Health effects of milk consumption: phenome-wide Mendelian randomization study

Therapeutic Target Discovery for Multiple Myeloma: Identifying Druggable Genes via Mendelian Randomization

Background: Multiple myeloma (MM) is a hematological malignancy originating from the plasma cells present in the bone marrow. Despite significant therapeutic advancements, relapse and drug resistance remain major clinical challenges, highlighting the urgent need for novel therapeutic targets. Methods: To identify potential druggable genes associated with MM, we performed Mendelian randomization (MR) analysis. Causal candidates were further validated using a single-tissue transcriptome-wide association study (TWAS), and colocalization analysis was conducted to assess shared genetic signals between gene expression and disease risk. Potential off-target effects were assessed through an MR phenome-wide association study (MR-PheWAS). Additionally, molecular docking and functional assays were used to evaluate candidate drug efficacy. Results: The MR analysis identified nine druggable genes (FDR < 0.05), among which Orosomucoid 1 (ORM1) and Oviductal Glycoprotein 1 (OVGP1) were supported by both TWAS and colocalization evidence (PPH4 > 0.75). Experimental validation demonstrated the significant downregulation of ORM1 and OVGP1 in MM cells (p < 0.05). Pregnenolone and irinotecan, identified as agonists of ORM1 and OVGP1, respectively, significantly inhibited MM cell viability, while upregulating their expression (p < 0.05). Conclusions: Our study highlights ORM1 and OVGP1 as novel therapeutic targets for MM. The efficacy of pregnenolone and irinotecan in suppressing MM cell growth suggests their potential for clinical application. These findings provide insights into MM pathogenesis and offer a promising strategy for overcoming drug resistance.

Effects of different types of milk consumption on type 2 diabetes and the mediating effect of AA: A Mendelian randomization study of East Asian populations

There is currently a lack of research examining the association between the consumption of different dairy products and type 2 diabetes (T2D) in East Asian populations. To address this gap, the present study employs Mendelian randomization to investigate the potential effects of 3 different types of milk consumption (including whole milk, semi-skim milk, and skim milk) on the risk of developing T2D. The results indicate that both whole milk and skim milk are associated with an increased risk of T2D (whole milk: odds ratio [OR] = 1.022, 95% CI: 1.001-1.044; skim milk: OR = 1.023, 95% CI: 1.007-1.039). Mediation analysis revealed that asparagine acts as a mediator between skim milk consumption and T2D, with a mediation effect of 0.003 (95% CI: 0.000 to 0.008), accounting for 14.269% of the total effect.

Effects of Different Cow-Milk Beta-Caseins on the Gut-Brain Axis: A Narrative Review of Preclinical, Animal, and Human Studies

The gut and brain communicate through bidirectional neural, endocrine, and immune signals to coordinate central nervous system activity with gastrointestinal function. Dysregulated inflammation can promote immune cell activation and increase entero-endocrine signaling and intestinal permeability; hence, a functional gut-brain axis is necessary for a healthy digestive system. The consumption of milk products can lead to gut discomfort via effects on gastrointestinal tract function and the inflammatory state, which, in turn, affect the brain. A1 β-casein and A2 β-casein are major components of bovine-milk protein, and their digestion may result in different physiological effects following the consumption of milk products. Peptides derived from A1 β-casein, such as β-casomorphins, may increase gut dysfunction and inflammation, thereby modulating the availability of bioactive metabolites in the bloodstream and contribute to changes in cognitive function. This narrative review examines the functional interrelationships between the consumption of cow-milk-derived β-caseins and their effect on the brain, immune system, and the gut, which together comprise the gut-brain axis.

Exploring beyond diagnoses in electronic health records to improve discovery: a review of the phenome-wide association study

Objective

The phenome-wide association study (PheWAS) systematically examines the phenotypic spectrum extracted from electronic health records (EHRs) to uncover correlations between phenotypes and exposures. This review explores methodologies, highlights challenges, and outlines future directions for EHR-driven PheWAS.

Materials and Methods

We searched the PubMed database for articles spanning from 2010 to 2023, and we collected data regarding exposures, phenotypes, cohorts, terminologies, replication, and ancestry.

Results

Our search yielded 690 articles. Following exclusion criteria, we identified 291 articles published between January 1, 2010, and December 31, 2023. A total number of 162 (55.6%) articles defined phenomes using phecodes, indicating that research is reliant on the organization of billing codes. Moreover, 72.8% of articles utilized exposures consisting of genetic data, and the majority (69.4%) of PheWAS lacked replication analyses.

Discussion

Existing literature underscores the need for deeper phenotyping, variability in PheWAS exposure variables, and absence of replication in PheWAS. Current applications of PheWAS mainly focus on cardiovascular, metabolic, and endocrine phenotypes; thus, applications of PheWAS in uncommon diseases, which may lack structured data, remain largely understudied.

Conclusions

With modern EHRs, future PheWAS should extend beyond diagnosis codes and consider additional data like clinical notes or medications to create comprehensive phenotype profiles that consider severity, temporality, risk, and ancestry. Furthermore, data interoperability initiatives may help mitigate the paucity of PheWAS replication analyses. With the growing availability of data in EHR, PheWAS will remain a powerful tool in precision medicine.

Dairy intake and cognitive function in older adults in three cohorts: a mendelian randomization study

BACKGROUND

Meta-analyses of observational studies on the effect of dairy on cognitive function have yielded inconclusive results, potentially due to unmeasured confounding. To avoid the no-unmeasured confounding assumption, we used lactase persistence genetic variant as an instrumental variable, for which the CC genotype is associated with lower lactase production and, consequently, lower dairy consumption. We used it to assess the effect of long-term consumption of total and non-fermented dairy on cognitive function.

METHODS

We included 43,836 individuals over 55 years old with genotyping, dietary data, and cognitive function measurements from three population-based studies: CoLaus|PsyCoLaus (Switzerland), the Rotterdam Study (the Netherlands) and the Canadian Longitudinal Study on Aging (CLSA - Canada). We performed a one-sample Mendelian randomization using two-stage least-squares regression. First, we estimated total and non-fermented dairy consumption by T-allele frequency. Second, we used the estimated dairy consumption in linear regression models on general cognition, assessed by the Mini-Mental State Examination (MMSE) and the Mental Alternation Test, executive function, verbal fluency, verbal learning, and memory.

RESULTS

Per T-allele, total dairy intake and non-fermented was 24.8 and 15.3 g/day higher in PsyCoLaus, 57.9 and 49.8 g/day in the Rotterdam Study, and 0.31 and 0.29 times/day in CLSA, respectively. We found no association between the genetically predicted difference and the MMSE in PsyCoLaus and the Rotterdam Study. However, lactase persistent individuals scored 3.4 (95% CI 2.1- 4.7) and 3.5 (95% CI 2.3-4.7) points more in the Mental Alternation Test for total and fermented dairy, respectively, in CLSA. Similarly, lactase persistent participants in CLSA had higher verbal fluency, verbal learning and executive function, but no differences were found in the other cohorts. Such inconsistencies might stem from different FFQs across cohorts and consumption ranges. Nonetheless, the generally small magnitude of effect sizes may suggest that there is no real effect between total or non-fermented dairy intake and cognitive function.

CONCLUSION

The evidence for a causal effect of dairy consumption on general cognitive function is weak, consistent with previous results from classic analysis from observational studies. Interventions targeting dairy are unlikely to have a relevant effect on cognitive function.

Percentage of fat in milk consumption and risk of six cancers: a Mendelian randomization study

Background

The causal relationship between percentage of fat in milk consumption and cancer risk lacks sufficient investigation. The purpose of this study was to explore whether the percentage of fat in milk consumption is a factor that affects the risk variation of several common types of cancer.

Methods

Mendelian randomization (MR) was performed to estimate the unconfounded causal relationship between the percentage of fat in milk consumption and the risk of six cancers related to milk intake, as well as to assess the associations between body fat percentage and these cancers. Data corresponding to the percentage of fat in milk consumption (n=411,503), body fat percentage (n=401,772), breast cancer (n=139,274), ovarian cancer (n=66,450), endometrial cancer (n=121,885), colorectal cancer (n=32,072), prostate cancer (n=140,254), and bladder cancer (n=373,295) were obtained from the Integrative Epidemiology Unit (IEU) or the genome-wide association study (GWAS) Catalog databases. The primary analytical strategy employed the inverse-variance weighted (IVW) method. Sensitivity analysis, including assessments of heterogeneity and pleiotropy, was conducted to assess the robustness of the findings.

Results

The percentage of fat in milk consumption only exhibited a causal relationship with breast cancer (β=2.993, P=0.01). The study identified significant causal effects of body fat percentage on the risk of several cancers, including ovarian cancer (β=0.225, P=0.002), endometrial cancer (β=0.669, P<0.001), and colorectal cancer (β=0.344, P<0.001), as well as a protective effect on prostate cancer (β=-0.104, P=0.046). Sensitivity analysis demonstrated that the findings were robust.

Conclusions

Our study findings indicated that a higher percentage of fat in milk consumption was associated with an increased risk of breast cancer, providing valuable insights for cancer prevention strategies among the European population.

Association of different types of milk with depression and anxiety: a prospective cohort study and Mendelian randomization analysis

Background

The relationship between different types of milk and depression and anxiety remains unclear, with limited evidence from prospective cohort studies. This study aims to evaluate this relationship using data from the UK Biobank cohort and to explore its potential causality through Mendelian randomization (MR) analysis.

Methods

Cox proportional hazards models were used to assess the association between different milk types and the risk of depression and anxiety among 357,568 UK Biobank participants free of these conditions at baseline. To further explore causality, a 2-sample MR analysis was conducted using data from the FinnGen study.

Results

During a median follow-up period of 13.5 years (interquartile range, 12.6-14.2 years), among 357,568 participants (mean [SD] age, 56.83 [8.06] years, 171,246 male individuals [47.9%]), a total of 13,065 and 13,339 participants were diagnosed with depression and anxiety, respectively. In the fully adjusted model (adjusted for sociodemographics characteristics, lifestyle behaviors and health indicators), full cream milk was related to a lower risk of anxiety (HR = 0.84, 95% CI: 0.75-0.94). Semi-skimmed milk had a lower risk of depression (HR = 0.88, 95% CI: 0.80-0.96) and anxiety (HR = 0.90, 95% CI: 0.82-0.98). No significant relationships were found between skimmed milk and depression/anxiety. Other types were related to an increased risk of depression (HR = 1.14, 95% CI: 1.02-1.28). After Bonferroni correction, the 2-sample MR analysis revealed a potential protective causal relationship between semi-skimmed milk and depression (OR = 0.83, 95% CI: 0.73-0.95, p = 0.006) and anxiety (OR = 0.71, 95% CI: 0.59-0.85, p < 0.001).

Conclusion

These findings indicate that semi-skimmed milk consumption may be linked to a lower risk of depression and anxiety, potentially highlighting its role in dietary strategies to promote mental health.

Unraveling the mechanisms underlying diabetic cataracts: insights from Mendelian randomization analysis

BACKGROUND

Diabetic cataract (DC) is a major cause of blindness, with its pathogenesis involving oxidative stress and ferroptosis, according to recent studies.

METHODS

We performed a Mendelian Randomization (MR) study using GWAS data to select SNPs and assess the causal link between diabetes and cataracts. DC datasets were analyzed for differential gene expression, WGCNA, and protein-protein interactions to identify key oxidative stress and ferroptosis genes. An SVM-RFE algorithm developed a diagnostic model, and ImmuCellAI analyzed immune infiltration patterns.

RESULTS

MR analysis confirmed diabetes as a cataract risk factor and identified core genes related to oxidative stress and ferroptosis in DC. Four key genes (Hspa5/Nfe2l2/Atf3/Stat3) linked to both processes were discovered. Immune infiltration analysis revealed an imbalance associated with these genes.

CONCLUSIONS

A functional interaction between oxidative stress and ferroptosis genes in DC is suggested, with a 4-gene model, indicating their potential as a 'bridge' in DC pathogenesis.

Non-fermented and fermented milk intake in relation to risk of ischemic heart disease and to circulating cardiometabolic proteins in swedish women and men: Two prospective longitudinal cohort studies with 100,775 participants

BACKGROUND

The effect of milk on the risk of ischemic heart disease (IHD) and acute myocardial infarction (MI) is unclear. We aimed to examine the association between non-fermented and fermented milk consumption on these endpoints and investigate the relationship between milk intake and cardiometabolic-related proteins in plasma.

METHODS

Our study is based on two Swedish prospective cohort studies that included 59,998 women and 40,777 men without IHD or cancer at baseline who provided repeated measures of diet and lifestyle factors and plasma proteomics data in two subcohorts. Through registry linkage, 17,896 cases with IHD were documented during up to 33 years of follow-up, including 10,714 with MI. We used time-updated multivariable Cox regression analysis to examine non-fermented or fermented milk intake with time to IHD or MI. Using high-throughput multiplex immunoassays, 276 cardiometabolic plasma proteins were measured in two subcohorts. We applied multivariable-adjusted regression models using a discovery-replication design to examine protein associations with increasing consumption of non-fermented or fermented milk.

RESULTS

The results for non-fermented milk differed by sex (p-value for interaction = 0.01). In women, we found a pattern of successively greater risk of IHD and MI at non-fermented milk intake levels higher than 1.5 glasses/day. Compared with an intake of 0.5 glass/day (100 mL/day), non-fermented milk intake of 2 glasses/day in women conferred a multivariable-adjusted hazard ratio (HR) of 1.05 (95% CI 1.01-1.08) for IHD, an intake of 3 glasses/day an HR of 1.12 (95% CI 1.06-1.19), and an intake of 4 glasses/day an HR of 1.21 (95% CI 1.10-1.32). Findings were similar for whole, medium-fat, and low-fat milk. We did not detect higher risks of IHD with increasing milk intakes in men. Fermented milk intake was unrelated to the risk of IHD or MI in either sex. Increasing non-fermented milk intake in women was robustly associated with a higher concentration of plasma ACE2 and a lower concentration of FGF21.

CONCLUSIONS

We show a positive association between high amounts of non-fermented milk intake and IHD in women but not men. We suggest metabolic pathways related to ACE2 and FGF21 potentially underlie the association.

Effects of multiple fluid intake on Urolithiasis by mendelian randomization study

Urolithiasis, a common and recurrent condition, imposes a significant global health burden. This study investigates the causal relationship between various types of fluid intake and urolithiasis using univariable and multivariable Mendelian randomization (MR) approaches. Genetic data for urolithiasis were obtained from the FinnGen Consortium (n = 400,681), while genetic measures for nine fluid types were sourced from meta-analyses of genome-wide association studies (GWAS). The analysis revealed that genetically predicted coffee intake (OR: 0.571, 95% confidence interval (CI): 0.341-0.958, p = 0.034) and ground coffee intake (OR: 0.219, 95% CI: 0.005-0.923, p = 0.038) were protective factors for upper urinary calculi. Additionally, a standard deviation (SD) increase in tea intake was associated with a 53% reduction in risk (OR: 0.473, 95% CI: 0.320-0.700, p < 0.001). Conversely, milk intake (OR: 1.072, 95% CI: 1.018-1.130) and alcohol intakefrequency (OR: 1.304, 95% CI: 1.083-1.570, p = 0.005) increased the risk of upper urinary calculi. These findings highlight the association of tea with reduced risk of urolithiasis, instead for milk and alcohol intake, in formulating prevention strategies for urolithiasis.

Consumption of milk and other dairy products and incidence of Parkinson's disease: a prospective cohort study in French women

Previous studies showed positive associations between milk intake and Parkinson's disease (PD) in men but not in women, but few studies were available in women. Due to the long prodromal PD phase, reverse causation represents a major threat to investigations of diet in PD; cohort studies with a long follow-up are needed. We investigated associations between intake of milk and other dairy products with PD incidence in women from the E3N cohort study (1993-2018). PD diagnoses were validated using medical records and drug claim databases. Diet was assessed via a dietary questionnaire. Hazard ratios (HR) were estimated using multivariable Cox regression models. Exposures were lagged by 5y in main analyses and longer lags in sensitivity analyses. We examined the impact of adjustment for premotor symptoms (constipation/depression). During a mean follow-up of 18.8y, 845 of 71,542 women developed PD. Main analyses showed a J-shaped association between total milk intake and PD (P-non linearity = 0.045), with a significant linear positive association among drinkers (HR/1-SD = 1.09, 95% CI = 1.01-1.18, P = 0.024), that was explained in secondary analyses by a different pattern of association for plain milk (alone or with cereals) and milk added to drinks (tea/coffee/chicory). PD incidence increased significantly with plain milk consumption (HR/1-SD = 1.08 [1.02-1.14], P = 0.014). A U-shaped relation was observed for milk added to drinks (P-non linearity = 0.038), with lower PD incidence in women with moderate consumption (HR = 0.77 [0.61-0.97], P = 0.030) and no difference between non-drinkers and those with the highest consumption (HR = 0.98 [0.79-1.21], P = 0.848). Findings were similar in analyses using longer lags and adjusted for constipation/depression. Consumption of other dairy products was not associated with PD. A J-shaped association between total milk intake and PD was explained by a different pattern of association for plain milk intake and milk added to drinks. Reverse causation is unlikely to explain a positive association of plain milk with PD incidence in women. The U-shaped relation for milk added to drinks could be explained by an interaction between milk and coffee/tea/chicory. Further studies are warranted to elucidate the underlying mechanisms.

A comprehensive analysis of the health effects associated with smoking in the largest population using UK Biobank genotypic and phenotypic data

Background

Smoking is a widespread behavior, while the relationship between smoking and various diseases remains a topic of debate.

Objective

We conducted analysis to further examine the identified associations and assess potential causal relationships.

Methods

We utilized seven single nucleotide polymorphisms (SNPs) known to be linked to smoking extracting genotype data from the UK Biobank, a large-scale biomedical repository encompassing comprehensive health-related and genetic information of European descent. Phenome-wide association study (PheWAS) analysis was conducted to map the association of genetically predicted smoking status with 1,549 phenotypes. The associations identified in the PheWAS were then meticulously examined through two-sample Mendelian randomization (MR) analysis, utilizing data from the UK Biobank (n = 487,365) and the Sequencing Consortium of Alcohol and Nicotine Use (GSCAN) (n = 337,334). This approach allowed us to comprehensively characterize the links between smoking and disease patterns.

Results

The PheWAS analysis produced 34 phenotypes that demonstrated significant associations with smoking (P = 0.05/1460). Importantly, sickle cell anemia and type 2 diabetes exhibited the most significant SNPs (both 85.71% significant SNPs). Furthermore, the MR analyses provided compelling evidence supporting causal associations between smoking and the risk of following diseases: obstructive chronic bronchitis (IVW: Beta = 0.48, 95% confidence interval (CI) 0.36-0.61, P = 1.62×10-13), cancer of the bronchus (IVW: Beta = 0.92, 95% CI 0.68-1.17, P = 2.02×10-13), peripheral vascular disease (IVW: Beta = 1.09, 95% CI 0.71-1.46, P = 1.63×10-8), emphysema (IVW: Beta = 1.63, 95% CI 0.90-2.36, P = 1.29×10-5), pneumococcal pneumonia (IVW: Beta = 0.30, 95% CI 0.11-0.49, P = 1.60×10-3), chronic airway obstruction (IVW: Beta = 0.83, 95% CI 0.30-1.36, P = 2.00×10-3) and type 2 diabetes (IVW: Beta = 0.53, 95% CI 0.16-0.90, P = 5.08×10-3).

Conclusion

This study affirms causal relationships between smoking and obstructive chronic bronchitis, cancer of the bronchus, peripheral vascular disease, emphysema, pneumococcal pneumonia, chronic airway obstruction, type 2 diabetes, in the European population. These findings highlight the broad health impacts of smoking and support smoking cessation efforts.

Genetically Determined Circulating Lactase/Phlorizin Hydrolase Concentrations and Risk of Colorectal Cancer: A Two-Sample Mendelian Randomization Study

Previous research has found that milk is associated with a decreased risk of colorectal cancer (CRC). However, it is unclear whether the milk digestion by the enzyme lactase-phlorizin hydrolase (LPH) plays a role in CRC susceptibility. Our study aims to investigate the direct causal relationship of CRC risk with LPH levels by applying a two-sample Mendelian Randomization (MR) strategy. Genetic instruments for LPH were derived from the Fenland Study, and CRC-associated summary statistics for these instruments were extracted from the FinnGen Study, PLCO Atlas Project, and Pan-UK Biobank. Primary MR analyses focused on a cis-variant (rs4988235) for LPH levels, with results integrated via meta-analysis. MR analyses using all variants were also undertaken. This analytical approach was further extended to assess CRC subtypes (colon and rectal). Meta-analysis across the three datasets illustrated an inverse association between genetically predicted LPH levels and CRC risk (OR: 0.92 [95% CI, 0.89-0.95]). Subtype analyses revealed associations of elevated LPH levels with reduced risks for both colon (OR: 0.92 [95% CI, 0.89-0.96]) and rectal cancer (OR: 0.92 [95% CI, 0.87, 0.98]). Consistency was observed across varied analytical methods and datasets. Further exploration is warranted to unveil the underlying mechanisms and validate LPH's potential role in CRC prevention.

Milk consumption and the risk of type 2 diabetes: A systematic review of Mendelian randomization studies

AIMS

Previously, no relationship between milk consumption and the risk of type 2 diabetes has been found in prospective cohorts. However, Mendelian randomization allows researchers to almost bypass much residual confounding, providing a more precise effect estimate. This systematic review aims to investigate the risk of type 2 diabetes and levels of HbA1c by assessing all Mendelian Randomization studies investigating this subject matter.

DATA SYNTHESIS

PubMed and EMBASE were searched from October 2021 through February 2023. Inclusion and exclusion criteria were formulated to filter out irrelevant studies. Studies were qualitatively assessed with STROBE-MR together with a list of five MR criteria. Six studies were identified, containing several thousand participants. All studies used the SNP rs4988235 as the main exposure and type 2 diabetes and/or HbA1c as the main outcome. Five studies were graded as "good" with STROBE-MR, with one graded as "fair". For the six MR criteria, five studies were graded "good" in four criteria, while two studies were graded "good" in two criteria. Overall, genetically predicted milk consumption did not seem to be associated with an increased risk of type 2 diabetes.

CONCLUSIONS

This systematic review found that genetically predicted milk consumption did not seem to increase the risk of type 2 diabetes. Future Mendelian randomization studies concerning this topic should consider conducting two-sample Mendelian Randomization studies, in order to derive a more valid effect estimate.

A Comprehensive Look at the -13910 C>T LCT Gene Polymorphism as a Molecular Marker for Vitamin D and Calcium Levels in Young Adults in Central and Eastern Europe: A Preliminary Study

Intolerance to dairy products resulting from the abnormal digestion of milk sugar (lactose) is a common cause of human gastrointestinal disorders. The aim of this study was to show that the -13910 C>T LCT gene polymorphism, together with genotypes of selected VDR gene polymorphisms and diet and nutritional status parameters, can impact the prevalence of vitamin D and calcium deficiency in young adults. This study was conducted on a group of 63 people, which comprised 21 individuals with primary adult lactase deficiency, and a control group of 42 individuals with no hypolactasia. The LCT and VDR gene genotypes were assessed using PCR restriction fragment length polymorphism (PCR-RFLP) analysis. A validated HPLC method was used to determine serum concentrations of 25(OH)D₂ and 25(OH)D₃. Atomic absorption spectrometry was used to determine calcium levels. Their diets (self-reported 7-day estimated food record), estimated calcium intakes based on the ADOS-Ca questionnaire and basic anthropometric parameters were assessed. The CC genotype associated with hypolactasia was found in 33.3% of the subjects. The presence of the CC variant of the LCT gene polymorphism in the study group of young Polish adults was found to be associated with significantly lower milk (134.7 ± 66.7 g/d vs. 342.5 ± 176 g/d; p = 0.012) and dairy product consumption (78.50 ± 36.2 g/d vs. 216.3 ± 102 g/d; p = 0.008) compared with lactase persistence. At the same time, people with adult-type primary intolerance were found to have statistically significant lower serum levels of vitamin D and calcium (p < 0.05). There was a higher chance of vitamin D and calcium deficiency and a lower intake in the group exhibiting lactase non-persistence (OR > 1). The AA variant of the VDR gene's BsmI polymorphism present in people with hypolactasia may further contribute to an increased risk of vitamin D deficiency. Exclusion of lactose from the diet, combined with impaired vitamin D metabolism, may also lead to inhibited calcium absorption by the body. Further research should be carried out on a larger group of subjects to clarify the relationship between lactase activity and vitamin D and calcium levels in young adults.