A region-based gene association study combined with a leave-one-out sensitivity analysis identifies SMG1 as a pancreatic cancer susceptibility gene

The causal relationship between 179 lipid species and urolithiasis: a bidirectional and multivariable Mendelian randomization study combined with meta-analysis

BACKGROUND

Previous research has suggested a potential link between urolithiasis and lipid species levels. A Mendelian randomization (MR) study was conducted to investigate whether a causal relationship exists between genetic susceptibility to plasma lipids and the risk of urolithiasis.

METHODS

Data on lipid species were collected from genome-wide association (GWAS) analyses of plasma lipidomes. For the initial analysis, GWAS data on urolithiasis were extracted using the GWAS ID ebi-a-GCST90018935. The inverse variance weighted (IVW) approach was utilized as the main method for MR analysis. Multivariable MR, multiple supplementary analyses, and comprehensive sensitivity analyses were also conducted. Additional independent datasets were utilized for replication analysis and meta-analysis.

RESULTS

Findings from the IVW method, repeated analyses, and meta-analysis revealed six significant causal effects of lipid species on urolithiasis. The specific lipid species identified were: phosphatidylcholine (PC; 16:1_20:4) levels [OR: 0.92; 95%CI: 0.87, 0.96; P = 6 × 10- 4], PC (16:0_20:4) levels [OR: 0.94; 95%CI: 0.90, 0.98; P = 0.0017], phosphatidylethanolamine (PE; 18:2_0:0) levels [OR: 1.10; 95%CI: 1.04, 1.15; P = 4 × 10- 4], PE (16:0_20:4) levels [OR: 1.05; 95%CI: 1.01, 1.09; P = 0.0028], PE (18:1_18:1) levels [OR: 1.06; 95%CI: 1.01, 1.11; P = 0.0136], and sterol ester (SE; 27:1/20:4) levels [OR: 0.93; 95%CI: 0.89, 0.96; P = 1.5 × 10- 4].

CONCLUSION

The MR study proposes a potential causal link between six plasma lipids and urolithiasis. Particularly, SEs (27:1/20:4), PC (16:0_20:4), and PC (16:1_20:4) may serve as potential inhibitors of calcium-containing urolithiasis growth. The integration of genomics and lipidomics in MR analysis holds promise for early screening, prevention, and treatment of urinary tract stones.

A virtual approach: Systematic review and meta-analysis of virtual reality-based therapies for convergence insufficiency

Convergence insufficiency (CI) is a common binocular vision disorder that significantly impacts visual comfort and quality of life. It has been hypothesized that CI therapy can also be provided effectively with Virtual reality (VR). Recently, a few studies were conducted on virtual reality-based CI therapy. However, to the best of the authors' knowledge, no systematic review and meta-analysis has been performed on the effectiveness of VR-based CI therapy. Therefore, this study aims to fill this critical gap and investigate the effectiveness of VR-based CI therapy. Consequently, it may be helpful to the clinicians, patients, and researchers to choose therapy, and develop future research studies. A systematic search was conducted on Google scholar, Scopus, PubMed and Science Direct until October 1, 2024. A total of 649 studies were screened, of which 3 studies were eligible to be included. We evaluated the quality and risk of bias for the included studies. Using the random-effects model, we found an overall mean difference of 3.38 (95% CI: 1.61, 5.16) before and after VR-based therapy. I² was 54.82% in our study, which indicates moderate heterogeneity. Then, we performed a Q test and found Q (df = 2) = 4.3593 and p-value = 0.1131, which indicates that albeit some heterogeneity observed in our analysis, it was not statistically significant. We also performed Leave-One-Out sensitivity analysis, which indicates that the overall findings of our analysis were relatively stable and not excessively dependent on any single selected study. No significant evidence of publication bias was found by using a funnel plot, Begg's test (Kendall's Tau = 1, p-value = 0.33), and Egger's test (intercept = 2.45, p-value = 0.40). Although we found VR based CI therapy has a positive effect, small sample size and variability in study methodologies make the current evidence insufficient to draw definitive conclusions regarding its effectiveness. Further studies are required to have more robust and reliable data.

Age at first sexual intercourse, age at menarche, and age at menopause: a mendelian randomization study on lung cancer risk

Background

There is increasing evidence that sex hormones are involved in the development of lung cancer, but the correlation between the reproductive behavior that changes sex hormone levels and lung cancer is not yet clear. Many previous studies have investigated the association between reproductive factors and lung cancer risk, but the results have been inconsistent. Therefore, we conducted a two-sample Mendelian randomization (MR) analysis to explore the potential relationship between age at first sexual intercourse (AFS), age at menarche, and age at menopause, and lung cancer.

Methods

We performed a MR analysis of the data from the genome-wide association study (GWAS) of European ancestry to evaluate the independent effects of three reproductive behaviors on lung cancer overall (LUCA), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), and small cell lung cancer (SCLC). We mainly used the inverse-variance weighting method for the MR analysis. Sensitivity was determined by a MR-pleiotropy residual sum and outlier analysis, a weighted median analysis, a MR-Egger analysis, and a leave-one-out analysis.

Results

The MR analysis results revealed that older AFS had a causal relationship with LUCA [odds ratio (OR) =0.6283, 95% confidence interval (CI): 0.4959-0.7961, P=0.0001), LUAD (OR =0.7042, 95% CI: 0.4967-0.9984, P=0.049), and LUSC (OR =0.6231, 95% CI: 0.4386-0.8853, P=0.0083).

Conclusions

Our results revealed a causal relationship between older AFS and a lower risk of lung cancer. Our findings emphasize the importance of providing sex education, as early sexual intercourse may have undesirable effects. In addition, early psychological treatment is also essential.

Association of obstructive sleep apnea syndrome with polycystic ovary syndrome through bidirectional Mendelian randomization

Background

Observational studies have established a link between polycystic ovary syndrome (PCOS) and obstructive sleep apnea syndrome (OSAS), with obesity being a significant confounding factor that complicates the understanding of causality. This study seeks to clarify the causal relationship by utilizing bidirectional two-sample Mendelian randomization (MR) analysis.

Methods

A bidirectional MR strategy was implemented to investigate the potential causal relationship between PCOS and OSAS. Instrumental variables (IVs) for PCOS were sourced from a dataset comprising 3,609 cases and 229,788 controls. For OSAS, statistical data were obtained from a genome-wide association study (GWAS) involving 38,998 subjects, alongside a control group of 336,659 individuals. Our MR analysis utilized several methods, including inverse variance weighted (IVW), weighted mode, weighted median, simple mode, and MR-Egger, primarily focusing on the IVW technique. Sensitivity tests were conducted to ensure the robustness of our findings.

Results

Utilizing the IVW method, we identified a notable causal association from OSAS to PCOS, with an odds ratio (OR) of 1.463 and a 95% confidence interval (CI) of 1.086-1.971 (p = 0.012). In the opposite direction, PCOS also appeared to significantly affect OSAS development, indicated by an OR of 1.041 and a 95% CI of 1.012-1.072 (p = 0.006). The MR-Egger intercept test showed no evidence of directional pleiotropy, affirming the credibility of our causal findings (p > 0.05).

Conclusion

This study suggests a bidirectional causal relationship between PCOS and an increased risk of OSAS. These insights could guide future screening and prevention strategies for both conditions.

Association of Barrett's esophagus with obstructive sleep apnea syndrome: a bidirectional analysis of Mendelian randomization

Background

Observational studies have reported associations between Barrett's esophagus (BE) and obstructive sleep apnea syndrome (OSAS), but the causal relationship remained unclear due to potential confounding biases. Our study aimed to elucidate this causal relationship by deploying a two-sample Mendelian randomization (MR) methodology.

Methods

Instrumental variables (IVs) for Barrett's esophagus were obtained from a public database that comprised 13,358 cases and 43,071 controls. To investigate OSAS, we utilized summary statistics from a comprehensive genome-wide association study (GWAS) encompassing 38,998 cases of OSAS and 336,659 controls. Our MR analyses adopted multiple techniques, including inverse variance weighted (IVW), weighted median, weighted mode, MR-Egger, and simple mode.

Results

The IVW analysis established a causal relationship between Barrett's esophagus and OSAS, with an odds ratio (OR) of 1.19 and a 95% confidence interval (CI) of 1.11-1.28 (p = 8.88E-07). Furthermore, OSAS was identified as a contributing factor to the onset of Barrett's esophagus, with an OR of 1.44 and a 95% CI of 1.33-1.57 (p = 7.74E-19). Notably, the MR-Egger intercept test found no evidence of directional pleiotropy (p > 0.05).

Conclusion

This study identifies a potential association between BE and an increased occurrence of OSAS, as well as the reverse relationship. These insights could influence future screening protocols and prevention strategies for both conditions.

Aberrant DNA Methylation Status and mRNA Expression Level of SMG1 Gene in Chronic Myeloid Leukemia: A Case-Control Study

OObjective: Chronic myeloid leukemia (CML) is a myeloproliferative malignancy with different stages. Aberrant epigenetic modifications, such as DNA methylation, have been introduced as a signature for diverse cancers which also plays a crucial role in CML pathogenesis and development. Suppressor with morphogenetic effect on genitalia (SMG1) gene recently has been brought to the spotlight as a potent tumor suppressor gene that can be suppressed by tumors for further progress. The present study aims to investigate SMG1 status in CML patients.

MATERIALS AND METHODS

In this case-control study, peripheral blood from 30 patients with different phases of CML [new case (N)=10, complete molecular remission (CMR)=10, blastic phase (BP)=10] and 10 healthy subjects were collected. Methylation status and expression level of SMG1 gene promoter was assessed by methylation-specific polymerase chain reaction (MSP) and quantitative reverse-transcription PCR, respectively.

RESULTS

MSP results of SMG1 gene promotor in the new case group were methylated (60% methylated, 30% hemimethylated and 10% unmethylated). All CMR and control group patients were unmethylated in the SMG1 gene promoter. In the BP group, methylated SMG1 promoter was seen (50% of patients had a methylated status and 50% had hemimethylated status). In comparison with the healthy subjects, expression level of SMG1 in the new case group was decreased (P<0.01); in the CMR group and BP-CML groups, it was increased (P<0.05). No significant correlation between patients' hematological features and SMG1 methylation was seen.

CONCLUSION

Our results demonstrated that aberrant methylation of SMG1 occurred in CML patients and it had a significant association with SMG1 expression. SMG1 gene promoter showed diverse methylated status and subsequent expression levels in different phases of CML. These findings suggested possible participation of SMG1 suppression in the CML pathogenesis.

Oncology clinic-based germline genetic testing for exocrine pancreatic cancer enables timely return of results and unveils low uptake of cascade testing

BACKGROUND

Traditional medical genetics models are unable to meet the growing demand for germline genetic testing (GT) in patients with exocrine pancreatic cancer (PC). This study investigates the impact of an ambulatory oncology clinic-based GT model.

METHODS

From 2012 to 2021, patients with PC were prospectively enrolled and considered for GT. Two chronological cohorts were compared: (1) the preuniversal genetic testing (pre-UGT) cohort, which received GT based on clinical criteria or family history; and (2) the post-UGT cohort, where an 86-gene panel was offered to all patients with PC.

RESULTS

Of 847 eligible patients, 735 (86.8%) were enrolled (pre-UGT, n=579; post-UGT, n=156). A higher proportion of the post-UGT cohort received prospective GT (97.4% vs 58.5%, p<0.001). The rate of pathogenic germline alterations (PGA) across both cohorts was 9.9%, with 8.0% of PGAs in PC susceptibility genes. The post-UGT cohort had a higher prevalence of overall PGAs (17.2% vs 6.6%, p<0.001) and PGAs in PC susceptibility genes (11.9% vs 6.3%, p<0.001). The median turnaround time from enrolment to GT report was shorter in the post-UGT cohort (13 days vs 42 days, p<0.001). Probands with a PGA disclosed their GT results to 84% of their first-degree relatives (FDRs). However, only 31% of informed FDRs underwent GT, and the number of new cases per index case was 0.52.

CONCLUSION

A point-of-care GT model is feasible and expedites access to GT for patients with PC. Strategies to increase the uptake of cascade testing are needed to maximise the clinical impact of an oncology clinic-based GT model.

Intra-Tumoral CD8+ T-Cell Infiltration and PD-L1 Positivity in Homologous Recombination Deficient Pancreatic Ductal Adenocarcinoma

The immune contexture of pancreatic ductal adenocarcinoma (PDAC) is generally immunosuppressive. A role for immune checkpoint inhibitors (ICIs) in PDAC has only been demonstrated for the rare and hypermutated mismatch repair (MMR) deficient (MMR-d) subtype. Homologous recombination repair (HR) deficient (HR-d) PDAC is more prevalent and may encompass up to 20% of PDAC. Its genomic instability may promote a T-cell mediated anti-tumor response with therapeutic sensitivity to ICIs. To investigate the immunogenicity of HR-d PDAC, we used multiplex immunohistochemistry (IHC) to compare the density and spatial distribution of CD8+ cytotoxic T-cells, FOXP3+ regulatory T-cells (Tregs), and CD68+ tumor-associated macrophages (TAMs) in HR-d versus HR/MMR-intact PDAC. We also evaluated the IHC positivity of programmed death-ligand 1 (PD-L1) across the subgroups. 192 tumors were evaluated and classified as HR/MMR-intact (n=166), HR-d (n=25) or MMR-d (n=1) based on germline testing and tumor molecular hallmarks. Intra-tumoral CD8+ T-cell infiltration was higher in HR-d versus HR/MMR-intact PDAC (p<0.0001), while CD8+ T-cell densities in the peri-tumoral and stromal regions were similar in both groups. HR-d PDAC also displayed increased intra-tumoral FOXP3+ Tregs (p=0.049) and had a higher CD8+:FOXP3+ ratio (p=0.023). CD68+ TAM expression was similar in HR-d and HR/MMR-intact PDAC. Finally, 6 of the 25 HR-d cases showed a PD-L1 Combined Positive Score of >=1, whereas none of the HR/MMR-intact cases met this threshold (p<0.00001). These results provide immunohistochemical evidence for intra-tumoral CD8+ T-cell enrichment and PD-L1 positivity in HR-d PDAC, suggesting that HR-d PDAC may be amenable to ICI treatment strategies.

The genetics of ductal adenocarcinoma of the pancreas in the year 2020: dramatic progress, but far to go

The publication of the "Pan-Cancer Atlas" by the Pan-Cancer Analysis of Whole Genomes Consortium, a partnership formed by The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC), provides a wonderful opportunity to reflect on where we stand in our understanding of the genetics of pancreatic cancer, as well as on the opportunities to translate this understanding to patient care. From germline variants that predispose to the development of pancreatic cancer, to somatic mutations that are therapeutically targetable, genetics is now providing hope, where there once was no hope, for those diagnosed with pancreatic cancer.

Identification of Novel BRCA1 and RAD50 Mutations Associated With Breast Cancer Predisposition in Tunisian Patients

Background

Deleterious mutations on BRCA1/2 genes are known to confer high risk of developing breast and ovarian cancers. The identification of these mutations not only helped in selecting high risk individuals that need appropriate prevention approaches but also led to the development of the PARP-inhibitors targeted therapy. This study aims to assess the prevalence of the most frequent BRCA1 mutation in Tunisia, c.211dupA, and provide evidence of its common origin as well as its clinicopathological characteristics. We also aimed to identify additional actionable variants using classical and next generation sequencing technologies (NGS) which would allow to implement cost-effective genetic testing in limited resource countries.

Patients and Methods

Using sanger sequencing, 112 breast cancer families were screened for c.211dupA. A set of patients that do not carry this mutation were investigated using NGS. Haplotype analysis was performed to assess the founder effect and to estimate the age of this mutation. Correlations between genetic and clinical data were also performed.

Results

The c.211dupA mutation was identified in 8 carriers and a novel private BRCA1 mutation, c.2418dupA, was identified in one carrier. Both mutations are likely specific to North-Eastern Tunisia. Haplotype analysis supported the founder effect of c.211dupA and showed its recent origin. Phenotype-genotype correlation showed that both BRCA1 mutations seem to be associated with a severe phenotype. Whole Exome Sequencing (WES) analysis of a BRCA negative family revealed a Variant of Unknown Significance, c.3647C > G on RAD50. Molecular modeling showed that this variant could be classified as deleterious as it is responsible for destabilizing the RAD50 protein structure. Variant prioritization and pathway analysis of the WES data showed additional interesting candidate genes including MITF and ANKS6.

Conclusion

We recommend the prioritization of BRCA1-c.211dupA screening in high risk breast cancer families originating from the North-East of Tunisia. We also highlighted the importance of NGS in detecting novel mutations, such as RAD50-c.3647C > G. In addition, we strongly recommend using data from different ethnic groups to review the pathogenicity of this variant and reconsider its classification in ClinVar.

Circular RNA VMA21 ameliorates sepsis-associated acute kidney injury by regulating miR-9-3p/SMG1/inflammation axis and oxidative stress

Accumulating evidence suggests that circular RNAs have the abilities to regulate gene expression during the progression of sepsis‐associated acute kidney injury. Circular RNA VMA21 (circVMA21), a recent identified circular RNA, could reduce apoptosis to alleviate intervertebral disc degeneration in rats and protect WI‐38 cells from lipopolysaccharide‐induced injury. However, the role of circVMA21 in sepsis‐associated acute kidney injury (sepsis‐associated AKI) is unknown. In this study, we first demonstrated that circVMA21 alleviated sepsis‐associated AKI by reducing apoptosis and inflammation in rats and HK‐2 cells. Additionally, to explore the molecule mechanism underlying the amelioration, after the bioinformatics analysis, we confirmed that miR‐9‐3p directly bound to circVMA21 by luciferase and RNA immunoprecipitation assay, and the effector protein of miR‐9‐3p was SMG1. Furthermore, the oxidative stress caused by sepsis‐associated AKI was down‐regulated by circVMA21. In conclusion, circVMA21 plays an important role in the regulating sepsis‐associated AKI via adjusting miR‐9‐39/SMG1/inflammation axis and oxidative stress.