatic cancers arise through a series of genetic events both inherited and acquired. Inherited genetic changes, both high penetrance and low penetrance, are an important component of pancreatic cancer risk, and may be used to characterize populations who will benefit from early detection. Furthermore, pancreatic cancer patients with inherited mutations may be particularly sensitive to certain targeted agents, providing an opportunity to personalized treatment. Family history of pancreatic cancer is one of the strongest risk factors for the disease, and is associated with an increased risk of caners at other sites, including but not limited to breast, ovarian and colorectal cancer. The goal of this chapter is to discuss the importance of family history of pancreatic cancer, and the known genes that account for a portion of the familial clustering of pancreatic cancer.