Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

PRCP is a promising drug target for intracranial aneurysm rupture supported via multi-omics analysis

BACKGROUND

Cerebral aneurysms are life-threatening cerebrovascular disorders. Currently, there are no effective treatments for preventing disease progression. Mendelian randomisation (MR) is widely used to repurify licensed drugs and identify new therapeutic targets. Therefore, this study aims to investigate effective drug targets for preventing the formation and rupture of cerebral aneurysms and analyse their potential mechanisms.

METHODS

We performed a comprehensive study integrating two-sample MR analysis, colocalisation analysis and summary data-based Mendelian randomisation (SMR) to assess the causal effects of blood and brain druggable cis-expression quantitative trait loci (cis-eQTLs) on intracranial aneurysm (IA), unruptured intracranial aneurysm (UIA) and subarachnoid haemorrhage of IA rupture (SAH). Druggable genes were obtained from the study by Chris Finan et al, cis-eQTLs from the eQTLGen and PsychENCODE consortia. Results were validated using proteomic and transcriptomic data. Single-gene functional analyses probed potential mechanisms, culminating in the construction of a drug-gene regulation network.

RESULTS

Through the MR analysis, we identified four potential drug targets in the blood, including prolylcarboxypeptidase (PRCP), proteasome 20S subunit alpha 4 (PSMA4), LTBP4 and GPR160 for SAH. Furthermore, two potential drug targets (PSMA4 and SLC22A4) were identified for IA and one potential drug target (KL) for UIA after accounting for multiple testing (P(inverse-variance weighted)<8.28e-6). Strong evidence of colocalisation and SMR analysis confirmed the relevance of PSMA4 and PRCP in outcomes. Elevated PRCP circulating proteins correlated with a lower SAH risk. PRCP gene expression was significantly downregulated in the disease cohort.

CONCLUSIONS

This study supports that elevated PRCP gene expression in blood is causally associated with the decreased risk of IA rupture. Conversely, increased PSMA4 expression in the blood is causally related to an increased risk of IA rupture and formation.

Genetic evidence from Mendelian randomization links CD40 levels to increased risk of estrogen receptor-positive breast cancer

This study uses Mendelian randomization (MR) to investigate the causal roles of CD40 and CD40L in BC.Data from genome-wide association studies (GWAS) on BC (overall, ER-positive, and ER-negative subtypes) and CD40/CD40L levels were obtained from the IEU database. Causal associations were assessed using the inverse-variance weighted (IVW) method, with additional robustness checks performed via MR-Egger, weighted median, and weighted mode methods. Sensitivity analyses, including Cochran's Q test and MR-PRESSO, were conducted to assess heterogeneity and pleiotropy. Reverse MR analyses were also performed to examine if BC influences CD40/CD40L levels.A borderline significant association was found between CD40 levels and overall BC risk (IVW OR 1.027, 95% CI 1.000-1.054, p = 0.049), with a more robust association observed for ER-positive BC (OR 1.048, 95% CI 1.016-1.082, p = 0.003). No significant associations were found between CD40 levels and ER-negative BC. CD40L did not show any significant associations with BC. Reverse MR analysis indicated no causal effect of BC on CD40/CD40L levels. CD40 is causally associated with a borderline increase in overall BC risk and a more significant increase in ER-positive BC risk. These findings suggest a potential role for CD40 in BC, particularly in ER-positive cases.

Genomic alterations in normal breast tissues preceding breast cancer diagnosis

BACKGROUND

Normal breast tissues adjacent to cancer often harbor many of the same genomic alterations as the cancer itself. However, it remains unclear whether histologically normal breast tissues carry genomic changes related to cancer development years before a cancer diagnosis.

METHODS

Whole exome sequencing was performed to examine germline and somatic alterations in histologically normal breast tissues from women who subsequently developed breast cancer (n = 79, pre-diagnosis tissues) and compared these with results from breast tissues of women who did not (n = 81). No patient had germline mutations in cancer predisposition genes.

RESULTS

The pre-diagnosis tissues had significantly more high functional impact germline variants per sample than the healthy controls (P = 0.034), 36.5% of affected genes were cancer hallmark genes, among these 62.4% were involved with evading growth suppressors and 5.7% with genome instability. The average number of somatic mutations were similar between the two cohorts. Mutation signature analysis revealed COSMIC signatures 3 (associated with impaired homologous recombination) as a dominant signature more frequent in pre-diagnosis tissues. At gene and variant level, nine common germline polymorphisms in two immune regulatory genes, FCGBP and TPSBP2, and along with three somatic mutations in F13A1, FRY and TMLHE, were significantly more frequently mutated in the pre-diagnosis samples.

CONCLUSIONS

Individuals who develop breast cancer have a higher germline variant burden in normal breast tissues leading to subtle deficiencies in DNA repair that in the context of other germline and somatic mutations could facilitate malignant transformation.

A metabolic shift to the serine pathway induced by lipids fosters epigenetic reprogramming in nontransformed breast cells

Lipid metabolism and the serine, one-carbon, glycine (SOG) and methionine pathways are independently and significantly correlated with estrogen receptor-negative breast cancer (ERneg BC). Here, we propose a link between lipid metabolism and ERneg BC through phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme in the de novo serine pathway. We demonstrate that the metabolism of the paradigmatic medium-chain fatty acid octanoic acid leads to a metabolic shift toward the SOG and methionine pathways. PHGDH plays a role in both the forward direction, contributing to the production of S-adenosylmethionine, and the reverse direction, generating the oncometabolite 2-hydroxyglutarate, leading to epigenomic reprogramming and phenotypic plasticity. The methionine cycle is closely linked to the transsulfuration pathway. Consequently, we observe that the shift increases the antioxidant glutathione, which mitigates reactive oxygen species (ROS), enabling survival of a subset of cells that have undergone DNA damage. These metabolic changes contribute to several hallmarks of cancer.

Association between sex steroid hormones and α-klotho: Results from the NHANES 2013-2016 and Mendelian randomization study

PURPOSE

This study aimed to explore the association and causal links between sex steroid hormones and the anti-aging protein α-Klotho, extending to investigate the mediation effects of potential mediators.

METHODS

Based on data from the National Health and Nutrition Examination Survey (NHANES) 2013-2016, this study performed weighted multivariable-adjusted logistic regression to evaluate the association between sex steroid hormones and α-Klotho. Then, utilizing summary data from genome-wide association studies (GWAS), a bidirectional two-sample Mendelian randomization (MR) was conducted to assess the causal relationship between sex steroid hormones and α-Klotho. Finally, mediation analysis was conducted to delineate the influence of five identified potential mediators on the sex steroid hormones-α-Klotho association.

RESULTS

In men, significant positive correlations with α-Klotho were consistent across both unadjusted and fully adjusted models for total testosterone (TT), bio-available testosterone (Bio-T), estradiol (E2) and sex hormone-binding globulin (SHBG) (Model 3: TT: β = 3.54, 95 % CI: 1.63-5.44, P = 0.0003; Bio-T: β = 1.74, 95 % CI: 0.73-2.74, P = 0.0007; E2: β = 0.25, 95 % CI: 0.11-0.38, P = 0.0003; SHBG: β = 0.95, 95 % CI: 0.63-1.27, P < 0.0001); In premenopausal women, we detected a potential nonlinear relationship between TT levels and α-Klotho, with α-Klotho levels rising to a peak at a TT level of 72.2 ng/mL, after which they declined. Furthermore, results from MR analyses reaffirmed positive associations of TT and Bio-T with α-Klotho in men (TT: β = 3.54, 95 % CI: 1.63-5.44, P = 0.0003; Bio-T: β = 1.74, 95 % CI: 0.73-2.74, P = 0.0007). Finally, significant mediation effects were observed for uric acid (β = 0.27, 95 % CI: 0.15-0.67, P < 0.0001) and creatinine (β = 0.05, 95 % CI: 0.01-0.16, P = 0.0060), accounting for 26.7 % and 5.23 % of the total mediation effect, respectively.

CONCLUSION

In conclusion, our results demonstrate that both TT and Bio-T enhance the expression of α-Klotho in men. The positive association observed may be partly mediated by uric acid and creatinine.

Genetic regulation of TERT splicing affects cancer risk by altering cellular longevity and replicative potential

The chromosome 5p15.33 region, which encodes telomerase reverse transcriptase (TERT), harbors multiple germline variants identified by genome-wide association studies (GWAS) as risk for some cancers but protective for others. Here, we characterize a variable number tandem repeat within TERT intron 6, VNTR6-1 (38-bp repeat unit), and detect a strong link between VNTR6-1 alleles (Short: 24-27 repeats, Long: 40.5-66.5 repeats) and GWAS signals rs2242652 and rs10069690 within TERT intron 4. Bioinformatics analyses reveal that rs10069690-T allele increases intron 4 retention while VNTR6-1-Long allele expands a polymorphic G-quadruplex (G4, 35-113 copies) within intron 6, with both variants contributing to variable TERT expression through alternative splicing and nonsense-mediated decay. In two cell lines, CRISPR/Cas9 deletion of VNTR6-1 increases the ratio of TERT-full-length (FL) to the alternative TERT-β isoform, promoting apoptosis and reducing cell proliferation. In contrast, treatment with G4-stabilizing ligands shifts splicing from TERT-FL to TERT-β isoform, implicating VNTR6-1 as a splicing switch. We associate the functional variants VNTR6-1, rs10069690, and their haplotypes with multi-cancer risk and age-related telomere shortening. By regulating TERT splicing, these variants may contribute to fine-tuning cellular longevity and replicative potential in the context of stress due to tissue-specific endogenous and exogenous exposures, thereby influencing the cancer risk conferred by this locus.

Potential drug targets for systemic lupus erythematosus identified through Mendelian randomization analysis

So far, there is no clear pathogenesis and no cure for systemic lupus erythematosus (SLE). The therapeutic benefits of existing drug therapies are far from ideal. The proteome is a major source of therapeutic targets. Therefore, new drug targets for SLE need to be discovered. Based on the STROBE-Mendelian randomization (MR) checklist, we performed MR to explore potential drug targets for SLE, using genome-wide association study summary statistics of plasma and cerebrospinal fluid (CSF) and further replicated in the external validation. Bidirectional MR, reverse causality testing by Steiger filtering, Bayesian co-localization were used. In addition, protein-protein interaction networks (PPI) were performed to reveal potential associations between proteins and current SLE drugs. At false discovery rate (FDR) significance (PFDR < .05), MR analysis revealed 8 proteins. Five proteins decreased the SLE risks, whereas the other 3 proteins increased the SLE risks. None of the 8 proteins had reverse causality except sICAM-1. Bayesian co-localization suggested that 5 proteins shared the same variant with SLE. PPI network suggested that intercellular adhesion molecular 1 (ICAM-1), Fc-gamma-RIIb (FCG2B) and N-terminal pro-B-type natriuretic peptide (N-terminal pro-BNP) interacted with targets of current SLE medications. Our integrative analysis revealed that SLE risk is causally associated with ICAM-1, FCG2B, and N-terminal pro-BNP. These 3 proteins have the potential to become drug targets of SLE, especially for ICAM-1 and FCG2B. More further studies are also warranted to support this finding.

Latent Association Between Diets and Glioma Risk: A Mendelian Randomization Analysis

BACKGROUND

Gliomas, particularly high-grade gliomas such as glioblastoma, represent a major challenge due to their poor prognosis. While dietary factors have been proposed as potential modulators of glioma risk, causal inference has been hindered by confounding and reverse causality in observational studies. This study employs Mendelian randomization to investigate the causal relationship between dietary factors and glioma risk.

METHODS

A two-sample MR framework was applied, utilizing genome-wide association study data for 22 dietary exposures and glioma risks, including both GBM and non-GBM subtypes. Instrumental variables (genetic variants) were identified for each dietary factor to address confounding and pleiotropy. Causal inference was conducted using inverse-variance weighted regression, complemented by MR-Egger and MR-PRESSO analyses to assess and correct for potential pleiotropy.

RESULTS

A positive causal association was observed between the intake of cooked vegetables and the GBM risk (OR = 6.55, 95% CI: 1.86-23.12, p = 0.00350). While alcohol intake demonstrated a protective effect for non-GBM risk (OR = 0.770, 95% CI: 0.61-0.97, p = 0.029), beer was substantially linked to an increased risk of non-GBM gliomas (OR = 4.82, 95% CI: 1.84-12.59, p = 0.0014). Other dietary factors did not exhibit significant causal associations.

CONCLUSIONS

These findings suggest that certain dietary factors, including cooked vegetable intake, beer consumption, and alcohol intake, may exert a causal influence on glioma risk. This study provides new insights into the potential dietary determinants of glioma and underscores the need for further investigation into modifiable risk factors for glioma prevention.

Testosterone and colorectal cancer: a bidirectional Mendelian randomization study

Background

Although Mendelian randomization (MR) studies have been conducted on the causal relationship of testosterone on colorectal cancer (CRC), the result remains controversial. We aimed to explore the genetically determined relationships between total testosterone (TT) and bioavailable testosterone (BT) with CRC using a larger sample size and more stringent methods to exclude confounding factors.

Methods

Based on genome wide association studies (GWAS) data of TT, BT and CRC, we utilized bidirectional two-sample MR methods to analyze their interrelationships. Causal relationship analysis was conducted using inverse variance weighting (IVW), MR-Egger, weighted median, simple mode and weighted mode. Sensitivity analyses were performed to examine the stability of the causal relationships.

Results

The bidirectional MR analysis revealed one standard deviation (SD) increase in genetically predicted BT increased the risk of CRC [IVW: odds ratio (OR) =1.834, 95% confidence interval (CI): 1.121-3.001, P=0.02] and there was no causal relationship of CRC on BT. There was no causal relationship between CRC and TT.

Conclusions

The findings of this study revealed a causal effect of BT on the risk of CRC, and CRC may not affect BT levels. Additionally, there was no causal relationship found between CRC and TT. Our results enhance the understanding of the real causal relationship between testosterone and CRC.

Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes

BACKGROUND

Genetic studies have associated thousands of enhancers with breast cancer (BC). However, the vast majority have not been functionally characterized. Thus, it remains unclear how BC-associated enhancers contribute to cancer.

RESULTS

Here, we perform single-cell CRISPRi screens of 3513 regulatory elements associated with breast cancer to measure the impact of these regions on transcriptional phenotypes. Analysis of > 500,000 single-cell transcriptomes in two breast cancer cell lines shows that perturbation of BC-associated enhancers disrupts breast cancer gene programs. We observe BC-associated enhancers that directly or indirectly regulate the expression of cancer genes. We also find one-to-multiple and multiple-to-one network motifs where enhancers indirectly regulate cancer genes. Notably, multiple BC-associated enhancers indirectly regulate TP53. Comparative studies illustrate subtype specific functions between enhancers in ER + and ER - cells. Finally, we develop the pySpade package to facilitate analysis of single-cell enhancer screens.

CONCLUSIONS

Overall, we demonstrate that enhancers form regulatory networks that link cancer genes in the genome, providing a more comprehensive understanding of the contribution of enhancers to breast cancer development.

Genome-wide association studies are enriched for interacting genes

BACKGROUND

With recent advances in single cell technology, high-throughput methods provide unique insight into disease mechanisms and more importantly, cell type origin. Here, we used multi-omics data to understand how genetic variants from genome-wide association studies influence development of disease. We show in principle how to use genetic algorithms with normal, matching pairs of single-nucleus RNA- and ATAC-seq, genome annotations, and protein-protein interaction data to describe the genes and cell types collectively and their contribution to increased risk.

RESULTS

We used genetic algorithms to measure fitness of gene-cell set proposals against a series of objective functions that capture data and annotations. The highest information objective function captured protein-protein interactions. We observed significantly greater fitness scores and subgraph sizes in foreground vs. matching sets of control variants. Furthermore, our model reliably identified known targets and ligand-receptor pairs, consistent with prior studies.

CONCLUSIONS

Our findings suggested that application of genetic algorithms to association studies can generate a coherent cellular model of risk from a set of susceptibility variants. Further, we showed, using breast cancer as an example, that such variants have a greater number of physical interactions than expected due to chance.

Genetically predicted brain cortical structure mediates the causality between insulin resistance and cognitive impairment

Background

Insulin resistance is tightly related to cognition; however, the causal association between them remains a matter of debate. Our investigation aims to establish the causal relationship and direction between insulin resistance and cognition, while also quantifying the mediating role of brain cortical structure in this association.

Methods

The publicly available data sources for insulin resistance (fasting insulin, homeostasis model assessment beta-cell function and homeostasis model assessment insulin resistance, proinsulin), brain cortical structure, and cognitive phenotypes (visual memory, reaction time) were obtained from the MAGIC, ENIGMA, and UK Biobank datasets, respectively. We first conducted a bidirectional two-sample Mendelian randomization (MR) analysis to examine the susceptibility of insulin resistance on cognitive phenotypes. Additionally, we applied a two-step MR to assess the mediating role of cortical surficial area and thickness in the pathway from insulin resistance to cognitive impairment. The primary Inverse-variance weighted, accompanied by robust sensitivity analysis, was implemented to explore and verify our findings. The reverse MR analysis was also performed to evaluate the causal effect of cognition on insulin resistance and brain cortical structure.

Results

This study identified genetically determined elevated level of proinsulin increased reaction time (beta=0.03, 95% confidence interval [95%CI]=0.01 to 0.05, p=0.005), while decreasing the surface area of rostral middle frontal (beta=-49.28, 95%CI=-86.30 to -12.27, p=0.009). The surface area of the rostral middle frontal mediated 20.97% (95%CI=1.44% to 40.49%) of the total effect of proinsulin on reaction time. No evidence of heterogeneity, pleiotropy, or reverse causality was observed.

Conclusions

Briefly, our study noticed that elevated level of insulin resistance adversely affected cognition, with a partial mediation effect through alterations in brain cortical structure.

Erythema nodosum, malignant melanoma and non-melanoma skin cancer in relation to inflammatory bowel disease: a Mendelian randomization study

Inflammatory bowel disease (IBD) is a multisystem condition that could affect the cutaneous systems, namely cutaneous extraintestinal manifestations (EIMs). It has been suggested that IBD is associated with erythema nodosum (EN), malignant melanoma (MM) and non-melanoma skin cancer (NMSC). However, the potential causal relationship between IBD and the mentioned above cutaneous EIMs is still unclear. This study aims to determine the effect of IBD on EN, MM and NMSC within a Mendelian randomization (MR) design. Summary-level data for IBD, EN, MM, NMSC were obtained from large-scale genome-wide association studies. We utilized five different methods, including the inverse variance weighted model (IVW), MR Egger, Weighted median, Simple mode, Weighted mode in the MR analysis, then the Cochran's Q test, the MR-Egger pleiotropy test, the MR-PRESSO global pleiotropy test and leave-one-out sensitivity test were used to evaluate the heterogeneity and pleiotropy of identified IVs. To further ensure the validity of our findings, we evaluated the strength of the instrumental variables using the F-statistic and estimated the statistical power of our study. Findings were verified using an independent validation dataset, as well as through different MR methods with different model assumptions. MR analysis suggested that genetically determined IBD had a detrimental causal effect on NMSC (IVW: odds ratio [OR] = 1.002037, 95% confidence interval [CI] = 1.0001150-1.003962, P = 0.03776677), but not on EN (IVW: [OR] = 1.0937191, 95% [CI] = 0.9685831-1.235022, P = 0.1484349) and MM (IVW: [OR] = 0.9998064, 95% [CI] = 0.9994885-1.000124, P = 0.2326482). Besides, a positive causal effect of IBD on NMSC was verified in an independent validation dataset (IVW: [OR] = 1.002651, 95% [CI] = 1.0006524-1.004654, P = 0.009307506). The present study corroborated the causal relationship between IBD and NMSC. In contrast, our results showed no evidence of a causal association of IBD on EN and MM. These findings provide new insights into increasing attention to patients with IBD to prevent concurrent NMSC.

KPNA3 regulates histone locus body formation by modulating condensation and nuclear import of NPAT

The histone locus body (HLB) is a membraneless organelle that determines the transcription of replication-dependent histones. However, the mechanisms underlying the appropriate formation of the HLB in the nucleus but not in the cytoplasm remain unknown. HLB formation is dependent on the scaffold protein NPAT. We identify KPNA3 as a specific importin that drives the nuclear import of NPAT by binding to the nuclear localization signal (NLS) sequence. NPAT undergoes phase separation, which is inhibited by KPNA3-mediated impairment of self-association. In this, a C-terminal self-interaction facilitator (C-SIF) motif, proximal to the NLS, binds the middle 431-1,030 sequence to mediate the self-association of NPAT. Mechanistically, the anchoring of KPNA3 to the NPAT-NLS sterically blocks C-SIF motif-dependent NPAT self-association. This leads to the suppression of aberrant NPAT condensation in the cytoplasm. Collectively, our study reveals a previously unappreciated role of KPNA3 in modulating HLB formation and delineates a steric hindrance mechanism that prevents inappropriate cytoplasmic NPAT condensation.

Multi-trait Genome-Wide Analysis Identified 20 Novel Loci for Sarcopenia-Related Traits in UK Biobank

This study aims to identify novel loci associated with sarcopenia-related traits in UK Biobank (UKB) through multi-trait genome-wide analysis. To identify novel loci associated with sarcopenia, we integrated the genome-wide association studies (GWAS) of usual walking pace (UWP) and hand grip strength (HGS) to conduct a joint association study known as multi-trait analysis of GWAS (MTAG). We performed a transcriptome-wide association study (TWAS) to analyze the results of MTAG in relation to mRNA expression data for genes identified in skeletal muscle. Additionally, we utilized Weighted Gene Co-Expression Network Analysis (WGCNA) and Protein-Protein Interaction (PPI) networks to explore the relationships between the identified genes and hub genes related to sarcopenia. We identified 15 novel loci associated with UWP and 5 novel loci associated with HGS at the genome wide significance level (GWS, p < 5 × 10 - 8 ). After TWAS (p TWAS < 6.659 × 10 - 6 , 0.05 / 7509 ), we found two significant genes: PPP1R3A, located at 7q31.1 and associated with HGS, and ZBTB38, located at 3q23 and associated with UWP. 11 identified genes associated with hub genes for sarcopenia were obtained through WGCNA. Our findings offer new insights into biological mechanisms underlying sarcopenia and identify several novel genes related to sarcopenia that warrant in-depth study.

Analysis of the incidence and outcomes of breast cancer in women with schizophrenia

OBJECTIVE

Breast cancer (BC) is the leading cause of female cancer death in the world and the second leading cause of female cancer death in the U.S, Mortality from breast cancer is even higher in individuals with schizophrenia. The aim of our project was to evaluate the incidence of breast cancer in women with schizophrenia and to compare outcomes between breast cancer patients who were or were not on antipsychotics prior to diagnosis.

METHODS

This retrospective study used data from the TriNetX database. Women ≥18 years old diagnosed with schizophrenia were identified. The incidence of primary BC diagnosis between January 2011 and December 2023 was evaluated and stratified by ethnicity. We then conducted a retrospective cohort study to compare outcomes of women ≥18 years who did or did not use antipsychotics one year before BC diagnosis. Patients' propensity score was matched based on age, obesity, tobacco use, socioeconomic status, cancer stage, chemoradiation, axillary lymph node dissection (ALND), sentinel lymph node biopsy (SLNB), and hormone therapy use. Outcomes of interest were 5-year overall survival, recurrence, chemotherapy need, and lymphedema.

RESULTS

1,398,475 women ≥18 years old with schizophrenia were identified. Breast cancer incidence in these patients was 0.53 ​% in 2011 and 0.53 ​% in 2022, with a peak in 2017 (1.29 ​%). Non-Hispanic patients were diagnosed with BC approximately 1.3 times more than Hispanic patients. The outcomes study included 183,062 matched patients, with 91,531 per cohort. 5-year survival with the Kaplan-Meier analysis was significantly greater in women not on antipsychotics (72 ​%) compared to those on antipsychotics (60 ​%), log-rank test p-value <0.0001. The risk of local recurrence (13.4 ​% versus 22.6 ​%, p-value <0.0001), chemotherapy need (41.2 ​% versus 48.4 ​%, p-value <0.0001), and lymphedema (7.7 ​% versus 11.5 ​%, p-value <0.0001) were also significantly lower in women who did not take antipsychotics.

CONCLUSION

Breast cancer incidence in patients with schizophrenia identified through TriNetX has not experienced a significant uptrend or downtrend over the past decade. Non-Hispanic patients with schizophrenia have a higher incidence of BC than Hispanic patients. Matched breast cancer patients on antipsychotics at least one year prior to diagnosis had higher mortality, recurrence, chemotherapy need, and risk of lymphedema.

HLA gene polymorphism is a modifier of age-related breast cancer penetrance in carriers of BRCA1 pathogenic alleles

PURPOSE

Female carriers of germline BRCA1 mutations almost invariably develop breast cancer (BC); however, the age at onset is a subject of variation. We hypothesized that the age-related penetrance of BRCA1 mutations may depend on inherited variability in the host immune system.

METHODS

Next-generation sequencing was utilized for genotyping of HLA class I/II genes (HLA-A, HLA-B, HLA-C, HLA-DPB1, HLA-DQB1, and HLA-DRB1/3/4/5) in patients with BRCA1-associated BC with early (< / = 38 years, n = 215) and late (> / = 58 years, n = 108) age at onset.

RESULTS

HLA-DQB1*06:03P prevalence was higher in the late-onset group due to the excess of allele carriers [25/108 (23.1%) vs. 22/215 (10.2%); OR 2.96, p < 0.001]. For all HLA-I loci, there was a trend toward an increase in the number of homozygotes in the early-onset group. This trend reached statistical significance for the HLA-A [14.4% vs. 6.5%, p = 0.037; OR 2.4, p = 0.042]. The frequencies of HLA-DPB1, HLA-DQB1, and HLA-DRB1/3/4/5 homozygous genotypes did not differ between young-onset and late-onset patients. The maximum degree of homozygosity detected in this study was 6 out of 7 HLA class I/II loci; all six carriers of these genotypes were diagnosed with BC at the age < / = 38 years [OR 6.97, p = 0.187].

CONCLUSION

HLA polymorphism may play a role in modifying the penetrance of BRCA1 pathogenic variants. Certain HLA alleles or HLA homozygosity may modify the risk of BC in BRCA1 carriers.

Targeting Oestrogen Receptor Signalling in Breast Cancer Therapy

There has been over 130 years of research into the treatment of breast cancer using approaches that target oestrogen receptor signalling. Here, we summarise the development of the key pillars of such endocrine therapy, namely, oestrogen deprivation, achieved through ovarian suppression and/or aromatase inhibition, and oestrogen receptor blockade, through selective oestrogen receptor modulators, downregulators and novel compounds entering early phase development. The translation of these compounds from advanced to early breast cancer settings is discussed with a focus on the placebo-controlled breast cancer prevention studies to most accurately describe the side effect profiles of the main approaches.

Assessing the causal role of the structural connectome in temporomandibular disorders: A Mendelian randomization study

OBJECTIVE

We examined the relationships between the structural connectome and temporomandibular disorders (TMDs).

METHODS

Bidirectional Mendelian randomization analyses were conducted using Genome-wide association studies data on the structural connectome and TMDs.

RESULTS

Positive associations with TMD risk were found for white matter structural connectivity from the left hemisphere limbic network to putamen, left hemisphere salience_ventral attention network to caudate, right hemisphere visual network to thalamus, and right hemisphere salience_ventral attention network to right hemisphere control network, while negative associations were observed for connectivity from the left hemisphere control and somatomotor networks to pallidum, left hemisphere somatomotor network to right hemisphere dorsal attention network, and right hemisphere somatomotor network to hippocampus (p< 0.05). In TMD patients, connectivity from the Left-hemisphere visual network to putamen was reduced, whereas connectivity from the Left-hemisphere limbic network to left-hemisphere control network was increased (p< 0.05).

CONCLUSION

Our findings provide insights into the TMD pathogenesis.

Investigation of the α9-nicotinic receptor single nucleotide polymorphisms induced oncogenic properties and molecular mechanisms in breast cancer

α9-nAChR, a subtype of nicotinic acetylcholine receptor, is significantly overexpressed in female breast cancer tumor tissues compared to normal tissues. Previous studies have proposed that specific single nucleotide polymorphisms (SNPs) in the CHRNA9 (α9-nAChR) gene are associated with an increased risk of breast cancer in interaction with smoking. The study conducted a breast cancer risk assessment of the α9-nAChR SNP rs10009228 (NM_017581.4:c.1325A > G) in the Taiwanese female population, including 308 breast cancer patients and 198 healthy controls revealed that individuals with the heterozygous A/G or A/A wild genotype have an increased susceptibility to developing breast cancer in the presence of smoking compared to carriers of the G/G variant genotype. Our investigation confirmed the presence of this missense variation, resulting in an alteration of the amino acid sequence from asparagine (N442) to serine (S442) to facilitate phosphorylation within the α9-nAchR protein. Additionally, overexpression of N442 (A/A) in breast cancer cells significantly enhanced cell survival, migration, and cancer stemness compared to S442 (G/G). Four-line triple-negative breast cancer patient-derived xenograft (TNBC-PDX) models with distinct α9-nAChR rs10009228 SNP genotypes (A/A, A/G, G/G) further demonstrated that chronic nicotine exposure accelerated tumor growth through sustained activation of the α9-nAChR downstream oncogenic AKT/ERK/STAT3 pathway, particularly in individuals with the A/G or A/A genotype. Collectively, our study established the links between genetic variations in α9-nAChR and smoking exposure in promoting breast tumor development. This emphasizes the need to consider gene-environment interactions carefully while developing effective breast cancer prevention and treatment strategies.

Genetic regulation of TERT splicing contributes to reduced or elevated cancer risk by altering cellular longevity and replicative potential

The chromosome 5p15.33 region, which encodes telomerase reverse transcriptase (TERT), harbors multiple germline variants identified by genome-wide association studies (GWAS) as risk for some cancers but protective for others. We characterized a variable number tandem repeat within TERT intron 6 (VNTR6-1, 38-bp repeat unit) and observed a strong association between VNTR6-1 alleles (Short: 24-27 repeats, Long: 40.5-66.5 repeats) and GWAS signals within TERT intron 4. Specifically, VNTR6-1 fully explained the GWAS signals for rs2242652 and partially for rs10069690. VNTR6-1, rs10069690 and their haplotypes were associated with multi-cancer risk and age-related telomere shortening. Both variants reduce TERT expression through alternative splicing and nonsense-mediated decay: rs10069690-T increases intron 4 retention and VNTR6-1-Long expands a polymorphic G quadruplex (G4, 35-113 copies) within intron 6. Treatment with G4-stabilizing ligands decreased the fraction of the functional telomerase-encoding TERT full-length isoform, whereas CRISPR/Cas9 deletion of VNTR6-1 increased this fraction and apoptosis while reducing cell proliferation. Thus, VNTR6-1 and rs10069690 regulate the expression and splicing of TERT transcripts encoding both functional and nonfunctional telomerase. Altered TERT isoform ratios might modulate cellular longevity and replicative potential at homeostasis and in response to environmental factors, thus selectively contributing to the reduced or elevated cancer risk conferred by this locus.

Circulating levels of vitamins and risk of lymphoma: insights from a two-sample Mendelian randomization

BACKGROUND

To explore the genetic causal association between lymphoma and the circulating levels of vitamins through Mendelian randomization (MR).

RESEARCH DESIGN AND METHODS

We performed MR analysis using publicly available genome-wide association study (GWAS) summary data. Seven indicators related to the circulating levels of vitamins (vitamin D, vitamin C, vitamin B6, vitamin B12, folic acid, vitamin E, and carotene) served as exposures, while lymphoma was the outcome. The genetic causal association between these circulating levels of vitamin indicators and lymphoma was assessed using the inverse variance weighted (IVW) method.

RESULTS

Based on IVW method, vitamin B12 (OR = 0.48; 95% CI: 0.28-5.19; p = 0.018) and folic acid (OR = 0.62; 95% CI: 0.40-0.96; p = 0.032) both showed substantial evidence of a relationship with lymphoma. Moreover, the Weighted median method similarly indicated potential evidence of an association between vitamin B12 (OR = 0.40; 95% CI: 0.18-0.90; p = 0.027) and lymphoma. The Simple mode, and Weighted mode methods showed no potential genetic causal association (p > 0.05 in the two analyses).

CONCLUSIONS

This study suggests a potential association between folic acid and vitamin B12 and lymphoma. Further research is required to assess the reproducibility of this finding in different contexts and to gain deeper insights into the potential underlying mechanisms.

Causal relationships between epilepsy and the microstructure of the white matter: A Mendelian randomization study

To examine the causal bidirectional relationships between epilepsy and microstructural changes in the white matter (WM). A genome-wide association study meta-analysis of the International League Against Epilepsy Consortium on Epilepsy and 360 WM imaging-derived phenotypes (IDPs) from the UK Biobank was used for the analysis. Genetic correlation analyses were conducted based on summary statistics of various "IDP-epilepsy" pairs for 2-sample Mendelian randomization (MR) analysis to explore the causal relationships. We used the inverse variance weighted (IVW) method as the primary MR analysis approach, and conducted sensitivity analyses for pleiotropy and heterogeneity. Forward MR analysis revealed that alterations in the 16 WM IDPs increased the risk of epilepsy (q value < 0.05). Changes in the 38 WM IDPs were associated with a decreased risk of epilepsy (q value < 0.05). In the reverse analysis, seizures from all epilepsy types changed 5 WM IDPs, whereas seizures from juvenile myoclonic epilepsy altered 11 WM IDPs (q value < 0.05). This study revealed causal associations between changes in the WM microstructure and epilepsy subtypes. These findings offer new directions for early prevention and treatment of epilepsy.

Towards functional maps of non-coding variants in cancer

Large scale cancer genomic studies in patients have unveiled millions of non-coding variants. While a handful have been shown to drive cancer development, the vast majority have unknown function. This review describes the challenges of functionally annotating non-coding cancer variants and understanding how they contribute to cancer. We summarize recently developed high-throughput technologies to address these challenges. Finally, we outline future prospects for non-coding cancer genetics to help catalyze personalized cancer therapy.

Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene-level

Integrating genome-wide association study (GWAS) and transcriptomic datasets can help identify potential mediators for germline genetic risk of cancer. However, traditional methods have been largely unsuccessful because of an overreliance on total gene expression. These approaches overlook alternative splicing, which can produce multiple isoforms from the same gene, each with potentially different effects on cancer risk. Here, we integrate genetic and multi-tissue isoform-level gene expression data from the Genotype Tissue-Expression Project (GTEx, N = 108-574) with publicly available European-ancestry GWAS summary statistics (all N > 20,000 cases) to identify both isoform- and gene-level risk associations with six cancers (breast, endometrial, colorectal, lung, ovarian, prostate) and six related cancer subtype classifications (N = 12 total). Compared to traditional methods leveraging total gene expression, directly modeling isoform expression through transcriptome-wide association studies (isoTWAS) substantially increases discovery of transcriptomic mechanisms underlying genetic associations. Using the same RNA-seq datasets, isoTWAS identified 164% more significant unique gene associations compared to TWAS (6,163 and 2,336, respectively), with isoTWAS-prioritized genes enriched 4-fold for evolutionarily-constrained genes (P = 6.1 × 10-13). isoTWAS tags transcriptomic associations at 52% more independent GWAS loci compared to TWAS across the six cancers. Additionally, isoform expression mediates an estimated 63% greater proportion of cancer risk SNP heritability compared to gene expression when evaluating cis-genetic influence on isoform expression. We highlight several notable isoTWAS associations that demonstrate GWAS colocalization at the isoform level but not at the gene level, including, CLPTM1L (lung cancer), LAMC1 (colorectal), and BABAM1 (breast). These results underscore the critical importance of modeling isoform-level expression to maximize discovery of genetic risk mechanisms for cancers.

Serum iron status and the risk of female infertility in European populations: A two-sample Mendelian randomization study

The relationship between iron status and female infertility has been observed in several studies, yet its causal nature remains ambiguous. We employed univariate Mendelian randomization (MR) analyses to explore the potential causal connection between these 2 factors. For our analysis, genetic instrumental variables pertaining to iron status were selected using data from the Iron Status Genetics Consortium, encompassing 48,972 individuals of European descent from 19 cohorts (11 discovery and 8 replication). For female infertility data, we referred to FinnGen Consortium Release 9, which includes 11,442 cases and 107,564 controls. Our MR approach utilized both a conservative strategy (involving single nucleotide polymorphisms pertinent to general iron status) and a liberal strategy (encompassing single nucleotide polymorphisms linked to any iron status indicator). The conservative approach relied on inverse variance-weighted methods, whereas the liberal strategy integrated inverse variance weighted with MR-Egger regression, the weighted median approach, and simple mode techniques. The conservative strategy did not reveal a significant link between iron status and female infertility risk. Conversely, the liberal strategy indicated a positive correlation specifically between serum iron levels and female infertility risk (odds ratio from MR: 1.225; 95% confidence interval: 1.064-1.410; P = .030), while no significant associations were found for other iron indicators (P > 0.05). Our MR investigation suggests a potential positive association between serum iron levels and the risk of female infertility, while other iron markers do not appear to significantly influence this risk. These findings highlight the need for further research into the possible connection between serum iron status and female infertility risk.

Genome wide association studies are enriched for interacting genes

Background

With recent advances in single cell technology, high-throughput methods provide unique insight into disease mechanisms and more importantly, cell type origin. Here, we used multi-omics data to understand how genetic variants from genome-wide association studies influence development of disease. We show in principle how to use genetic algorithms with normal, matching pairs of single-nucleus RNA- and ATAC-seq, genome annotations, and protein-protein interaction data to describe the genes and cell types collectively and their contribution to increased risk.

Results

We used genetic algorithms to measure fitness of gene-cell set proposals against a series of objective functions that capture data and annotations. The highest information objective function captured protein-protein interactions. We observed significantly greater fitness scores and subgraph sizes in foreground vs.matching sets of control variants. Furthermore, our model reliably identified known targets and ligand-receptor pairs, consistent with prior studies.

Conclusions

Our findings suggested that application of genetic algorithms to association studies can generate a coherent cellular model of risk from a set of susceptibility variants. Further, we showed, using breast cancer as an example, that such variants have a greater number of physical interactions than expected due to chance.

Investigation of the causal relationship between cholelithiasis and Parkinson's disease: A bidirectional Mendelian randomization study

Background

Parkinson's disease (PD) and cholelithiasis are a huge public health burden. Although observational studies have suggested a potential link between PD and cholelithiasis, the causal relationship between the two remains uncertain. To address this gap, we performed a two-sample bidirectional Mendelian randomization analysis using genetic tools.

Method

Genome-wide association study summary statistics for all traits were obtained from publicly available databases. We used strict control steps in instrumental variable selection to screen for single nucleotide polymorphisms (SNPs) from summary-level genome-wide association studies. In addition, all F-statistics were >10, indicating no weak instrumental bias. The inverse variance weighting (IVW) method was the primary method used to assess causal associations. Four other MR methods (MR-Egger, Weighted Median, Simple mode, and Weighted mode) were also used to complement IVW. Various sensitivity tests were also performed to assess reliability: (1) Cochrane's Q test for assessing heterogeneity, (2) MR-Egger intercept test and MR-PRESSO global test for assessing horizontal multiplicity, and (3) leave-one-out sensitivity test for determining stability.

Results

We selected a total of 30 SNPs as instrumental variables. It was demonstrated that cholelithiasis had a causal effect on the risk of PD (OR = 1.146, 95% CI: 1.062-1.236, p < 0.001) in IVW method.

Conclusion

The results of our analysis revealed an increased risk effect of cholelithiasis against PD, which may give light on new approaches to PD prevention and therapy.

Implementing the Risk Stratification and Clinical Management of Breast Cancer Families Using Polygenic Risk Score Evaluation: A Pilot Study

BACKGROUND

The identification of women at high risk of breast cancer (BC) is crucial for personalized screening strategies. Pathogenic and likely pathogenic variants (PVs/LPVs) in susceptibility risk genes explain part of the individual risk. Moreover, a polygenic background, summarized as a polygenic risk score (PRS), contributes to the risk of BC and may modify the individual risk in carrier and non-carrier members of BC families.

METHODS

We performed a retrospective pilot study evaluating PRS in women from a subset of high- (BRCA1 and BRCA2) and moderate-risk (PALB2 and ATM) BC families. We included PVs/LPVs carriers and non-carriers and evaluated a PRS based on 577,113 BC-associated variants. Using BOADICEA, we calculated the adjusted lifetime BC risk.

RESULTS

Our data showed that in BRCA1/BRCA2 carriers, PVs have a major role in stratifying the lifetime risk, while PRS improves risk estimation in non-carriers of these families. A different scenario may be observed in PALB2 and ATM families where PRS combined with PV/LPV carrier status gives a more informative lifetime risk.

CONCLUSIONS

This study showed that in BC families, the PRS might help to quantify the weight of the genetic familial background, improving the individual risk stratification and contributing to personalized clinical management for carrier and non-carrier women.

Polymyalgia rheumatica and giant cell arteritis: A bidirectional Mendelian randomization study

Polymyalgia rheumatica (PMR) and giant cell arteritis (GCA) as 2 types of autoimmune diseases are frequently concomitant, and Mendelian randomization (MR) was applied in this study to assess the causal relationship between them. In this study, single-nucleotide polymorphism (SNP) was used as the instrumental variable for Mendelian analysis, and the SNP data of GCA and PMR were obtained from the FinnGen Biobank databases. SNPs are significantly correlated with GCA and PMR and were screened based on preset thresholds. Inverse variance weighted analysis was used as the main analysis, supplemented with MR-Egger and weighted median. The evidence of the impact of GCA on PMR risk was found in inverse variance weighted results (odds ratio, 1.22 [95% confidence interval, 1.11-1.34]; P < .01), and the evidence of the impact of PMR on GCA risk has also been found (odds ratio, 1.58 [95% confidence interval, 1.28-1.96]; P < .01). Finally, the stability and reliability of the results were tested using the retention method, heterogeneity test, and horizontal gene pleiotropy test. MR analysis indicates that GCA increases the risk of PMR and PMR is an important risk factor for GCA, with a causal relationship. The potential value of reasonable management of PMR in patients with GCA has received high attention. In addition, novel GCA therapeutics may be indicated for PMR, and it is a potential for further investigation.

Causal association of epigenetic age acceleration and risk of subacute thyroiditis: a bidirectional Mendelian randomization study

BACKGROUND

Epigenetic age accelerations (EAAs) are a promising new avenue of research, yet their investigation in subacute thyroiditis (SAT) remains scarce. Our study endeavors to fill this void by exploring the potential causal association between EAAs and SAT.

METHODS

Our study utilized publicly available genome-wide association study (GWAS) data of European ancestry to conduct a bidirectional Mendelian randomization (MR) study. Five MR methods were employed to measure causal association between EAAs and SAT multiple analyses were utilized to perform quality control.

RESULTS

Our study evaluated causal association between SAT and four EAAs, included GrimAge acceleration (GrimAA), Hannum age acceleration (HannumAA), PhenoAge acceleration (PhenoAA), intrinsic epigenetic age acceleration (IEAA). Results showed that there is a significant causal association between PhenoAA and SAT (OR 1.109, 95% CI 1.000-1.228, p = 0.049, by IVW method). On the contrary, SAT was associated with IEAA (OR 0.933, 95% CI 0.884-0.984, p = 0.011, by IVW method; OR 0.938, 95% CI 0.881-0.998, p = 0.043, by weighted median method). Leave-one-out sensitivity analysis, heterogeneity test, pleiotropy test, and MR-PRESSO analysis provide good quality control.

CONCLUSION

The bidirectional MR analysis concluded that an increase in PhenoAA was correlated with a higher risk of SAT, indicating a potential causal relationship between PhenoAA and risk of SAT. Conversely, SAT was found to be closely associated with IEAA, suggesting that SAT may accelerate the aging process. Slowing down biological aging has emerged as a new research direction in curbing SAT.

Causality of blood metabolites and metabolic pathways on peripheral arteriosclerosis: a Mendelian randomization study

Background

Peripheral arteriosclerosis is caused by any atherosclerosis outside the heart and brain. However, the underlying biological mechanisms are not fully understood. This study aims to explore the causal relationship between blood metabolites and peripheral arteriosclerosis.

Methods

A Mendelian randomization (MR) analysis was implemented to estimate the causality of blood metabolites on peripheral arteriosclerosis. A genome-wide association study (GWAS) of 1,400 metabolites was used as the exposure, whereas two different GWAS datasets of peripheral arteriosclerosis were the outcomes. Inverse-variance weighted (IVW) was the main analysis of causal analysis. MR-Egger, the simple mode, weighted median and weighted mode were used to increase the stability and robustness of the results. Cochran Q test, MR-Egger intercept test, the funnel plot, and MR-Pleiotropy RESidual Sum and Outlier were used for sensitivity analyses. Furthermore, metabolic pathway enrichment analysis was performed using MetaboAnalyst5.0.

Results

In this MR study, eight blood metabolites have a strong causal relationship with peripheral arteriosclerosis, including 1-myristoyl-2-arachidonoyl-GPC (14:0/20:4), 1-palmitoyl-2-arachidonoyl-gpc (16:0/20:4n6), 1-(1-enyl-stearoyl)-2-arachidonoyl-GPE, 1-palmitoyl-2-dihomo-linolenoyl-GPC, Gamma-glutamylleucine, Deoxycholic acid glucuronide and two named X- (X-24546, X-26111). In addition, five important metabolic pathways in peripheral arteriosclerosis were identified through metabolic pathway analysis.

Conclusion

This study provides evidence for the causal relationship between blood metabolites and peripheral arteriosclerosis, and these eight blood metabolites provide new perspectives for screening and prevention of peripheral arteriosclerosis in the future.

Type 1 diabetes and combined acute and chronic complications are associated with risk of progression of liver fibrosis: a Mendelian randomization study

Background

There has been controversy and uncertainty regarding the causal relationship between type 1 diabetes, its consequences, liver fibrosis, and cirrhosis. In order to determine the causal relationship, we conducted a Mendelian randomization study (MR).

Methods

For the first time, we subjected multiple diabetes data to analyze its relationship with the progression of liver fibrosis. Once the instrumental variables had been extracted, we assessed them employing Cochran's Q multi-analysis, inverse variance weighted, MR-Egger, MR-PRESSO, weighted mode, and weighted median.

Results

Genetically predicted type 1 diabetes (OR = 1.13, 95% CI: 1.04-1.23, ** P = 3.42 × 10-3), type 1 diabetes without complications (OR = 1.12, 95% CI: 1.03-1.23, * P = 1.26 × 10-2), type 1 diabetes with coma (OR = 1.09, 95% CI: 1-1.18, * P = 4.74 × 10-2), type 1 diabetes with ketoacidosis (OR = 1.07, 95% CI: 1.01-1.13, * P = 1.3 × 10-2), type 1 diabetes with neurological complications (OR = 1.18, 95% CI: 1.11-1.26, *** P = 4.05 × 10-7), type 1 diabetes with ophthalmic complications (OR = 1.16, 95% CI: 1.05-1.28, ** P = 3.06 × 10-3), type 1 diabetes with renal complications (OR = 1.07, 95% CI: 1-1.13, *P = 3.45 × 10-2), type 1 diabetes with other specified/multiple/unspecified complications (OR = 1.12, 95% CI: 1.02-1.23, * P = 1.41 × 10-2) were all associated with an increased risk of liver fibrosis progression.

Conclusions

According to our MR investigation, type 1 diabetes and both its acute and chronic implications may increase the likelihood that liver fibrosis could continue to develop. Additionally, type 1 diabetes with neurological and ocular problems is more likely to accelerate the development of liver fibrosis and inflammation, which offers new insights for genetic investigations.

Using polygenic risk modification to improve breast cancer prevention: study protocol for the PRiMo multicentre randomised controlled trial

INTRODUCTION

Established personal and familial risk factors contribute collectively to a woman's risk of breast or ovarian cancer. Existing clinical services offer genetic testing for pathogenic variants in high-risk genes to investigate these risks but recent information on the role of common genomic variants, in the form of a Polygenic Risk Score (PRS), has provided the potential to further personalise breast and ovarian cancer risk assessment. Data from cohort studies support the potential of an integrated risk assessment to improve targeted risk management but experience of this approach in clinical practice is limited.

METHODS AND ANALYSIS

The polygenic risk modification trial is an Australian multicentre prospective randomised controlled trial of integrated risk assessment including personal and family risk factors with inclusion of breast and ovarian PRS vs standard care. The study will enrol women, unaffected by cancer, undergoing predictive testing at a familial cancer clinic for a pathogenic variant in a known breast cancer (BC) or ovarian cancer (OC) predisposition gene (BRCA1, BRCA2, PALB2, CHEK2, ATM, RAD51C, RAD51D). Array-based genotyping will be used to generate breast cancer (313 SNP) and ovarian cancer (36 SNP) PRS. A suite of materials has been developed for the trial including an online portal for patient consent and questionnaires, and a clinician education programme to train healthcare providers in the use of integrated risk assessment. Long-term follow-up will evaluate differences in the assessed risk and management advice, patient risk management intentions and adherence, patient-reported experience and outcomes, and the health service implications of personalised risk assessment.

ETHICS AND DISSEMINATION

This study has been approved by the Human Research Ethics Committee of Peter MacCallum Cancer Centre and at all participating centres. Study findings will be disseminated via peer-reviewed publications and conference presentations, and directly to participants.

TRIAL REGISTRATION NUMBER

ACTRN12621000009819.

Association between primary biliary cholangitis with diabetes and cardiovascular diseases: A bidirectional multivariable Mendelian randomization study

BACKGROUND AND AIMS

Primary biliary cholangitis (PBC) is an autoimmune disease often accompanied by multisystem damage. This study aimed to explore the causal association between genetically predicted PBC and diabetes, as well as multiple cardiovascular diseases (CVDs).

METHODS

Genome-wide association studies (GWAS) summary data of PBC in 24,510 individuals of European ancestry from the European Association for the Study of the Liver was used to identify genetically predicted PBC. We conducted 2-sample single-variable Mendelian randomization (SVMR) and multivariable Mendelian randomization (MVMR) to estimate the impacts of PBC on diabetes (N = 17,685 to 318,014) and 20 CVDs from the genetic consortium (N = 171,875 to 1,030,836).

RESULTS

SVMR provided evidence that genetically predicted PBC is associated with an increased risk of type 1 diabetes (T1D), type 2 diabetes (T2D), myocardial infarction (MI), heart failure (HF), hypertension, atrial fibrillation (AF), stroke, ischemic stroke, and small-vessel ischemic stroke. Additionally, there was no evidence of a causal association between PBC and coronary atherosclerosis. In the MVMR analysis, PBC maintained independent effects on T1D, HF, MI, and small-vessel ischemic stroke in most models.

CONCLUSION

Our findings revealed the causal effects of PBC on diabetes and 7 CVDs, and no causal relationship was detected between PBC and coronary atherosclerosis.

Case-Case Genome-Wide Analyses Identify Subtype-Informative Variants That Confer Risk for Breast Cancer

Breast cancer includes several subtypes with distinct characteristic biological, pathologic, and clinical features. Elucidating subtype-specific genetic etiology could provide insights into the heterogeneity of breast cancer to facilitate the development of improved prevention and treatment approaches. In this study, we conducted pairwise case-case comparisons among five breast cancer subtypes by applying a case-case genome-wide association study (CC-GWAS) approach to summary statistics data of the Breast Cancer Association Consortium. The approach identified 13 statistically significant loci and eight suggestive loci, the majority of which were identified from comparisons between triple-negative breast cancer (TNBC) and luminal A breast cancer. Associations of lead variants in 12 loci remained statistically significant after accounting for previously reported breast cancer susceptibility variants, among which, two were genome-wide significant. Fine mapping implicated putative functional/causal variants and risk genes at several loci, e.g., 3q26.31/TNFSF10, 8q22.3/NACAP1/GRHL2, and 8q23.3/LINC00536/TRPS1, for TNBC as compared with luminal cancer. Functional investigation further identified rs16867605 at 8q22.3 as a SNP that modulates the enhancer activity of GRHL2. Subtype-informative polygenic risk scores (PRS) were derived, and patients with a high subtype-informative PRS had an up to two-fold increased risk of being diagnosed with TNBC instead of luminal cancers. The CC-GWAS PRS remained statistically significant after adjusting for TNBC PRS derived from traditional case-control GWAS in The Cancer Genome Atlas and the African Ancestry Breast Cancer Genetic Consortium. The CC-GWAS PRS was also associated with overall survival and disease-specific survival among patients with breast cancer. Overall, these findings have advanced our understanding of the genetic etiology of breast cancer subtypes, particularly for TNBC. Significance: The discovery of subtype-informative genetic risk variants for breast cancer advances our understanding of the etiologic heterogeneity of breast cancer, which could accelerate the identification of targets and personalized strategies for prevention and treatment.

The gut-facial aging axis: A two-sample Mendelian randomization and mediation analysis of gut microbiota, gut microbiota metabolic pathways, and blood metabolites

BACKGROUND

Facial aging (FA) is a complex process influenced by both genetic and environmental factors. Gut microbiota (GM), gut microbiota metabolic pathways (GMMPs), and blood metabolites (BMs) have been implicated in the regulation of FA, but the causal and mediating effects of these factors remain unclear.

METHODS

We used summary-level data from genome-wide association studies (GWAS) of 16S rRNA gene sequencing data for GM (n = 18 340), GWAS of GMMPs (n = 7738), BMs (n = 24 925), and GWAS of FA (n = 423 999). We applied Mendelian randomization (MR) methods to estimate the causal effects of GM, GMMPs, and BMs on FA. We performed mediation analysis to quantify the proportion of the effects mediated by blood metabolites.

RESULTS

We identified nine genus, two phylum, two families of GM, nine GM metabolic pathways, and 73 BMs that showed potential causal effects on FA. After Bonferroni correction, three BMs remained causally associated with FA, including average number of methylene groups per double bond (β, -0.023; 95% CI, -0.032∼-0.014; p = 3.120×10-7) and average number of methylene groups in a fatty acid chain (β, -0.031; 95% CI, -0.045∼-0.016; p = 2.062×10-5), which had strong negative causal effects on FA, and ratio of bisallylic groups to total fatty acids (β, 0.023; 95% CI, 0.017∼-0.029; p = 8.441×10-15), which had a strong positive causal effect on FA. Mediation analysis revealed that histidine, average number of methylene groups in a fatty acid chain, and triglycerides in chylomicrons and largest VLDL particles mediated the effects of anaerofilum and/ or superpathway of Laspartate and Lasparagine biosynthesis on FA.

CONCLUSION

Our study provides novel insights into the causal and mediating effects of GM, GMMPs, and BMs on FA. These findings may have implications for the development of new strategies for preventing or delaying FA.

No bidirectional association between serum 25-hydroxyvitamin D and erectile dysfunction: Mendelian randomization and genetic association studies

Background

The causal relationship between the level of serum 25-hydroxyvitamin D [25(OH)D] and the risk of erectile dysfunction (ED) is still unclear.

Aim

We tried to determine the causal relationship between the level of serum 25(OH)D and ED risk.

Methods

In this study, we used genome-wide association study data from the UK Biobank to analyse the relationship between serum 25(OH)D (as the exposure) and ED (as the outcome). Linkage disequilibrium score regression (LDSC) was used to assess the genetic correlation between 2 traits. The CAUSE (Causal Analysis using Summary Effect estimates) method and Mendelian randomization (MR) were employed to evaluate the bidirectional causal relationship. The MRlap method was utilized to assess the impact of sample overlap on the results. To assess potential heterogeneity and horizontal pleiotropy, we utilized methods such as MR-Egger, MR-PRESSO (Mendelian Randomization Pleiotropy Residual Sum and Outlier), weighted median, and others.

Outcomes

The primary outcome was defined as self or physician-reported ED, or using oral ED medication, or a history of surgery related to ED.

Results

The LDSC analysis did not reveal a significant genetic correlation between serum 25(OH)D and ED (rg = 0.2787, P = .3536). Additionally, the CAUSE (P value testing that the causal model is a better fit >.05) and MR analyses (odds ratio, 0.8951; 95% confidence interval, 0.7480-1.0710; P = .2260) did not support a causal relationship between 25(OH)D and ED, and our study did not detect any heterogeneity and pleiotropy.

Clinical implications

This study provides evidence on whether vitamin D needs to be ingested to prevent or treat ED.

Strengths and limitations

We used LDSC and MR to avoid bias. However, the population in this study was limited to European ancestry.

Conclusion

No causal relationship was found between 25(OH)D and ED.

Causal relationship between gut microbiota and ankylosing spondylitis and potential mediating role of inflammatory cytokines: A mendelian randomization study

Associations between gut microbiota and ankylosing spondylitis have been discovered in previous studies, but whether these associations reflect a causal relationship remains inconclusive. Aiming to reveal the bidirectional causal associations between gut microbiota and ankylosing spondylitis, we utilized publicly available genome wide association study summary data for 211 gut microbiota (GM) taxa and ankylosing spondylitis (AS) to conduct two sample mendelian randomization analyses. Mediation analysis was performed to explore mediating inflammatory cytokines. We found that genetically predicted higher abundance of Lactobacillaceae family, Rikenellaceae family and Howardella genus had suggestive associations with decreased risk of ankylosing spondylitis while genetic proxied higher abundance of Actinobacteria class and Ruminococcaceae_NK4A214_group genus was associated with increased risk of ankylosing spondylitis. IL23 and IFN-γ were potential mediating cytokines for GM dysbiosis, especially for Actinobacteria class, leading to AS. Our study provided a new exploration direction for the treatment of AS. Lactobacillaceae family, Rikenellaceae family, Howardella genus, Actinobacteria class and Ruminococcaceae_NK4A214_group genus are expected to become new therapeutic targets and monitoring indicators for AS.

Causal Relationship between Mitochondrial Biological Function and Periodontitis: Evidence from a Mendelian Randomization Study

A growing number of studies indicate that mitochondrial dysfunction serves as a pathological mechanism for periodontitis. Therefore, this two-sample Mendelian randomization (MR) study was carried out to explore the causal associations between mitochondrial biological function and periodontitis, because the specific nature of this causal relationship remains inconclusive in existing MR studies. Inverse variance weighting, Mendelian randomization-Egger, weighted mode, simple mode, and weighted median analyses were performed to assess the causal relationships between the exposure factors and periodontitis. The results of the present study revealed a causal association between periodontitis and medium-chain specific acyl-CoA dehydrogenase (MCAD), malonyl-CoA decarboxylase (MLYCD), glutaredoxin 2 (Grx2), oligoribonuclease (ORN), and pyruvate carboxylase (PC). Notably, MCAD and MLYCD are causally linked to periodontitis, and serve as protective factors. However, Grx2, ORN, and PC function as risk factors for periodontitis. Our study established a causal relationship between mitochondrial biological function and periodontitis, and such insights may provide a promising approach for treating periodontitis via mitochondrial regulation.

The Combined Effects of the Most Important Dietary Patterns on the Incidence and Prevalence of Chronic Renal Failure: Results from the US National Health and Nutrition Examination Survey and Mendelian Analyses

BACKGROUND

We aimed to comprehensively assess the relationship of specific dietary patterns and various nutrients with chronic kidney disease (CKD) and its progression.

METHODS

The observational study data were from the NHANES 2005-2020. We calculated four dietary pattern scores (healthy eating index 2020 (HEI-2020), dietary inflammatory index (DII), alternative mediterranean diet (aMed), and dietary approaches to stop hypertension (DASH)) and the intakes of various nutrients and defined CKD, CKD-very high risk, and kidney dialysis. Associations between dietary patterns and nutrients and disease were assessed by means of two logistic regression models. Two-sample MR was performed with various food and nutrients as the exposure and CKD, kidney dialysis as the outcome. Sensitivity analyses were conducted to verify the reliability of the results.

RESULTS

A total of 25,167 participants were included in the analyses, of whom 4161 had CKD. HEI-2020, aMed, and DASH were significantly negatively associated with CKD and CKD-very high risk at higher quartiles, while DII was significantly positively associated. A higher intake of vitamins and minerals may reduce the incidence and progression of CKD to varying degrees. The MR results, corrected for false discovery rates, showed that a higher sodium intake was associated with a higher prevalence of CKD (OR: 3.91, 95%CI: 2.55, 5.99).

CONCLUSIONS

Adhering to the three dietary patterns of HEI-2020, aMed, and DASH and supplementing with vitamins and minerals benefits kidney health.

Association between blood metabolites and basal cell carcinoma risk: a two-sample Mendelian randomization study

Background

Circulating metabolites, which play a crucial role in our health, have been reported to be disordered in basal cell carcinoma (BCC). Despite these findings, evidence is still lacking to determine whether these metabolites directly promote or prevent BCC's progression. Therefore, our study aims to examine the potential effects of circulating metabolites on BCC progression.

Material and methods

We conducted a two-sample Mendelian randomization (MR) analysis using data from two separate genome-wide association studies (GWAS). The primary study included data for 123 blood metabolites from a GWAS with 25,000 Finnish individuals, while the secondary study had data for 249 blood metabolites from a GWAS with 114,000 UK Biobank participants.GWAS data for BCC were obtained from the UK Biobank for the primary analysis and the FinnGen consortium for the secondary analysis. Sensitivity analyses were performed to assess heterogeneity and pleiotropy.

Results

In the primary analysis, significant causal relationships were found between six metabolic traits and BCC with the inverse variance weighted (IVW) method after multiple testing [P < 4 × 10-4 (0.05/123)]. Four metabolic traits were discovered to be significantly linked with BCC in the secondary analysis, with a significance level of P < 2 × 10-4 (0.05/249). We found that all the significant traits are linked to Polyunsaturated Fatty Acids (PUFAs) and their degree of unsaturation.

Conclusion

Our research has revealed a direct link between the susceptibility of BCC and Polyunsaturated Fatty Acids and their degree of unsaturation. This discovery implies screening and prevention of BCC.

Causal relationship between Alzheimer's disease and unstable angina: a bidirectional Mendelian randomization analysis

Background

Research from observational studies has demonstrated a link between Alzheimer's disease (AD) and a higher risk of cardiovascular disease (CVD). Uncertainty surrounds the exact genetic cause of AD and coronary heart disease, particularly unstable angina (UA). Mendelian randomization (MR) analysis was used to examine the causal genetic link between AD and UA to evaluate the impact of AD on UA.

Methods

The purpose of the bidirectional MR analysis was to investigate the link between exposure and illness causation. Genetic instrumental variables for AD were obtained from European populations using genome-wide association studies (GWAS). The primary causal conclusions were obtained using the inverse variance weighted approach (IVW), and other sensitivity analysis techniques were employed. Sensitivity analyses were carried out to evaluate heterogeneity and horizontal pleiotropy to guarantee accurate MR results.

Results

An elevated risk of UA was linked to genetically predicted AD (IVW: OR=3.439, 95% CI: 1.565-7.555, P=0.002). A substantial genetic relationship between UA and the risk of AD was not supported by any evidence in the reverse study (IVW: OR=0.998, 95% CI: 0.995-1.001, P=0.190). Various MR techniques produced consistent results. Sensitivity analysis revealed no discernible heterogeneity or horizontal pleiotropy.

Conclusions

One risk factor for UA that we found in our bidirectional Mendelian randomization trial was AD. This highlights the necessity of researching the underlying molecular mechanisms linked to AD and UA as well as the possibility of creating individualized treatment plans based on genetic data.

Causal Involvement of Immune Cells in Chronic Obstructive Pulmonary Disease: A Mendelian Randomization Study

Background

The immune cells play a substantial role in the development and progression of chronic obstructive pulmonary disease (COPD). We aim to investigate the causal involvement of immune cells in COPD via a Mendelian randomization (MR) analysis.

Methods

Published genome-wide association studies (GWAS) statistics on immune cells were analyzed, with genetic variants identified as instrumental variables (IVs). Inverse-variance weighting (IVW), weighted median, and MR-Egger regression methods were employed, along with simple mode and weighted mode adopted in the two-sample MR analysis. Sensitivity analysis was conducted to examine the heterogeneity, horizontal pleiotropy, and stability of the causal relationship.

Results

IVW results suggested that CCR2 on CD62L+ plasmacytoid dendritic cells (DC), CCR2 on plasmacytoid DC, CD11b on CD66b++ myeloid cells, CD19 on CD20- CD38- CD24+ memory B cell subset, CD25 on transitional B cells, and CD25++CD8br %CD8br T cells were risk factors for the development of COPD. Besides, CD127 on effector memory-like cytotoxic T lymphocytes lacking expression of co-stimulatory molecule 28 (CD28-EM CTLs) and HLA DR+ NK ACs expressing human leukocyte antigen DR molecules while being natural killer cells (%NK ACs) were protective factors for COPD.

Conclusion

This study unveiled a causal relationship between immune cell phenotype and COPD. These findings offer new insights for the prevention and treatment of COPD using COPD-associated immune cells.

A Bidirectional Mendelian Randomization Study of Gut Microbiota and Cerebral Small Vessel Disease

BACKGROUND

The causal nature of gut microbiota and cerebral small vessel disease (CSVD) is still obscure regardless of evidence supporting their observational correlations.

OBJECTIVES

The primary objective of this research is to investigate the potentially pathogenic or protective causal impacts of specific gut microbiota on various neuroimaging subtypes of CSVD.

METHODS

We obtained the latest summary-level genome-wide databases for gut microbiota and 9 CSVD traits. The univariable and multivariable Mendelian randomization (MR) studies were conducted to examine the possible causal link between exposure and outcome. Meanwhile, we conducted sensitivity analyses sequentially, containing the heterogeneity, pleiotropy, and leave-one-out analysis. Additionally, to clarify the potential bidirectional causality, the causality from CSVD traits to the identified gut microbiota was implemented through reverse MR analysis.

RESULTS

The univariable MR analysis identified 22 genetically predicted bacterial abundances that were correlated with CSVD traits. Although conditioning on macronutrient dietary compositions, 2 suggestive relationships were retained using the multivariable MR analysis. Specifically, the class Negativicutes and order Selenomonadales exhibited a negative causal association with strictly lobar cerebral microbleeds, one neuroimaging trait of CSVD. There is insufficient evidence indicating the presence of heterogeneity and horizontal pleiotropy. Furthermore, the identified causal relationship was not driven by any single nucleotide polymorphism. The results of the reverse MR analysis did not reveal any statistically significant causality from CSVD traits to the identified gut microbiota.

CONCLUSIONS

Our study indicated several suggestive causal effects from gut microbiota to different neuroimaging subtypes of CSVD. These findings provided a latent understanding of the pathogenesis of CSVD from the perspective of the gut-brain axis.

Genetic susceptibility to breast cancer increases the risk of neutropenia and agranulocytosis: insights from Mendelian randomization

PURPOSE

The causal relationship between breast cancer and its estrogen receptor (ER) subtypes and neutropenia and agranulocytosis is unclear.

METHODS

In two-sample Mendelian randomization (MR), we used inverse variance weighting (IVW), Bayesian weighted MR (BWMR), MR-Egger, weighted median, simple mode, and weighted mode methods to analyze causality for ER-positive breast cancer, ER-negative breast cancer, overall breast cancer, and drug-induced neutropenia and agranulocytosis. To validate the results, we performed the analysis again using GWAS data on neutropenia from different databases. In multivariable MR (MVMR), we assessed the independent effects of ER-positive and ER-negative breast cancer on causality.

RESULTS

Two-sample MR analysis showed a causal relationship between ER-positive breast cancer (IVW odds ratio (OR) = 1.319, P = 7.580 × 10-10), ER-negative breast cancer (OR = 1.285, P = 1.263 × 10-4), overall breast cancer (OR = 1.418, P = 2.123 × 10-13), and drug-induced neutropenia and a causal relationship between ER-positive breast cancer (OR = 1.349, P = 1.402 × 10-7), ER-negative breast cancer (OR = 1.235, P = 7.615 × 10-3), overall breast cancer (OR = 1.429, P = 9.111 × 10-10), and neutropenia. Similarly, ER-positive breast cancer (OR = 1.213, P = 5.350 × 10-8), ER-negative breast cancer (OR = 1.179, P = 1.300 × 10-3), and overall breast cancer (OR = 1.275, P = 8.642 × 10-11) also had a causal relationship with agranulocytosis. MVMR analysis showed that ER-positive breast cancer remained causally associated with drug-induced neutropenia (OR = 1.233, P = 4.188 × 10-4), neutropenia (OR = 1.283, P = 6.363 × 10-4), and agranulocytosis (OR = 1.142, P = 4.549 × 10-3). Heterogeneity analysis and pleiotropy test showed that our results were reliable.

CONCLUSION

Our study provides genetic evidence for a causal association between breast cancer and its estrogen receptor subtypes and neutropenia. In clinical practice, in addition to focusing on therapeutic factors, additional attention should be given to breast cancer patients to avoid severe neutropenia.

Causal relationship between primary sclerosing cholangitis and systemic lupus erythematosus: a bidirectional Mendelian randomization study

BACKGROUND

Observational studies have found a link between two autoimmune diseases, namely, primary sclerosing cholangitis (PSC) and systemic lupus erythematosus (SLE). However, the relationship remains unclear.

METHODS

Bidirectional Mendelian randomization (MR) analysis and statistical methods, including inverse variance weighting, weighted median, and MR-Egger tests, were performed using data from genome-wide association studies to detect a causal relationship between PSC and SLE. Sensitivity analyses were subsequently performed to assess the robustness of the results. Univariate MR methods were also investigated.

RESULTS

Results of MR analysis suggested that PSC was associated with an increased risk for SLE (odds ratio: 1.33, 95% confidence interval: 1.10-1.61, P=0.0039) However, SLE had no significant causal relationship with PSC.

CONCLUSION

Results of MR analysis revealed that patients with PSC were at an increased risk for SLE, which provides new insights into the relationship between these two autoimmune diseases.

Association of ESR1 Germline Variants with TP53 Somatic Variants in Breast Tumors in a Genome-wide Study

In breast tumors, somatic mutation frequencies in TP53 and PIK3CA vary by tumor subtype and ancestry. Emerging data suggest tumor mutation status is associated with germline variants and genetic ancestry. We aimed to identify germline variants that are associated with somatic TP53 or PIK3CA mutation status in breast tumors. A genome-wide association study was conducted in 2,850 women of European ancestry with breast cancer using TP53 and PIK3CA mutation status (positive or negative) as well as specific functional categories [e.g., TP53 gain-of-function (GOF) and loss-of-function, PIK3CA activating] as phenotypes. Germline variants showing evidence of association were selected for validation analyses and tested in multiple independent datasets. Discovery association analyses found five variants associated with TP53 mutation status with P values <1 × 10-6 and 33 variants with P values <1 × 10-5. Forty-four variants were associated with PIK3CA mutation status with P values <1 × 10-5. In validation analyses, only variants at the ESR1 locus were associated with TP53 mutation status after multiple comparisons corrections. Combined analyses in European and Malaysian populations found ESR1 locus variants rs9383938 and rs9479090 associated with the presence of TP53 mutations overall (P values 2 × 10-11 and 4.6 × 10-10, respectively). rs9383938 also showed association with TP53 GOF mutations (P value 6.1 × 10-7). rs9479090 showed suggestive evidence (P value 0.02) for association with TP53 mutation status in African ancestry populations. No other variants were significantly associated with TP53 or PIK3CA mutation status. Larger studies are needed to confirm these findings and determine if additional variants contribute to ancestry-specific differences in mutation frequency.

SIGNIFICANCE

Emerging data show ancestry-specific differences in TP53 and PIK3CA mutation frequency in breast tumors suggesting that germline variants may influence somatic mutational processes. This study identified variants near ESR1 associated with TP53 mutation status and identified additional loci with suggestive association which may provide biological insight into observed differences.

Relationship between age at menarche and breast cancer in individuals, as well as in first-degree kin and estrogen receptor status: a Mendelian randomization study

Target

We executed a Mendelian randomization (MR) investigation employing two distinct cohorts of genetic instrumental variables to elucidate the causal nexus between age at menarche (AAM) and the incidence of disparate breast cancer (BC) subtypes, in addition to the incidence of BC among first-degree kin.

Methods

We aggregated statistical data pertaining to AAM and BC from various consortia representing a homogenous population cohort. MR analysis was conducted employing inverse variance weighted (IVW) methodology as the principal approach, complemented by weighted median and MR-Egger regression techniques for an exhaustive evaluation. To evaluate the presence of pleiotropy, we applied the MR-Egger intercept test, MR-PRESSO, and leave-one-out sensitivity analysis.

Results

Upon exclusion of confounding SNP, an increment of one standard deviation in AAM was inversely correlated with the incidence of BC. (odds ratio [OR] 0.896, 95% confidence interval [CI] 0.831-0.968)/(OR 0.998, 95% CI 0.996-0.999) and estrogen receptor-positive (ER+) BC incidence (OR 0.895, 95% CI 0.814-0.983). It was also associated with reducing the risk of maternal BC incidence (OR 0.995, 95% CI 0.990-0.999) and sibling BC incidence (OR 0.997, 95% CI 0.994-0.999). No significant association was found between AAM and estrogen receptor-negative (ER-) BC incidence (OR 0.936, 95% CI 0.845-1.037).

Conclusion

Our study substantiated the causal relationship between a delayed AAM and a diminished risk of BC in probands, as well as in their maternal progenitors and siblings. Furthermore, the analysis suggests that AAM exerts a considerable potential causal influence on the risk of developing Luminal-a/b subtype of BC.

Inflammatory bowel disease and risk of autoimmune hepatitis: A univariable and multivariable Mendelian randomization study

OBJECTIVE

This study aimed to use Mendelian randomization (MR) to investigate the potential causal association between inflammatory bowel disease (IBD) and autoimmune hepatitis (AIH).

METHODS

Two-sample MR was performed to estimate the causal effect of IBD on AIH. The primary analysis employed the inverse variance weighted (IVW) method in univariable MR analysis, supplemented by additional methods including MR-Egger, weighted median, simple mode, and weighted mode. The p values were adjusted by FDR p-value adjustment. In the replication analysis, the primary IVW analysis was repeated and then pooled by meta-analysis. Sensitivity analyses were performed using Cochran's Q test, MR-Egger intercept test, MR-PRESSO, leave-one-out, and funnel plot analysis to evaluate the robustness of the MR findings. Additionally, multivariable MR (MVMR) was employed to estimate the direct causal effect of IBD on the risk of AIH.

RESULTS

In univariable MR analysis, a significant positive causal association was observed between IBD (both Crohn's disease (CD) or ulcerative colitis (UC)) and the risk of AIH (for CD and AIH, the IVW odds ratio (OR) = 1.10, 95% confidence interval (CI) = 1.00-1.16, P = 0.045, FDR P = 0.045; for UC and AIH, the IVW OR = 1.07, 95% CI = 1.00-1.13, P = 0.038, FDR P = 0.076). Furthermore, no significant positive correlation between IBD and the risk of AIH (OR = 1.13, 95% CI = 0.94-1.35, P = 0.194). Sensitivity analysis revealed no pleiotropic bias. MVMR analysis further confirmed the direct causal effect of CD or UC on the risk of AIH after adjusting for the common risk factors (cigarettes per day and osteoporosis). In the replication analysis, the positive causal association between UC and the risk of AIH remain significant (the IVW odds ratio (OR) = 1.32, 95% CI = 1.18-1.48, P = 2.90E-06). While no significant positive association was observed between CD or IBD and the risk of AIH in the replication analysis, a suggestive positive association between the identified risk factors (UC, CD, and IBD) and the risk of AIH was detected in the meta-analysis (OR = 1.09, 95% CI = 1.05-1.13, P<0.0001).

CONCLUSION

This MR study revealed a positive impact of the identified risk factors (CD, UC and IBD) on the risk of AIH within the European population.