Mapping biological influences on the human plasma proteome beyond the genome

Biomarkers of aging: from molecules and surrogates to physiology and function

Many countries face an unprecedented challenge in aging demographics. This has led to an exponential growth in research on aging, which, coupled to a massive financial influx of funding in the private and public sectors, has resulted in seminal insights into the underpinnings of this biological process. However, critical validation in humans has been hampered by the limited translatability of results obtained in model organisms, additionally confined by the need for extremely time-consuming clinical studies in the ostensible absence of robust biomarkers that would allow monitoring in shorter time frames. In the future, molecular parameters might hold great promise in this regard. In contrast, biomarkers centered on function, resilience, and frailty are available at the present time, with proven predictive value for morbidity and mortality. In this review, the current knowledge of molecular and physiological aspects of human aging, potential antiaging strategies, and the basis, evidence, and potential application of physiological biomarkers in human aging are discussed.

Body fluid biomarkers and psychosis risk in The Accelerating Medicines Partnership® Schizophrenia Program: design considerations

Advances in proteomic assay methodologies and genomics have significantly improved our understanding of the blood proteome. Schizophrenia and psychosis risk are linked to polygenic scores for schizophrenia and other mental disorders, as well as to altered blood and saliva levels of biomarkers involved in hormonal signaling, redox balance, and chronic systemic inflammation. The Accelerating Medicines Partnership® Schizophrenia (AMP®SCZ) aims to ascertain biomarkers that both predict clinical outcomes and provide insights into the biological processes driving clinical outcomes in persons meeting CHR criteria. AMP®SCZ will follow almost 2000 CHR and 640 community study participants for two years, assessing biomarkers at baseline and two-month follow-up including the collection of blood and saliva samples. The following provides the rationale and methods for plans to utilize polygenic risk scores for schizophrenia and other disorders, salivary cortisol levels, and a discovery-based proteomic platform for plasma analyses. We also provide details about the standardized methods used to collect and store these biological samples, as well as the study participant metadata and quality control measures related to preanalytical factors that could influence the values of the biomarkers. Finally, we discuss our plans for analyzing the results of blood- and saliva-based biomarkers. Watch Dr. Perkins discuss their work and this article: https://vimeo.com/1062879582?share=copy#t=0 .

Human Plasma Proteomics Links Modifiable Lifestyle Exposome to Disease Risk

Environmental exposures influence disease risk, yet their underlying biological mechanisms remain poorly understood. We present the Human Exposomic Architecture of the Proteome (HEAP), a framework and resource integrating genetic, exposomic, and proteomic data to uncover how lifestyle influences disease through plasma proteins. Applying HEAP to 2,686 proteins in 53,014 UK Biobank participants, we identified over 11,000 exposure-protein associations across 135 lifestyle exposures. Exposures explained a substantial portion of proteomic variation, with 9% of proteins more influenced by lifestyle than genetics. Mediation analyses across 270 diseases revealed proteins linking exposures to disease risk; for instance, IGFBP1 and IGFBP2 mediated the effects of exercise and diet on type 2 diabetes. These findings were supported by concordant proteomic shifts in interventional studies of exercise and GLP1 agonists, underscoring therapeutic relevance. HEAP provides a resource for advancing disease prevention and precision medicine by revealing mechanisms through which lifestyle shapes human health.

Proteomic Correlates of Vitamin D Supplementation in the Atherosclerosis Risk in Communities (ARIC) Study

PURPOSE

Proteins are key effectors of biological functions and play roles in signaling, transport, growth, repair, and immunity. Vitamin D biomarkers may be reflected in the plasma proteome. The aim of this discovery study was to identify novel proteins associated with vitamin D supplementation.

EXPERIMENTAL DESIGN

We examined cross-sectional associations between vitamin D supplementation and plasma proteins in the Atherosclerosis Risk in Communities (ARIC) study at visit 5 (2011-2013). An untargeted proteomic platform (SomaScan version 4, SomaLogic) was used to quantify relative abundance for 4955 proteins. We compared protein levels in vitamin D supplement users and nonusers using covariate-adjusted multivariable linear regression models.

RESULTS

Of 5011 participants analyzed (mean age 76 [SD 5] years), 2255 (45%) used vitamin D supplements. Fifty-one proteins were associated with vitamin D supplementation at a false discovery rate-adjusted p < 0.05. Most proteins (33 of 51) were lower in users than nonusers. After adjusting for other supplement use (multivitamin/mineral, omega-3, B vitamins, and vitamin C), 7 proteins remained significantly associated with vitamin D supplementation.

CONCLUSIONS AND CLINICAL RELEVANCE

Chondroadherin, parathyroid hormone, transcobalamin-1, osteomodulin, collagen type II, and bone sialoprotein 2 were lower, while sclerostin was higher, in vitamin D users than nonusers. These proteins are potential markers of vitamin D in older adults and highlight vitamin D-related metabolic pathways.

The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends

Recent improvements in proteomics technologies have fundamentally altered our capacities to characterize human biology. There is an ever-growing interest in using these novel methods for studying the circulating proteome, as blood offers an accessible window into human health. However, every methodological innovation and analytical progress calls for reassessing our existing approaches and routines to ensure that the new data will add value to the greater biomedical research community and avoid previous errors. As representatives of HUPO's Human Plasma Proteome Project (HPPP), we present our 2024 survey of the current progress in our community, including the latest build of the Human Plasma Proteome PeptideAtlas that now comprises 4608 proteins detected in 113 data sets. We then discuss the updates of established proteomics methods, emerging technologies, and investigations of proteoforms, protein networks, extracellualr vesicles, circulating antibodies and microsamples. Finally, we provide a prospective view of using the current and emerging proteomics tools in studies of circulating proteins.

BMI trajectories from birth to young adulthood associate with distinct cardiometabolic profiles

BACKGROUND

Numerous studies have investigated links between body mass index (BMI) trajectories and cardiovascular risk, yet discrepancies in BMI measurement duration and timing of the cardiovascular-related outcome evaluation have led to inconsistent findings.

METHODS

We included participants from the Swedish birth cohort (BAMSE) and applied latent class mixture modeling to identify BMI trajectories using data of multiple BMI measures (≥ 4 times) from birth until 24-year follow-up (n = 3204). Subsequently, we analyzed the associations of BMI trajectories with lipids (n = 1974), blood pressure (n = 2022), HbA1c (n = 941), and blood leukocytes (n = 1973) using linear regression. We also investigated the circulating levels of 92 inflammation-related proteins (n = 1866) across BMI trajectories.

RESULTS

Six distinct BMI groups were identified, denoted as increasing-persistent high (n = 74; 2.3%), high-accelerated increasing (n = 209; 6.5%), increasing-accelerated resolving (n = 142; 4.4%), normal-above normal (n = 721; 22.5%), stable normal (n = 1608; 50.2%), and decreasing-persistent low (n = 450; 14.1%) BMI groups. The increasing-persistent high and high-accelerated increasing BMI groups had higher levels of total cholesterol [mean difference (95% confidence intervals): 0.30 (0.04-0.56) and 0.16 (0.02-0.31) mmol/L], triglyceride, low-density lipoprotein, hemoglobin A1C [3.61 (2.17-5.54) and 1.18 (0.40-1.98) mmol/mol], and low-density lipoprotein/high-density lipoprotein ratios, but a lower level of high-density lipoprotein than the stable normal BMI group. These two groups also had higher leukocyte cell counts and higher circulating levels of 28 inflammation-related proteins. No increased cardiometabolic markers were observed in the increasing-accelerated resolving BMI group.

CONCLUSIONS

Participants with persistently high or accelerated increasing BMI trajectories from birth to young adulthood have elevated levels of cardiometabolic risk markers at young adulthood than those with stable normal BMI. However, a raised BMI in childhood may not be inherently harmful to cardiometabolic health, provided it does not persist into adulthood.