Association between CCDC132, FDX1 and TNFSF13 gene polymorphisms and the risk of IgA nephropathy

Novel immune cross-talk between inflammatory bowel disease and IgA nephropathy

The mechanisms underlying the complex correlation between immunoglobulin A nephropathy (IgAN) and inflammatory bowel disease (IBD) remain unclear. This study aimed to identify the optimal cross-talk genes, potential pathways, and mutual immune-infiltrating microenvironments between IBD and IgAN to elucidate the linkage between patients with IBD and IgAN. The IgAN and IBD datasets were obtained from the Gene Expression Omnibus (GEO). Three algorithms, CIBERSORTx, ssGSEA, and xCell, were used to evaluate the similarities in the infiltrating microenvironment between the two diseases. Weighted gene co-expression network analysis (WGCNA) was implemented in the IBD dataset to identify the major immune infiltration modules, and the Boruta algorithm, RFE algorithm, and LASSO regression were applied to filter the cross-talk genes. Next, multiple machine learning models were applied to confirm the optimal cross-talk genes. Finally, the relevant findings were validated using histology and immunohistochemistry analysis of IBD mice. Immune infiltration analysis showed no significant differences between IBD and IgAN samples in most immune cells. The three algorithms identified 10 diagnostic genes, MAPK3, NFKB1, FDX1, EPHX2, SYNPO, KDF1, METTL7A, RIDA, HSDL2, and RIPK2; FDX1 and NFKB1 were enhanced in the kidney of IBD mice. Kyoto Encyclopedia of Genes and Genomes analysis showed 15 mutual pathways between the two diseases, with lipid metabolism playing a vital role in the cross-talk. Our findings offer insights into the shared immune mechanisms of IgAN and IBD. These common pathways, diagnostic cross-talk genes, and cell-mediated abnormal immunity may inform further experimental studies.

A Novel Cuproptosis-Related Prognostic Model and the Hub Gene FDX1 Predict the Prognosis and Correlate with Immune Infiltration in Clear Cell Renal Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC) is a common malignancy of the urological system with poor prognosis. Cuproptosis is a recently discovered novel manner of cell death, and the hub gene FDX1 could promote cuproptosis. However, the potential roles of cuproptosis-related genes (CRGs) and FDX1 for predicting prognosis, the immune microenvironment, and therapeutic response have been poorly studied in ccRCC. In the present study, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) data were downloaded. CRGs were subjected to prognosis analysis, and three of them were used to construct the prognostic model by least absolute shrinkage and selection operator (LASSO) regression. The CRGs prognostic model showed excellent performance. Moreover, based on the risk score of the model, the nomogram was developed to predict 1-year, 3-year, and 5-year survival. Furthermore, the hub gene of cuproptosis, FDX1, was an independent prognostic biomarker in multivariate Cox regression analysis. The pan-cancer analysis showed that FDX1 was significantly downregulated and closely related to prognosis in ccRCC among 33 cancer types. Lower FDX1 was also correlated with worse clinicopathologic features. The lower expression of FDX1 in ccRCC was verified in the external database and our own database, which may be caused by DNA methylation. We further demonstrated that the tumor mutational burden (TMB) and immune cell infiltration were related to the expression of FDX1. Immune response and drug sensitivity analysis revealed that immunotherapy or elesclomol may have a favorable treatment effect in the high FDX1 expression group and sunitinib or axitinib may work better in the low FDX1 expression group. In conclusion, we constructed a CRGs prognostic model and revealed that FDX1 could serve as a prognostic biomarker and predict therapeutic response in ccRCC. The study will provide a novel, precise, and individual treatment strategy for ccRCC patients.

Ferredoxin 1 is a cuproptosis-key gene responsible for tumor immunity and drug sensitivity: A pan-cancer analysis

Ferredoxin 1 (FDX1) functions by transferring electrons from NADPH to mitochondrial cytochrome P450 via the ferredoxin reductase and is the key regulator in copper-dependent cell death. Although mounting evidence supports a vital role for FDX1 in tumorigenesis of some cancers, no pan-cancer analysis of FDX1 has been reported. Therefore, we aimed to explore the prognostic value of FDX1 in pan-cancer and investigate its potential immune function. Based on data from The Cancer Genome Atlas, Cancer Cell Line Encyclopedia, Genotype Tissue-Expression, Human Protein Atlas, and Gene Set Cancer Analysis, we used a range of bioinformatics approaches to explore the potential carcinogenic role of FDX1, including analyzing the relationship between FDX1 expression and prognosis, DNA methylation, RNA methylation-related genes, mismatch repair (MMR) gene, microsatellite instability (MSI), tumor mutation burden (TMB), tumor microenvironment (TME), immune-related genes, and drug sensitivity in different tumors. The results show that FDX1 was lowly expressed in most cancers but higher in glioblastoma multiforme, stomach adenocarcinoma, and uterine corpus endometrial carcinoma. Moreover, FDX1 expression was positively or negatively associated with prognosis in different cancers. FDX1 expression was significantly associated with DNA methylation in 6 cancers, while there was a correlation between FDX1 expression and RNA methylation-related genes and MMR gene in most cancers. Furthermore, FDX1 expression was significantly associated with MSI in 8 cancers and TMB in 10 cancers. In addition, FDX1 expression was also significantly correlated with immune cell infiltration, immune-related genes, TME, and drug resistance in various cancers. An experiment in vitro showed FDX1 is downregulated by elesclomol, resulting in inhibiting cell viability of bladder cancer, clear cell renal cell carcinoma, and prostate cancer cells. Our study reveals that FDX1 can serve as a potential therapeutic target and prognostic marker for various malignancies due to its vital role in tumorigenesis and tumor immunity.

Molecular Subtyping Based on Cuproptosis-Related Genes and Characterization of Tumor Microenvironment Infiltration in Kidney Renal Clear Cell Carcinoma

The incidence of kidney renal clear cell carcinoma (KIRC) is rising worldwide, and the prognosis is poor. Cuproptosis is a new form of cell death that is dependent on and regulated by copper ions. The relationship between cuproptosis and KIRC remains unclear. In the current study, changes in cuproptosis-related genes (CRGs) in TCGA-KIRC transcriptional datasets were characterized, and the expression patterns of these genes were analyzed. We identified three main molecular subtypes and discovered that multilayer CRG changes were associated with patient clinicopathological traits, prognosis, elesclomol sensitivity, and tumor microenvironment (TME) cell infiltration characteristics. Then, a CRG score was created to predict overall survival (OS). The CRG score was found to be strongly linked to the TME. These findings may help elucidate the roles of CRGs in KIRC, potentially enhancing understanding of cuproptosis and supporting the development of more effective immunotherapy strategies.

Coiled-Coil Domain-Containing (CCDC) Proteins: Functional Roles in General and Male Reproductive Physiology

The coiled-coil domain-containing (CCDC) proteins have been implicated in a variety of physiological and pathological processes. Their functional roles vary from their interaction with molecular components of signaling pathways to determining the physiological functions at the cellular and organ level. Thus, they govern important functions like gametogenesis, embryonic development, hematopoiesis, angiogenesis, and ciliary development. Further, they are implicated in the pathogenesis of a large number of cancers. Polymorphisms in CCDC genes are associated with the risk of lifetime diseases. Because of their role in many biological processes, they have been extensively studied. This review concisely presents the functional role of CCDC proteins that have been studied in the last decade. Studies on CCDC proteins continue to be an active area of investigation because of their indispensable functions. However, there is ample opportunity to further understand the involvement of CCDC proteins in many more functions. It is anticipated that basing on the available literature, the functional role of CCDC proteins will be explored much further.

A Case-Control Study of ADCY9 Gene Polymorphisms and the Risk of Hepatocellular Carcinoma in the Chinese Han Population

Background: Adenylyl cyclase type 9 (ADCY9) modulates signal transduction by producing the second messenger cyclic AMP. It has been reported that ADCY9 gene polymorphisms were associated with cancer development. The aim of this study was to investigate whether ADCY9 gene polymorphisms could contribute to the susceptibility of hepatocellular carcinoma (HCC) in the Chinese Han population.

Methods: In the present study, five single-nucleotide polymorphisms (SNPs) in ADCY9 were genotyped using Agena MassARRAY platform in 876 subjects from China. Logistic regression was used to assess the effects of SNPs on HCC risk. Associations were also evaluated for HCC risk stratified by age and gender. False discovery rate (FDR) was used to correct multiple testing.

Results: After adjusting for age and gender, we found a significant relationship between heterozygous genotypes of rs2531995 and HCC risk (OR = 1.34, 95% CI = 1.01–1.77, p = 0.045). ADCY9 rs2230742 had a strong relationship with lower risk of HCC in allele (p = 0.006), co-dominant (p = 0.023), dominant (p = 0.010), and additive (p = 0.006) models. Stratified analysis showed that rs879620 increased HCC risk and rs2230742 was associated with lower risk of HCC in the individuals aged 55 or younger, rs2531992 significantly decreased HCC risk in the elder group (age > 55). For women, rs2230742 and rs2230741 were significantly associated with HCC risk in multiple models (p < 0.05). FDR analysis showed that rs2230742 could protect individuals from HCC risk in the allele model (FDR-p = 0.030). In addition, haplotype analysis indicated that C_rs879620A_rs2230742A_rs2230741 haplotype was a protective factor for HCC (OR = 0.67, 95% CI = 0.50–0.89, p = 0.007, FDR-p = 0.028).

Conclusion: Our findings suggest that ADCY9 gene polymorphisms are associated with HCC risk in the Chinese Han population.

Genetic variants of the MIR31HG gene are related to a risk of IgA nephropathy

IgA nephropathy (IgAN) is the most common primary glomerulonephritis worldwide. Previous studies reveal that genetic factors play a crucial role in IgAN progression. This study was conducted to investigate the association between MIR31HG variants and IgAN risk. A total of 836 subjects were recruited to detect the relationship of MIR31HG variants with IgAN susceptibility. Odds ratios (OR) and 95% confidence intervals (CI) were computed to evaluate the associations. Multifactor dimensionality reduction was performed to analyze the SNP-SNP interaction with IgAN risk. Our study showed that rs1332184 and rs55683539 significantly related to an increased risk of IgAN (OR 1.34, p = 0.041; OR 1.39, p = 0.025). Stratified analyses indicated rs72703442, rs55683539, and rs10965064 exhibited strongly enhanced risk of IgAN in age ≤ 35 years (OR 1.55, p = 0.023; OR 1.60, p = 0.012; OR 1.46, p = 0.037). Besides, we found rs1332184, rs55683539 and rs2181559 significantly increased the susceptibility of IgAN in males (OR 1.71, p = 0.003; OR 1.44, p = 0.042; OR 1.60, p = 0.010). We also observed that rs1332184 could enhance IgAN risk for Lee's grade ≥ III (OR 1.39, p = 0.045). Rs55683539 significantly increased a risk of IgAN (OR 1.58, p = 0.027), while rs2025327 had a lower risk of IgAN in Lee's grade < III (OR 0.46, p = 0.007). Interestingly, we found rs72703442 polymorphism was related to hemoglobin (p = 0.043), and rs10965064 was associated with Urine red blood cell (p = 0.040). Our study proposed that MIR31HG polymorphisms associate with susceptibility to IgAN in Chinese population.

Knockdown Of CCDC132 Attenuates Gastric Cancer Cells Proliferation And Tumorigenesis By Facilitating DNA Damage Signaling

Background

Aberrant endocytic recycling has fundamental functions on plasma membrane component turnover. Recent studies have identified an uncharacterized protein, CCDC132, in the endosome-associated recycling protein complex. Besides, our preliminary data first showed that CCDC132 was elevated in malignant neoplasms, especially in esophagus/stomach cancers. However, the functions and the underlying mechanisms of CCDC132 in gastric cancer (GC) biology remain unclear.

Methods

The CCDC132 mRNA expression in 4 GC cell lines and normal gastric epithelial cell lines was detected by qRT-PCR. Then, CCDC132 was downregulated in AGS and MGC-803 cells by lentivirus-induced RNA interfere, and cell viability assay, clone formation assay and apoptosis assay were carried out. The mechanism of CCDC132 on cell proliferation and apoptosis activation was explored using PathScan^® Stress, apoptosis signaling arrays and Western blot. We further investigated the pro-oncogenesis of CCDC132 in vivo. Meanwhile, immunohistochemistry was utilized to analyze the association between CCDC132 expression and clinicopathological features and prognosis. Finally, the correlation between CCDC132 and p53 was analyzed by Spearman’s rank correlation analysis.

Results

In this study, knockdown of CCDC132 significantly decreased cell proliferation and clone formation ability and facilitated apoptosis, and increased phosphorylation of p53 and Chk2 and protein levels of γ-H2AX, 53BP1, cleaved Caspase 3 and cleaved PARP. Additionally, knockdown of CCDC132 attenuated tumorigenesis and tumor growth of MGC-803 cell xenografts. CCDC132 expression was significantly higher in GC tissues compared with that in adjacent normal tissues and was positively correlated with nodal metastasis and TNM stage and negatively associated with prognosis. The survival rate of CCDC132 positive patients was lower than that of CCDC132-negative patients. Furthermore, CCDC132 expression was negatively related to p53.

Conclusion

This study unravels that knockdown of CCDC132 attenuates GC cell proliferation and tumorigenesis by facilitating DNA damage signaling, indicating that CCDC132 may serve as a potential target for GC therapy.

Three SNPs of FCRL3 and one SNP of MTMR3 are associated with immunoglobulin A nephropathy risk

PURPOSE

Immunoglobulin A nephropathy (IgAN) is determined by a combination of multiple genetic and environmental factors, but its etiology and pathogenesis are not well understood. We aim to determine whether variations in FCRL3 and MTMR3 correlate with IgAN risk indices in Chinese Han people.

METHODS

Eight single nucleotide polymorphisms (SNPs) of FCRL3 and MTMR3 were genotyped, and association analysis was performed. A total of 426 patients with IgAN and 498 healthy individuals, serving as the control group, were recruited for this association study.

RESULTS

There were significant associations between FCRL3 rs11264793 (OR = 0.78; 95 % CI = 0.63-0.98; p = 0.029), rs11264794 (OR = 0.81; 95 % CI = 0.67-0.98; p = 0.026) and rs7522061 (OR = 0.79; 95 % CI = 0.65-0.95; p = 0.012) and decreased risk of IgAN according to allele model results. Under genetic models, FCRL3 and MTMR3 were associated with the risk of IgAN. Interestingly, FCRL3 reduced the IgAN susceptibility only in females, while MTMR3 was a risk factor for IgAN only in males. In addition, FCRL3 rs11264793 and rs7522061 were significantly associated with a decreased risk of IgAN in different disease grades. Moreover, the haplotypes ACC (p = 0.02) and CTC (p = 0.017) of LD block rs11264794/rs7522061/rs11264799 in the FCRL3 gene were significantly associated with a decreased risk of IgAN.

CONCLUSIONS

We suggest that three SNPs of FCRL3 were associated with a decreased risk of IgAN, while one SNP of MTMR3 was associated with an increased risk of IgAN in Chinese Han populations. These findings may be useful in the development of early prognostics for IgAN.

Genetic Variations rs859, rs4646, and rs372883 in the 3'-Untranslated Regions of Genes Are Associated with a Risk of IgA Nephropathy

BACKGROUND

Previous studies indicate that genetic factors play an important role in the pathogenesis of IgA nephropathy (IgAN). To evaluate the association between single nucleotide polymorphisms (SNPs) in the 3'-untranslated region (3'-UTR) of genes and IgAN risk, we performed a case-control study in a Chinese Han population.

MATERIALS

Twelve SNPs were selected and genotyped in 384 IgAN patients and 357 healthy controls. Odds ratio (OR) and 95% confidence intervals (CI) were calculated by logistic regression adjusted for age and gender. Multifactor dimensionality reduction (MDR) was used to analyze the interaction of SNP-SNP with IgAN risk.

RESULTS

Our study demonstrated that IL-16 rs859 (OR = 0.75, p = 0.040) and CYP19A1 rs4646 (OR = 2.58, p = 0.017) polymorphism were related to the risk of IgAN. In stratified analyses by gender, CYP19A1 rs4646 (OR = 2.96, p = 0.015) and BACH1 rs372883 (OR = 1.81, p = 0.038) polymorphisms conferred susceptibility to IgAN in males. Besides, rs372883 reduced IgAN risk in females (OR = 0.44, p = 0.042). We also found rs859 polymorphism was correlated with grade I-II (OR = 0.42, p = 0.028) in subgroup analysis of Lee's classification. Additionally, we found rs4646 polymorphism was correlated with serum creatinine (p = 0.035).

CONCLUSION

Our results suggested that the IL-16 rs859, CYP19A1 rs4646, and BACH1 rs372883 polymorphisms have potential roles in the genetic susceptibility to IgAN in Chinese Han population.

Complement factor H gene polymorphism rs6677604 and the risk, severity and progression of IgA nephropathy: A systematic review and meta-analysis

AIM

Studies reporting the association between complement factor H gene rs6677604 polymorphism and susceptibility to IgA nephropathy (IgAN) had yielded inconsistent results. We performed a systematic review and meta-analysis to clarify the association between rs6677604 and IgAN susceptibility, disease severity and chronic progression.

METHODS

A comprehensive database search was performed to identify eligible studies. Meta-analyses were performed for rs6677604 allele frequency, genotypes and the association with IgAN susceptibility.

RESULTS

10 studies were included in the systematic review. Among them, four studies containing 10 distinct datasets (15,617 cases and 31,957 controls) were included in the meta-analysis. The pooled frequency of the minor allele (A) was significantly higher in Europeans than in Asians across both IgAN cases and controls, and the frequency of the minor allele (A) in IgAN cases was also significantly lower than that in controls across both European and Asian subgroups. Significant associations were detected between rs6677604 and risk of developing IgAN, when comparing allele A vs. G, genotype AA vs. GG, genotype AA vs. AG and genotype AG vs. GG. In analysis stratified by ethnicity, significant association was only observed in Europeans but not in Asians when comparing AA vs. GG or AA vs. AG.

CONCLUSION

Our pooled analysis showed a significant association between rs6677604-(A) allele and IgAN susceptibility, supporting the importance of complement activation in the pathogenesis of IgAN. The presence of rs6677604-(A) allele may be associated with a decreased the risk of IgAN in Europeans, but the association was not confirmed in Asians.

Association between the <b><i>ACYP2</i></b> Polymorphisms and IgAN Risk in the Chinese Han Population

<b><i>Background/Aims:</i></b> The association between <i>ACYP2</i>(Acylphosphatase 2) polymorphisms and immunoglobulin A nephropathy (IgAN) risk in the Chinese Han population remains unclear. We aimed to evaluate the association between <i>ACYP2</i> polymorphisms and IgAN risk by performing a case-control study. <b><i>Methods:</i></b> Eleven <i>ACYP2</i> single nucleotide polymorphisms (SNPs) from 416 IgAN patients and 495 healthy controls were genotyped using the Sequenom MassARRAY platform. Odds ratio (OR) and 95% confidence interval (CI) were calculated to evaluate the association of <i>ACYP2</i> polymorphisms with IgAN risk. <b><i>Results:</i></b> We observed that rs843720 was significantly associated with an increased risk of IgAN (allele G: OR = 1.23, 95% CI: 1.01–1.49, <i>p</i> = 0.036; dominant model: OR = 1.55, 95% CI: 1.01–2.37, <i>p =</i>0.044; log-additive model: OR = 1.43, 95% CI: 1.04–1.95, <i>p</i> = 0.026) before Bonferroni correction. The SNP rs12615793 was also significantly associated with an increased IgAN risk in the recessive model (OR = 3.33, 95% CI: 1.05–10.51, <i>p</i> = 0.042) before Bonferroni correction. <b><i>Conclusion:</i></b> These findings suggested that polymorphisms (rs843720 and rs12615793) of <i>ACYP2</i> may be pivotal in the development of IgAN. However, more functional and association studies with larger sample sizes should be performed to further validate our results in the future.

IgA Nephropathy Susceptibility Loci and Disease Progression

BACKGROUND AND OBJECTIVES

At least 20 susceptibility loci of IgA nephropathy have been identified by genome-wide association studies to date. Whether these loci were associated with disease progression is unclear.

DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS

We enrolled 613 adult patients with IgA nephropathy for a follow-up of ≥12 months. All 20 IgA nephropathy susceptibility loci were selected and their tag single nucleotide polymorphisms (SNPs) were genotyped. After strict quality control, 16 SNPs and 517 patients with IgA nephropathy were eligible for subsequent analysis. Progression was defined as ESKD or 50% decrease in eGFR. A stepwise Cox regression analysis of all SNPs on Akaike information criterion was performed to select the best model.

RESULTS

A four-SNP model, rs11150612 (ITGAM-ITGAX), rs7634389 (ST6GAL1), rs2412971 (HORMAD2), and rs2856717 (HLA-DQ/DR), was selected as the best predictive model. The genetic risk score calculated on the basis of the four SNPs was independently associated with disease progression before (hazard ratio [HR], 1.65; 95% confidence interval [95% CI], 1.29 to 2.12) and after adjustment by a recently reported clinical model (HR, 1.29; 95% CI, 1.03 to 1.62) or clinical-pathologic model (HR, 1.35; 95% CI, 1.03 to 1.77). Compared with low genetic risk, patients with middle genetic risk had a 2.12-fold (95% CI, 1.33 to 3.40) increase of progression risk, whereas patients with high genetic risk had 3.61-fold (95% CI, 2.00 to 6.52) progression risk increase. In addition, incorporation of genetic risk score could potentially increase discrimination of the clinical model (c-statistic increase from 0.83 to 0.86) or the clinical-pathologic model (c-statistic increase from 0.82 to 0.85) in predicting 5-year progression risk.

CONCLUSIONS

The four-SNP genetic risk score was independently associated with IgA nephropathy progression and could enhance the performance of clinical and clinical-pathologic risk models.

Association analysis of CHRNA3 polymorphisms with schizophrenia in a Chinese Han population: A case-control study

Schizophrenia (SCZ) is a highly heritable, chronic, severe psychiatric disorder associated with significant financial costs to families and societies. In this case-control study, we investigated the associations between seven SNPs in CHRNA3 gene and the risk of SCZ.A total of 1071 (384 cases and 687 controls) unrelated subjects were recruited for our association study. Seven candidate tagging SNPs in CHRNA3 gene (rs3743077, rs1317286, rs938682, rs12914385, rs2869546, rs3743075, rs8040868) selected in HapMap database were genotyped by Sequenom MassARRAY. Finally, association analysis was conducted under various models.According to our results, in genetic model analysis, rs12914385 and rs8040868 are associated with decreased risk of SCZ in female subgroup; rs3743075 is associated with decreased risk of SCZ in subgroup with age <45; while rs3743077 and rs2869546 are associated with increased risk of SCZ. Haplotype analysis suggested that the 3 variants comprised 1 block, and that the haplotype Ars938682Crs12914385Crs2869546 was significantly correlated with an increased risk of SCZ in the subgroup with age ≥45.Our data indicate potential associations between CHRNA3polymorphisms and SCZ susceptibility, and the significant variants identified in our study may be used as genetic biomarkers for SCZ susceptibility in Chinese Han population.

Angiotensin II receptor 1 gene variants are associated with high-altitude pulmonary edema risk

Previous studies demonstrated that Angiotensin II Receptor 1 (AGTR1) may play an important role in the development of high-altitude pulmonary edema. We envisaged a role for AGTR1 gene variants in the pathogenesis of HAPE and investigated their potential associations with HAPE in a Han Chinese population. We genotyped seven AGTR1 polymorphisms in 267 patients with diagnosed HAPE and 304 controls and evaluated their association with risk of HAPE. Statistically significant associations were found for the single nucleotide polymorphisms (SNPs) rs275651 (p = 0.017; odds ratio [OR] = 0.65) and rs275652 (p = 0.016; OR = 0.64). Another SNP rs10941679 showed a marginally significant association after adjusting for age and sex in the additive genetic model (adjusted OR = 1.44, 95% CI = 1.01-2.04, p = 0.040). Haplotype analysis confirmed that the haplotype "AG" was associated with a 35% reduction in the risk of developing HAPE, while the haplotype "AA" increased the risk of developing HAPE by 44%. These results provide the first evidence linking genetic variations in AGTR1 with HAPE risk in Han Chinese individuals.