Abstract Circulating plasma proteins are key biomarkers and therapeutic targets, now measurable at scale through high-throughput technologies, yet whether expanding proteomics platforms beyond the classical plasma secretome enhances genetic discovery and causal inference remains poorly understood. Here, we use an expanded SomaScan 7k platform to map the genetic architecture of a broader segment of the plasma proteome and to evaluate how proteome expansion affects pQTL discovery, causal inference and therapeutic target prioritisation. After quality control, we analysed 7,144 aptamers targeting 6,267 proteins in the harmonised dataset of two European cohorts: INTERVAL (n = 9,251 participants) and CHRIS (n = 4,194), and conducted genome-wide pQTL association analyses followed by meta-analysis. We identified 7,870 significant pQTLs (P-value < 1.26 × 10 −11 ; 1,784 cis , 6,086 trans ), of which 2,704 (34%) associations were not reported in five prior large-scale pQTL studies. Newly assessed proteins, which accounted for 53% (1,422/2,704) of the novel associations, were less likely to harbour cis -pQTLs associations (∼15%) than those in the previous platform version (∼28%), consistent with their lower expected plasma concentrations and predominantly intracellular localisation. Colocalization analyses revealed widespread sharing of genetic signals across proteins and characterised 22 pleiotropic trans -regulatory hotspots accounting for 68% of all trans -pQTLs. Through two-sample Mendelian randomization analyses on 2,003 phenotypes from the Million Veteran Program, UK Biobank, and FinnGen (combined N > 1.2 million), we identified 6,340 genetically supported protein–trait associations, highlighting disease mechanisms and potential therapeutic opportunities beyond currently drug-targeted circulating proteins. Together, these findings provide a systematic view of the genetic architecture of the expanded plasma proteome and demonstrate that plasma proteome expansion reveals genetically anchored disease biology beyond the classical secretome, while exposing inherent biological and technical constraints of studying low-abundance intracellular proteins in circulation.

Cardiovascular-kidney metabolic syndrome (CKM) represents an increasingly prevalent public health concern. Optimal strategies to prevent CKM-related outcomes are greatly needed. We assessed the association between various dietary patterns and CKM biomarkers in a general population study. We used cross-sectional data from 8066 adult participants of the Cooperative Health Research in South Tyrol (CHRIS) study. Self-reported dietary intake was assessed through the semi-quantitative GA2LEN Food Frequency questionnaire. We derived six established dietary pattern indices, and population-specific dietary patterns through principal component analysis. CKM biomarkers included: systolic and diastolic blood pressure, glycated haemoglobin, visceral fat, HDL, LDL and total cholesterol, triglycerides, creatinine-based estimated glomerular filtration rate, and urinary albumin-to-creatinine ratio. We investigated associations between each dietary index and CKM risk marker using multivariable linear regression models. We further examined potential effect modification by sex, body mass index, physical activity and smoking habit. Higher adherence to healthy dietary patterns rich in fruits, vegetables, whole grains, and low in saturated fats was associated with more favorable CKM marker levels. E.g, when comparing the fourth to the first quartile the healthy plant-based dietary index was associated with lower total and LDL cholesterol (β ≈ − 5.0 mg/dL, p < 0.001), lower blood pressure (β= − 1.24 mmHg, p = 0.001) and higher eGFR (β = 1.24 ml/min/1.73m2, p = 0.001). In contrast, the unhealthy plant based and a Western style diet were associated with higher SBP (β = 1.23–1.89 mmHg, p < 0.01), amongst others. For some markers, associations tended to be stronger in men, individuals with overweight or obesity, those with lower physical activity, and smokers (Pinteraction< 0.05). Adhering to a healthy plant rich diet low in saturated fats, added sugars and processed foods was associated with more favorable levels of CKM biomarkers, including blood lipids, blood pressure, glycated hemoglobin and eGFR.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is among the most prevalent liver disorders in Western countries. While steatosis is prevalent, molecular mechanisms associated with steatosis grades and how nutrition modulates related metabolic disturbances remain poorly understood. We analyzed data from 327 participants of the CHRIS NAFLD study with Type 2 diabetes (T2D) and matched controls, integrating 148 plasma proteins with 175 serum metabolites and lipids to identify circulating biomarkers associated with hepatic steatosis severity. Associations between dietary intake and steatosis were investigated, and a potential influence of diet on the identified biomarkers was evaluated through a sensitivity analysis. Participants were stratified by steatosis grade based on ultrasound-derived measurements. Steatosis grade was strongly positively correlated with BMI and T2D. Several proteins (e.g., GC, AFM, AZGP1, SERPINC1, VTN, LRG1) and metabolites (e.g., glutamate, tyrosine, valine, lysoPCs) were associated with the highest steatosis grade, mainly reflecting a broader metabolically unhealthy phenotype. Adherence to a plant-based diet was associated with lower steatosis grades independent of circulating proteins, metabolites, and lipids. Results suggest that circulating metabolic signatures of steatosis reflect broader metabolic dysregulation and are independent of dietary intake. These data support the use of blood-based multi-omics profiling to distinguish between metabolically healthy and unhealthy individuals, and may thus improve MASLD risk stratification. Multi-omics profiling reveals biomarkers associated with hepatic steatosis severity Substantial overlap between steatosis biomarkers and metabolic health indicators Steatosis-associated profiles reflect broad metabolic dysfunction Plant-based diet is associated with lower steatosis grade Dietary habits did not affect the identified steatosis blood biomarkers

Introduction: Genome-wide association studies (GWAS) identified a locus on chromosome 4q21.1, spanning the Family With Sequence Similarity 47 Member E (FAM47E), Starch Binding Domain 1 (STBD1), Coiled-Coil Domain Containing 158 (CCDC158), and Shroom Family Member 3 (SHROOM3) genes, to be associated with kidney function markers. Functional studies implicated SHROOM3 as the effector gene, demonstrating its developmental role to guarantee podocyte barrier integrity. However, the locus has also been associated with other clinical traits, including electrolytes, hematological, cardiovascular, and neurological traits, not all of which can be easily traced to the regulation of kidney function. We therefore conducted a systematic analysis of the whole locus' genetic profiles (haplotypes) to assess which phenotypic profiles they were associated with. Methods: For the 4 genes, we reconstructed haplotypes spanning 71 exonic and intronic variants for 12,834 participants in the Cooperative Health Research in South Tyrol (CHRIS) study based on genotypes imputed on a local whole-exome sequencing (WES) reference panel. Haplotypes were tested for associations with 72 clinical traits, 170 serum metabolites, and 148 plasma protein concentrations, using linear regression models. Results: We identified 11 haplotypes with a population frequency between 2% and 24%. Compared with the most common haplotype, most haplotypes were associated with higher creatinine-based estimated glomerular filtration rate (eGFR) and lower serum magnesium levels. In addition, specific haplotypes were also associated with biologically diverse groups of traits, including albuminuria, blood pressure, red blood cell traits, carnitines, and amino acids. Cluster analysis highlighted the existence of distinct genetic profiles in which individuals with specific haplotypes presented with specific phenotypic and metabolic signatures. Conclusion: The genetic variability of the FAM47E-SHROOM3 locus indicates the existence of population subgroups with distinct biomarker profiles.

Summary Genome-wide association studies (GWAS) generated thousands of loci associated with complex traits and diseases. However, to characterize of the pleiotropic, molecular and population genetic bounds of uncovered loci, investigations are conducted, that remain conceptually and practically separated. Also in the best case, such investigations proceed by one locus at a time. To address these limitations, we introduce an efficient and reproducible Snakemake pipeline for executing haplotype-based association analysis on GWAS-identified genetic loci, which is especially helpful in samples enriched with molecular omics data. Haplomics takes as input the genetic coordinates of each locus along with all available clinical and molecular phenotypes, the necessary covariates, and VCF genotype files, to reconstruct haplotypes and test them for associations with the phenotypes. The reconstructed haplotypes, the annotation of included variants, and association results are graphically displayed in an HTML report. We tested Haplomics in population-based study sample encompassing 391 traits, including 72 clinical markers, 171 serum metabolites, 148 plasma protein concentrations, and whole-exome sequencing (WES) imputed genotypes. We estimated WES-based haplotypes at 11 kidney function genetic loci from a GWAS and conducted association analyses throughout, identifying 19 significant associations after multiple testing correction. Haplomics is a scalable, easy-to-use and fast haplotype reconstruction and association pipeline that makes it possible to jointly conduct molecular and population-genetic characterization of multiple GWAS loci in unified analysis framework. Availability and implementation Haplomics is freely available on GitHub https://github.com/dariushghasemi/haplomics. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The CHRIS study was funded by the Autonomous Province of Bolzano/Bozen - South Tyrol -Department of Innovation, Research, University and Museums and supported by the European Regional Development Fund (FESR1157). This work was carried out within the TrainCKDis project, funded by the European Union Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement H2020-MSCA-ITN-2019 ID:860977 (TrainCKDis). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Ethics Committee of the Healthcare System of the Autonomous Province of Bolzano-South Tyrol approved the CHRIS baseline protocol on 19 April 2011 (21-2011). The study conforms to the Declaration of Helsinki, and with national and institutional legal and ethical requirements. The CHRIS Access Committee at Eurac Research Institute for Biomedicine in Bolzano, Italy, gave approval for this work to publish. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The data used in the current study can be requested with an application to: biomedicine{at}eurac.edu at the Eurac Research Institute for Biomedicine.

Background: Individuals affected by obesity present different health trajectories and do not suffer from cardiometabolic complications all in the same way. There is a need to better understand obesity subtypes and to develop approaches for stratification. In this study we investigated both metabolomic and proteomic signatures in serum and blood plasma samples discriminating metabolically healthy from unhealthy obesity. Methods: We investigated cross-sectional metabolomic and proteomic data from participants of the Cooperative Health Research in South Tyrol (CHRIS) study. Participants were grouped into metabolically healthy obesity (MHO) and metabolically unhealthy obesity (MUO) based on available health data in the study. A total of 461 individuals were included in the analysis, with n=130 MHO and n=331 MUO. Random forest (RF) classifiers were used to discriminate metabolically healthy from unhealthy obesity and to identify molecular features characteristic of MHO/MUO. Linear regression models were used to assess associations between each relevant metabolite/protein and MHO/MUO phenotypes independently of age, sex and body composition. Results: The MHO/MUO RF classifier achieved a performance of AUC = 0.709, 95% CI = (0.698,0.721). Three plasma proteins and 12 circulating metabolites were identified as relevant predictors of MHO/MUO phenotypes. Linear regression models confirmed the Apolipoprotein C-III (APOC3) association to be independent of age, visceral fat composition, medication or serum triglyceride levels. Conclusion: APOC3 was identified as a novel predictor for obesity stratification, highlighting the importance of circulating triglyceride levels in relation to metabolic health. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The CHRIS study was funded by the Autonomous Province of Bolzano - Department of Innovation, Research, University and Museums and supported by the European Regional Development Fund (FESR1157). The research was funded by the European Region Tyrol South Tyrol Trentino, project EUREGIO EFH (decision 2059 from 1 December 2017, Autonomous Province of Trento). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics Committee of the Healthcare System of the Autonomous Province of Bolzano-South Tyrol gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data and samples can be requested for clearly defined research via the CHRIS Portal (https://chrisportal.eurac.edu/).

BACKGROUND:The study of circulating blood proteins in population cohorts offers new avenues to explore lifestyle-related and genetic influences describing and shaping human health. METHODS:Utilizing high-throughput mass spectrometry, we quantified 148 highly abundant proteins, functioning in the innate and adaptive immune system, coagulation and nutrient transport in 3632 blood plasma, and 500 serum samples from the CHRIS and BASE-II cross-sectional population studies, respectively. Through multiple regression analyses, we aimed to identify the main factors influencing the circulating proteome at population level. RESULTS:Many demographic covariates and common medications affect the concentration of high-abundant plasma proteins, but the most significant changes are linked to the use of hormonal contraceptives (HCU). HCU particularly alters amongst others the levels of Angiotensinogen and Transcortin. We robustly replicated these findings in the BASE-II cohort. Furthermore, our results indicate that combined hormonal contraceptives with ethinylestradiol have a stronger effect compared to bioidentical estrogens. Our analysis detects no lasting impact of hormonal contraceptives on the plasma proteome. CONCLUSIONS:HCU is the dominant factor reshaping the high-abundant circulating blood proteome in two population studies. Given the high prevalence of HCU among young women, it is essential to account for this treatment in human proteome studies to avoid misinterpreting its impact as sex- or age-related effects. Although we did not investigate the influence of HCU-induced proteomic changes on human health, our data suggest that future studies on this topic are warranted.

BACKGROUND:Loss-of-function mutations in the PRKN gene, encoding Parkin, are the most common cause of autosomal recessive Parkinson's disease (PD). We have previously identified mitoch ondrial Stomatin-like protein 2 (SLP-2), which functions in the assembly of respiratory chain proteins, as a Parkin-binding protein. Selective knockdown of either Parkin or SLP-2 led to reduced mitochondrial and neuronal function in neuronal cells and Drosophila, where a double knockdown led to a further worsening of Parkin-deficiency phenotypes. Here, we investigated the minimal Parkin region involved in the Parkin-SLP-2 interaction and explored the ability of Parkin-fragments and peptides from this minimal region to restore mitochondrial function. METHODS:In fibroblasts, human induced pluripotent stem cell (hiPSC)-derived neurons, and neuroblastoma cells the interaction between Parkin and SLP-2 was investigated, and the Parkin domain responsible for the binding to SLP-2 was mapped. High resolution respirometry, immunofluorescence analysis and live imaging were used to analyze mitochondrial function. RESULTS:Using a proximity ligation assay, we quantitatively assessed the Parkin-SLP-2 interaction in skin fibroblasts and hiPSC-derived neurons. When PD-associated PRKN mutations were present, we detected a significantly reduced interaction between the two proteins. We found a preferential binding of SLP-2 to the N-terminal part of Parkin, with a highest affinity for the RING0 domain. Computational modeling based on the crystal structure of Parkin protein predicted several potential binding sites for SLP-2 within the Parkin RING0 domain. Amongst these, three binding sites were observed to overlap with natural PD-causing missense mutations, which we demonstrated interfere substantially with the binding of Parkin to SLP-2. Finally, delivery of the isolated Parkin RING0 domain and a Parkin mini-peptide, conjugated to cell-permeant and mitochondrial transporters, rescued compromised mitochondrial function in Parkin-deficient neuroblastoma cells and hiPSC-derived neurons with endogenous, disease causing PRKN mutations. CONCLUSIONS:These findings place further emphasis on the importance of the protein-protein interaction between Parkin and SLP-2 for the maintenance of optimal mitochondrial function. The possibility of restoring an abolished binding to SLP-2 by delivering the Parkin RING0 domain or the Parkin mini-peptide involved in this specific protein-protein interaction into cells might represent a novel organelle-specific therapeutic approach for correcting mitochondrial dysfunction in Parkin-linked PD.

Identifying biomarkers able to discriminate individuals on different health trajectories is crucial to understand the molecular basis of age-related morbidity. We investigated multi-omics signatures of general health and organ-specific morbidity, as well as their interconnectivity. We examined cross-sectional metabolome and proteome data from 3,142 adults of the Cooperative Health Research in South Tyrol (CHRIS) study, an Alpine population study designed to investigate how human biology, environment, and lifestyle factors contribute to people’s health over time. We had 174 metabolites and 148 proteins quantified from fasting serum and plasma samples. We used the Cumulative Illness Rating Scale (CIRS) Comorbidity Index (CMI), which considers morbidity in 14 organ systems, to assess health status (any morbidity vs. healthy). Omics-signatures for health status were identified using random forest (RF) classifiers. Linear regression models were fitted to assess directionality of omics markers and health status associations, as well as to identify omics markers related to organ-specific morbidity. Next to age, we identified 21 metabolites and 10 proteins as relevant predictors of health status and results confirmed associations for serotonin and glutamate to be age-independent. Considering organ-specific morbidity, several metabolites and proteins were jointly related to endocrine, cardiovascular, and renal morbidity. To conclude, circulating serotonin was identified as a potential novel predictor for overall morbidity.

Genome-wide association studies identified a locus on chromosome 4q21.1, spanning the FAM47E , STBD1 , CCDC158 , and SHROOM3 genes, as associated with kidney function markers. Functional studies implicated SHROOM3 , encoding an actin-binding protein involved in cell shaping, into podocyte barrier damage. Despite the locus was also found associated with electrolytes, hematological and cardiovascular traits, systematic explorations of functional variants across all the genes in the locus are lacking. We reconstructed haplotypes covering the whole locus on 12,834 participants to the Cooperative Health Research in South Tyrol (CHRIS) study, using genotypes imputed on a whole-exome sequencing reference panel of a subsample of 3,422 participants. Haplotypes included 146 exonic and intronic variants over the four genes and were tested for association with 73 serum, urine and anthropometric traits, 172 serum metabolite and 148 plasma protein concentrations using linear regression models. We identified 11 haplotypes with 2% to 24% frequency. Compared to the most common haplotype, most haplotypes were associated with higher levels of the creatinine-based estimated glomerular filtration rate and lower serum magnesium levels. The second most common haplotype (12% frequency) was additionally associated with lower dodecanoyl-, hydroxyvaleryl- and tiglyl-carnitine serum concentrations. A haplotype of 4% frequency was also associated with lower red blood cell count, hemoglobin, and hematocrit levels. A haplotype of 2% frequency was associated with serum glutamine and putrescine concentrations. Cluster analysis revealed distinct groups of traits and of haplotypes. The FAM47E - SHROOM3 locus exhibits haplotype variability that corresponds to marked pleiotropic effects, implicating the existence of population subgroups with distinct biomarker profiles. ### Competing Interest Statement CP is consultant for Quotient Therapeutics. DA is employed by AstraZeneca. The other authors declare no competing financial interests. ### Funding Statement The CHRIS study was funded by the Department of Innovation, Research and University of the Autonomous Province of Bolzano-South Tyrol and supported by the European Regional Development Fund (FESR1157). This work was carried out within the TrainCKDis project, funded by the European Union Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement H2020-MSCA-ITN-2019 ID:860977 (TrainCKDis). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee/IRB of the Eurac Research Institute for Biomedicine gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The data used in the current study can be requested with an application to access.request.biomedicine{at}eurac.edu at the Eurac Research Institute for Biomedicine.

AbstractIdentifying biomarkers able to discriminate individuals on different health trajectories is crucial to understand the molecular basis of age-related morbidity. We investigated multi-omics signatures of general health and organ-specific morbidity, as well as their interconnectivity. We examined cross-sectional metabolome and proteome data from 3,142 adults of the Cooperative Health Research in South Tyrol (CHRIS) study, an Alpine population study designed to investigate how human biology, environment, and lifestyle factors contribute to people’s health over time. We had 174 metabolites and 148 proteins quantified from fasting serum and plasma samples. We used the Cumulative Illness Rating Scale (CIRS) Comorbidity Index (CMI), which considers morbidity in 14 organ systems, to assess health status (any morbidity vs. healthy). Omics-signatures for health status were identified using random forest (RF) classifiers. Linear regression models were fitted to assess directionality of omics markers and health status associations, as well as to identify omics markers related to organ-specific morbidity.Next to age, we identified 21 metabolites and 10 proteins as relevant predictors of health status and results confirmed associations for serotonin and glutamate to be age-independent. Considering organ-specific morbidity, several metabolites and proteins were jointly related to endocrine, cardiovascular, and renal morbidity. To conclude, circulating serotonin was identified as a potential novel predictor for overall morbidity.

Background Plasma proteomics offers new avenues to explore non-genetic associations, such as biomarkers for lifestyle and environmental exposure in population studies. To date, most proteomic investigations in population studies have utilized affinity-reagent based technologies, which are ideal to quantify the low abundant fraction of the circulating proteome but may omit several of the abundant proteins that function in plasma. Methods Utilizing high throughput mass spectrometry, we quantified 148 highly abundant protein groups including immunoglobulins, coagulation factors, metabolic proteins, and components of the innate immune system, in the plasma of 3,632 participants from the Cooperative Health Research in South Tyrol (CHRIS) study. Using multiple regression analyses we then investigated associations with various factors including common medications. Results Beyond age and sex, the high abundant plasma proteome is predominantly influenced by hormonal contraceptives. For instance, Angiotensinogen (AGT) levels exhibit significant alteration with this treatment, suggesting that AGT levels could be a potential biomarker for contraceptive use. The effect of this drug class is more pronounced than other common medications or covariates. Furthermore, our analysis does not reveal any enduring signature associated with the use of these contraceptives. Conclusion In contrast to most used drugs, hormonal contraceptives exert a pronounced effect on the high abundant plasma proteome. Given its high prevalence among young female participants, the impact of hormonal contraceptives might be misconstrued as sex-or age-related effects on the plasma proteome. One should thus account for their use in any epidemiological or clinical plasma proteome study to prevent misleading results. ### Competing Interest Statement Markus Ralser is founder and shareholder of Elitptica Ltd. Michael Mülleder is a consultant and shareholder of Eliptica Ltd. ### Funding Statement The CHRIS study was funded by the Department of Innovation, Research and University of the Autonomous Province of Bolzano-South Tyrol and supported by the European Regional Development Fund (FESR1157). Measurements were partly funded by Wellcome Trust (IA 200829/Z/16) to Markus Ralser. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Ethics Committee of the Health Authority of the Autonomous Province of Bolzano (Südtiroler Sanitätsbetrieb/Azienda Sanitaria dell'Alto Adige) gave ethical approval for this work (protocol No. 21/2011, 19 April 2011). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes

Objective The objective of this study was to investigate the clinical manifestations and outcome of COVID-19 in patients with inflammatory rheumatic and musculoskeletal disease (iRMD) as compared with the general population.Methods This is a case-control study of patients selected from the South Tyrol public health service, Italy, with and without iRMD, affected by COVID-19. We included patients >= 18 years and with a positive SARS-CoV-2 PCR test between 1 October 2020 and 1 March 2021. Cases were identified by linking the diagnosis of a rheumatic disease with PCR test positivity; these were then matched in a 1:1.8 (planned 1:2) ratio for age, sex, and date of COVID-19 diagnosis with people from the general population. The outcomes of primary interest were hospitalization, and severe course (intensive care unit, mechanical ventilation/extracorporeal membrane oxygenation, death).Results The study population consisted of 561 COVID-19 patients, of which 201 (mean age 60.4 years; 65.2% female) were patients with iRMD and 360 were controls from the general population (59.8 years; 64.7% female). The majority of iRMD patients (88.6%) were receiving an immunosuppressive drug at the time of COVID-19 diagnosis, and 36.3% were receiving glucocorticoids. COVID-19 related hospitalization (12.4% vs 10.6%, P = 0.49), severe course (5.0% vs 5.3%, P = 1.00), and mortality (3.5% vs 4.4%, P = 0.66) were similar between the groups. Among the hospitalized patients, mechanical ventilation was more common in iRMD patients than in controls [n = 5 (20.0%) vs n = 1 (2.6%), P = 0.035].Conclusion Our study indicated similar rates for admission, severe course, and mortality between patients with iRMD and controls affected by COVID-19. Among the hospitalized patients, mechanical ventilation was more frequently required in the iRMD group.

Large-scale plasma proteomics in population studies offer new avenues to explore non-genetic associations, such as biomarkers for lifestyle and environmental exposure. Moreover, through longitudinal monitoring, they help in characterizing the onset and progression of diseases. Utilizing the SWATH DIA-MS-based proteomic approach with 5-minute chromatographic gradients, we examined the neat plasma proteome of 3,632 participants from the Cooperative Health Research in South Tyrol (CHRIS) study. We present precise protein quantities for 148 highly abundant plasma protein groups. Many of these proteins are challenging to quantify using affinity-based reagents. This set of highly abundant plasma proteins includes immunoglobulins, coagulation factors, metabolic proteins, and components of the innate immune system, such as the complement system. Our findings indicate that, beyond age and sex, the most significant biological variable affecting the plasma proteome was the use of hormonal contraceptives. The signature from this drug class was more pronounced compared to other common medications, which influenced only a subset of the measured proteins and exhibited smaller effect sizes. Notably, Angiotensinogen (AGT) levels were strongly influenced by contraceptive use, suggesting that AGT levels might serve as a potential biomarker for contraceptive usage. Due to its high prevalence, and apparently strong influence, this type of medication should be accounted for in any epidemiological or clinical study of the plasma proteome to avoid spurious findings.

Background Diet is known to affect kidney function. However, population-based studies provide contrasting evidence, resulting in a poor understanding of the effect of proteins from specific foods on kidney health. Methods We analyzed the effect of total daily protein intake (TDPI) and source-specific daily protein intake (DPI) on fasting serum creatinine (SCr) and estimated glomerular filtration rate (eGFR) in the Cooperative Health Research In South Tyrol (CHRIS) cross-sectional study ( n = 5889), using the GA 2 LEN food frequency questionnaire for TDPI and DPI estimation. We fitted multivariable adjusted mixed models of SCr and eGFR on TDPI and DPI quartiles (Q1-Q4) in the overall sample, and after removing individuals with known hypertension, diabetes or chronic kidney disease (CKD). Results Higher TDPI as well as DPI from overall animal sources, fish, and poultry, were associated with higher SCr (trend test p , p trend < 0.01), with larger effect after excluding individuals with known hypertension, diabetes or CKD. The eGFR was lower at higher TDPI (Q4 vs Q1: − 1.6 ml/min/1.73 m 2 ; 95% CI − 2.5, − 0.7; p trend = 3e−4) and DPI from fish (Q4 vs Q1: − 2.1 ml/min/1.73 m 2 ; 95% CI − 2.9, − 1.20; p trend = 4.3e−6), overall animal source (Q4 vs Q1: − 1.6 ml/min/1.73 m 2 ; 95% CI −2.5, − 0.8), processed meat (Q4 vs Q1: − 1.4 ml/min/1.73 m 2 ; p trend = 0.027), red meat, offal and processed meat (Q4 vs Q1: − 1.4 ml/min/1.73 m 2 ; p trend = 0.015) and poultry (Q4 vs Q1: − 0.9 ml/min/1.73 m 2 ; p trend = 0.015). Conclusions TDPI and DPI from specific animal sources were positively associated with SCr and negatively associated with eGFR. Lacking an alternative marker of kidney function, confounding involving muscle mass metabolism cannot be fully excluded. Graphical abstract

Atrial fibrillation (AF) is a supraventricular arrhythmia deriving from uncoordinated electrical activation with considerable associated morbidity and mortality. To expand the limited understanding of AF biological mechanisms, we performed two screenings, investigating the genetic and metabolic determinants of AF in the Cooperative Health Research in South Tyrol study. We found 110 AF cases out of 10,509 general population individuals. A genome-wide association scan (GWAS) identified two novel loci (p-value < 5 × 10−8) around SNPs rs745582874, next to gene PBX1, and rs768476991, within gene PCCA, with genotype calling confirmed by Sanger sequencing. Risk alleles at both SNPs were enriched in a family detected through familial aggregation analysis of the phenotype, and both rare alleles co-segregated with AF. The metabolic screening of 175 metabolites, in a subset of individuals, revealed a 41% lower concentration of lysophosphatidylcholine lysoPC a C20:3 in AF cases compared to controls (p-adj = 0.005). The genetic findings, combined with previous evidence, indicate that the two identified GWAS loci may be considered novel genetic rare determinants for AF. Considering additionally the association of lysoPC a C20:3 with AF by metabolic screening, our results demonstrate the valuable contribution of the combined genomic and metabolomic approach in studying AF in large-scale population studies.

The COVID-19 pandemic has been threatening the healthcare and socioeconomic systems of entire nations. While population-based surveys to assess the distribution of SARS-CoV-2 infection have become a priority, pre-existing longitudinal studies are ideally suited to assess the determinants of COVID-19 onset and severity.The Cooperative Health Research In South Tyrol (CHRIS) study completed the baseline recruitment of 13,393 adults from the Venosta/Vinschgau rural district in 2018, collecting extensive phenotypic and biomarker data, metabolomic data, densely imputed genotype and whole-exome sequencing data.Based on CHRIS, we designed a prospective study, called CHRIS COVID-19, aimed at: 1) estimating the incidence of SARS-CoV-2 infections; 2) screening for and investigating the determinants of incident infection among CHRIS participants and their household members; 3) monitoring the immune response of infected participants prospectively.An online screening questionnaire was sent to all CHRIS participants and their household members. A random sample of 1450 participants representative of the district population was invited to assess active (nasopharyngeal swab) or past (serum antibody test) infections. We prospectively invited for complete SARS-CoV-2 testing all questionnaire completers gauged as possible cases of past infection and their household members. In positive tested individuals, antibody response is monitored quarterly for one year. Untested and negative participants receive the screening questionnaire every four weeks until gauged as possible incident cases or till the study end.Originated from a collaboration between researchers and community stakeholders, the CHRIS COVID-19 study aims at generating knowledge about the epidemiological, molecular, and genetic characterization of COVID-19 and its long-term sequelae.

Levodopa is the standard long-term dopamine replacement therapy to treat Parkinson’s disease (PD) symptoms. With time, levodopa may induce debilitating dyskinesias (LID), the treatment of which represents a large clinically unmet need. However, time-to-LID onset varies between patients, reflecting a possible genetic component. We performed an hypothesis-free whole-exome sequencing (WES)-based screening of time-to-LID onset and attempted replication of previously published candidate gene studies. A WES association analysis was carried out in 134 PD patients in a meta-analytical framework. Replication was attempted in an independent study of 97 PD patients. Variants from previously reported candidate genes (OPRM1, COMT, BDNF) were also specifically examined. We significantly replicated, for the first time, an association of variant rs1799971 in the OPRM1 gene with time-to-LID onset. Furthermore, we identified two novel potentially functional variants, in the MAD2L2 (rs2233019) and MAP7 (rs35350783) genes, which were significantly associated at the discovery stage. In the replication study, the two variants showed direction-consistent effects but did not achieve the replication significance threshold. Our study provides the first WES results for time-to-LID onset, where we replicate association at OPRM1, and suggest new variants in MAD2L2 and MAP7 genes that are significant in discovery, but require larger datasets for replication. The results are being made publicly available to allow for independent external validation.