Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer.

The C1ORF112 gene initially drew attention when it was found to be strongly co-expressed with several genes previously associated with cancer and implicated in DNA repair and cell cycle regulation, such as RAD51 and the BRCA genes. The molecular functions of C1ORF112 remain poorly understood, yet several studies have uncovered clues as to its potential functions. Here, we review the current knowledge on C1ORF112 biology, its evolutionary history, possible functions, and its potential relevance to cancer. C1ORF112 is conserved throughout eukaryotes, from plants to humans, and is very highly conserved in primates. Protein models suggest that C1ORF112 is an alpha-helical protein. Interestingly, homozygous knockout mice are not viable, suggesting an essential role for C1ORF112 in mammalian development. Gene expression data show that, among human tissues, C1ORF112 is highly expressed in the testes and overexpressed in various cancers when compared to healthy tissues. C1ORF112 has also been shown to have altered levels of expression in some tumours with mutant TP53. Recent screens associate C1ORF112 with DNA replication and reveal possible links to DNA damage repair pathways, including the Fanconi anaemia pathway and homologous recombination. These insights provide important avenues for future research in our efforts to understand the functions and potential disease relevance of C1ORF112.

Gene co-expression analysis for functional classification and gene-disease predictions.

Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes. Here, we introduce and guide researchers through a (differential) co-expression analysis. We provide an overview of methods and tools used to create and analyse co-expression networks constructed from gene expression data, and we explain how these can be used to identify genes with a regulatory role in disease. Furthermore, we discuss the integration of other data types with co-expression networks and offer future perspectives of co-expression analysis.

Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies.

Schinzel-Giedion syndrome (SGS) is a rare developmental disorder characterized by multiple malformations, severe neurological alterations and increased risk of malignancy. SGS is caused by de novo germline mutations clustering to a 12bp hotspot in exon 4 of SETBP1. Mutations in this hotspot disrupt a degron, a signal for the regulation of protein degradation, and lead to the accumulation of SETBP1 protein. Overlapping SETBP1 hotspot mutations have been observed recurrently as somatic events in leukemia. We collected clinical information of 47 SGS patients (including 26 novel cases) with germline SETBP1 mutations and of four individuals with a milder phenotype caused by de novo germline mutations adjacent to the SETBP1 hotspot. Different mutations within and around the SETBP1 hotspot have varying effects on SETBP1 stability and protein levels in vitro and in in silico modeling. Substitutions in SETBP1 residue I871 result in a weak increase in protein levels and mutations affecting this residue are significantly more frequent in SGS than in leukemia. On the other hand, substitutions in residue D868 lead to the largest increase in protein levels. Individuals with germline mutations affecting D868 have enhanced cell proliferation in vitro and higher incidence of cancer compared to patients with other germline SETBP1 mutations. Our findings substantiate that, despite their overlap, somatic SETBP1 mutations driving malignancy are more disruptive to the degron than germline SETBP1 mutations causing SGS. Additionally, this suggests that the functional threshold for the development of cancer driven by the disruption of the SETBP1 degron is higher than for the alteration in prenatal development in SGS. Drawing on previous studies of somatic SETBP1 mutations in leukemia, our results reveal a genotype-phenotype correlation in germline SETBP1 mutations spanning a molecular, cellular and clinical phenotype.

GeneFriends: a human RNA-seq-based gene and transcript co-expression database.

Co-expression networks have proven effective at assigning putative functions to genes based on the functional annotation of their co-expressed partners, in candidate gene prioritization studies and in improving our understanding of regulatory networks. The growing number of genome resequencing efforts and genome-wide association studies often identify loci containing novel genes and there is a need to infer their functions and interaction partners. To facilitate this we have expanded GeneFriends, an online database that allows users to identify co-expressed genes with one or more user-defined genes. This expansion entails an RNA-seq-based co-expression map that includes genes and transcripts that are not present in the microarray-based co-expression maps, including over 10,000 non-coding RNAs. The results users obtain from GeneFriends include a co-expression network as well as a summary of the functional enrichment among the co-expressed genes. Novel insights can be gathered from this database for different splice variants and ncRNAs, such as microRNAs and lincRNAs. Furthermore, our updated tool allows candidate transcripts to be linked to diseases and processes using a guilt-by-association approach. GeneFriends is freely available from http://www.GeneFriends.org and can be used to quickly identify and rank candidate targets relevant to the process or disease under study.

A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels.

BACKGROUND: A deeper understanding of differences and similarities in transcriptional regulation between species can uncover important information about gene functions and the role of genes in disease. Deciphering such patterns between mice and humans is especially important since mice play an essential role in biomedical research. RESULTS: Here, in order to characterize evolutionary changes between humans and mice, we compared gene co-expression maps to evaluate the conservation of co-expression. We show that the conservation of co-expression connectivity of homologous genes is negatively correlated with molecular evolution rates, as expected. Then we investigated evolutionary aspects of gene sets related to functions, tissues, pathways and diseases. Genes expressed in the testis, eye and skin, and those associated with regulation of transcription, olfaction, PI3K signalling, response to virus and bacteria were more divergent between mice and humans in terms of co-expression connectivity. Surprisingly, a deeper investigation of the PI3K signalling cascade revealed that its divergence is caused by the most crucial genes of this pathway, such as mTOR and AKT2. On the other hand, our analysis revealed that genes expressed in the brain and in the bone, and those associated with cell adhesion, cell cycle, DNA replication and DNA repair are most strongly conserved in terms of co-expression network connectivity as well as having a lower rate of duplication events. Genes involved in lipid metabolism and genes specific to blood showed a signature of increased co-expression connectivity in the mouse. In terms of diseases, co-expression connectivity of genes related to metabolic disorders is the most strongly conserved between mice and humans and tumor-related genes the most divergent. CONCLUSIONS: This work contributes to discerning evolutionary patterns between mice and humans in terms of gene interactions. Conservation of co-expression is a powerful approach to identify gene targets and processes with potential similarity and divergence between mice and humans, which has implications for drug testing and other studies employing the mouse as a model organism.

GDF-15 improves the predictive capacity of Steatotic liver disease non-invasive tests for incident morbidity and mortality risk for cardio-renal-metabolic diseases and malignancies.

BACKGROUND & AIMS: Noninvasive tools (NITs) are currently used to stratify the risk of having or developing hepatic steatosis or fibrosis. Their performance and a proteomic-enabled improvement in forecasting long-term cardio-renal-metabolic morbidity, malignancies, as well as cause-specific and all-cause mortality, are lacking. Therefore, the performance of established NITs needs to be investigated in identifying cardio-renal-metabolic morbidity, malignancies, cause-specific and overall mortality and improve their performance with novel, proteomic-enabled NITs, including growth differentiation factor 15 (GDF-15), allowing multipurpose utilization. METHODS: 502,359 UK Biobank participants free of the study outcomes at baseline with a 14-year median follow-up were grouped into three categories: a) general population, b) potentially metabolic dysfunction-associated steatotic liver disease (MASLD) population, c) individuals with type 2 diabetes mellitus. The investigated NITs include Aspartate aminotransferase to Platelet Ratio Index (APRI), Fibrosis 4 Index (FIB-4), Fatty Liver Index (FLI), Hepatic Steatosis Index (HSI), Lipid Accumulation Product (LAP), and metabolic dysfunction-associated fibrosis (MAF-5) score. RESULTS: Adding GDF-15 to the existing NITs led to significantly increased prognostic performance compared to the traditional NITs in almost all instances, reaching substantially high C-indices, ranging between 0.601 and 0.808, with an overall >0.2 improvement in C-index. Overall, with the GDF-15 enhanced NITs, up to more than seven times fewer individuals need to be screened to identify more incident cases of adverse outcomes compared to the traditional NITs. The cumulative incidence of all outcomes, based on the continuous value percentiles of NITs, is increasing exponentially in the upper quintile of the GDF-15 enhanced NITs. CONCLUSIONS: The herein-developed GDF-15 enhanced indices demonstrate higher screening effectiveness and significantly improved prognostic abilities, which are reduced to practice through an easy-to-use web-based calculator tool (https://clinicalpredictor.shinyapps.io/multimorbidity-mortality-risk/).

A Digitally Enabled Combined Lifestyle Intervention for Weight Loss: Pilot Study in a Dutch General Population Cohort.

BACKGROUND: Overweight and obesity rates among the general population of the Netherlands keep increasing. Combined lifestyle interventions (CLIs) focused on physical activity, nutrition, sleep, and stress management can be effective in reducing weight and improving health behaviors. Currently available CLIs for weight loss (CLI-WLs) in the Netherlands consist of face-to-face and community-based sessions, which face scalability challenges. A digitally enabled CLI-WL with digital and human components may provide a solution for this challenge; however, the feasibility of such an intervention has not yet been assessed in the Netherlands. OBJECTIVE: The aim of this study was two-fold: (1) to determine how weight and other secondary cardiometabolic outcomes (lipids and blood pressure) change over time in a Dutch population with overweight or obesity and cardiometabolic risk participating in a pilot digitally enabled CLI-WL and (2) to collect feedback from participants to guide the further development of future iterations of the intervention. METHODS: Participants followed a 16-week digitally enabled lifestyle coaching program rooted in the Fogg Behavior Model, focused on nutrition, physical activity, and other health behaviors, from January 2020 to December 2021. Participants could access the digital app to register and track health behaviors, weight, and anthropometrics data at any time. We retrospectively analyzed changes in weight, blood pressure, and lipids for remeasured users. Surveys and semistructured interviews were conducted to assess critical positive and improvement points reported by participants and health care professionals. RESULTS: Of the 420 participants evaluated at baseline, 53 participated in the pilot. Of these, 37 (70%) were classified as overweight and 16 (30%) had obesity. Mean weight loss of 4.2% occurred at a median of 10 months postintervention. The subpopulation with obesity (n=16) showed a 5.6% weight loss on average. Total cholesterol decreased by 10.2% and low-density lipoprotein cholesterol decreased by 12.9% on average. Systolic and diastolic blood pressure decreased by 3.5% and 7.5%, respectively. Participants identified the possibility of setting clear action plans to work toward and the multiple weekly touch points with coaches as two of the most positive and distinctive components of the digitally enabled intervention. Surveys and interviews demonstrated that the digital implementation of a CLI-WL is feasible and well-received by both participants and health care professionals. CONCLUSIONS: Albeit preliminary, these findings suggest that a behavioral lifestyle program with a digital component can achieve greater weight loss than reported for currently available offline CLI-WLs. Thus, a digitally enabled CLI-WL is feasible and may be a scalable alternative to offline CLI-WL programs. Evidence from future studies in a Dutch population may help elucidate the mechanisms behind the effectiveness of a digitally enabled CLI-WL.

The necessity of incorporating non-genetic risk factors into polygenic risk score models.

The growing public interest in genetic risk scores for various health conditions can be harnessed to inspire preventive health action. However, current commercially available genetic risk scores can be deceiving as they do not consider other, easily attainable risk factors, such as sex, BMI, age, smoking habits, parental disease status and physical activity. Recent scientific literature shows that adding these factors can improve PGS based predictions significantly. However, implementation of existing PGS based models that also consider these factors requires reference data based on a specific genotyping chip, which is not always available. In this paper, we offer a method naïve to the genotyping chip used. We train these models using the UK Biobank data and test these externally in the Lifelines cohort. We show improved performance at identifying the 10% most at-risk individuals for type 2 diabetes (T2D) and coronary artery disease (CAD) by including common risk factors. Incidence in the highest risk group increases from 3.0- and 4.0-fold to 5.8 for T2D, when comparing the genetics-based model, common risk factor-based model and combined model, respectively. Similarly, we observe an increase from 2.4- and 3.0-fold to 4.7-fold risk for CAD. As such, we conclude that it is paramount that these additional variables are considered when reporting risk, unlike current practice with current available genetic tests.

Effective questionnaire-based prediction models for type 2 diabetes across several ethnicities: a model development and validation study.

Background: Type 2 diabetes disproportionately affects individuals of non-White ethnicity through a complex interaction of multiple factors. Therefore, early disease detection and prediction are essential and require tools that can be deployed on a large scale. We aimed to tackle this problem by developing questionnaire-based prediction models for type 2 diabetes prevalence and incidence for multiple ethnicities. Methods: In this proof of principle analysis, logistic regression models to predict type 2 diabetes prevalence and incidence, using questionnaire-only variables reflecting health state and lifestyle, were trained on the White population of the UK Biobank (n = 472,696 total, aged 37-73 years, data collected 2006-2010) and validated in five other ethnicities (n = 29,811 total) and externally in Lifelines (n = 168,205 total, aged 0-93 years, collected between 2006 and 2013). In total, 631,748 individuals were included for prevalence prediction and 67,083 individuals for the eight-year incidence prediction. Type 2 diabetes prevalence in the UK Biobank ranged between 6% in the White population to 23.3% in the South Asian population, while in Lifelines, the prevalence was 1.9%. Predictive accuracy was evaluated using the area under the receiver operating characteristic curve (AUC), and a detailed sensitivity analysis was conducted to assess potential clinical utility. We compared the questionnaire-only models to models containing physical measurements and biomarkers as well as to clinical non-laboratory type 2 diabetes risk tools and conducted a reclassification analysis. Findings: Our algorithms accurately predicted type 2 diabetes prevalence (AUC = 0.901) and eight-year incidence (AUC = 0.873) in the White UK Biobank population. Both models replicated well in the Lifelines external validation, with AUCs of 0.917 and 0.817 for prevalence and incidence, respectively. Both models performed consistently well across different ethnicities, with AUCs of 0.855-0.894 for prevalence and 0.819-0.883 for incidence. These models generally outperformed two clinically validated non-laboratory tools and correctly reclassified >3,000 additional cases. Model performance improved with the addition of blood biomarkers but not with the addition of physical measurements. Interpretation: Our findings suggest that easy-to-implement, questionnaire-based models could be used to predict prevalent and incident type 2 diabetes with high accuracy across several ethnicities, providing a highly scalable solution for population-wide risk stratification. Future work should determine the effectiveness of these models in identifying undiagnosed type 2 diabetes, validated in cohorts of different populations and ethnic representation. Funding: University Medical Center Groningen.

Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases.

Identification of therapeutic targets from genome-wide association studies (GWAS) requires insights into downstream functional consequences. We harmonized 8,613 RNA-sequencing samples from 14 brain datasets to create the MetaBrain resource and performed cis- and trans-expression quantitative trait locus (eQTL) meta-analyses in multiple brain region- and ancestry-specific datasets (n ≤ 2,759). Many of the 16,169 cortex cis-eQTLs were tissue-dependent when compared with blood cis-eQTLs. We inferred brain cell types for 3,549 cis-eQTLs by interaction analysis. We prioritized 186 cis-eQTLs for 31 brain-related traits using Mendelian randomization and co-localization including 40 cis-eQTLs with an inferred cell type, such as a neuron-specific cis-eQTL (CYP24A1) for multiple sclerosis. We further describe 737 trans-eQTLs for 526 unique variants and 108 unique genes. We used brain-specific gene-co-regulation networks to link GWAS loci and prioritize additional genes for five central nervous system diseases. This study represents a valuable resource for post-GWAS research on central nervous system diseases.

GeneFriends: an online co-expression analysis tool to identify novel gene targets for aging and complex diseases.

BACKGROUND: Although many diseases have been well characterized at the molecular level, the underlying mechanisms are often unknown. Nearly half of all human genes remain poorly studied, yet these genes may contribute to a number of disease processes. Genes involved in common biological processes and diseases are often co-expressed. Using known disease-associated genes in a co-expression analysis may help identify and prioritize novel candidate genes for further study. RESULTS: We have created an online tool, called GeneFriends, which identifies co-expressed genes in over 1,000 mouse microarray datasets. GeneFriends can be used to assign putative functions to poorly studied genes. Using a seed list of disease-associated genes and a guilt-by-association method, GeneFriends allows users to quickly identify novel genes and transcription factors associated with a disease or process. We tested GeneFriends using seed lists for aging, cancer, and mitochondrial complex I disease. We identified several candidate genes that have previously been predicted as relevant targets. Some of the genes identified are already being tested in clinical trials, indicating the effectiveness of this approach. Co-expressed transcription factors were investigated, identifying C/ebp genes as candidate regulators of aging. Furthermore, several novel candidate genes, that may be suitable for experimental or clinical follow-up, were identified. Two of the novel candidates of unknown function that were co-expressed with cancer-associated genes were selected for experimental validation. Knock-down of their human homologs (C1ORF112 and C12ORF48) in HeLa cells slowed growth, indicating that these genes of unknown function, identified by GeneFriends, may be involved in cancer. CONCLUSIONS: GeneFriends is a resource for biologists to identify and prioritize novel candidate genes involved in biological processes and complex diseases. It is an intuitive online resource that will help drive experimentation. GeneFriends is available online at: http://genefriends.org/.

Gathering insights on disease etiology from gene expression profiles of healthy tissues.

MOTIVATION: Gene expression profiles have been widely used to study disease states. It may be possible, however, to gather insights into human diseases by comparing gene expression profiles of healthy organs with different disease incidence or severity. We tested this hypothesis and developed an approach to identify candidate genes associated with disease development by focusing on cancer incidence since it varies greatly across human organs. RESULTS: We normalized organ-specific cancer incidence by organ weight and found that reproductive organs tend to have a higher mass-normalized cancer incidence, which could be due to evolutionary trade-offs. Next, we performed a genome-wide scan to identify genes whose expression across healthy organs correlates with organ-specific cancer incidence. We identified a large number of genes, including genes previously associated with tumorigenesis and new candidate genes. Most genes exhibiting a positive correlation with cancer incidence were related to ribosomal and transcriptional activity, translation and protein synthesis. Organs with enhanced transcriptional and translational activation may have higher cell proliferation and therefore be more likely to develop cancer. Furthermore, we found that organs with lower cancer incidence tend to express lower levels of known cancer-associated genes. Overall, these results demonstrate how genes and processes that predispose organs to specific diseases can be identified using gene expression profiles from healthy tissues. Our approach can be applied to other diseases and serve as foundation for further oncogenomic analyses. CONTACT: jp@senescence.info SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Effect of a Digitally-Enabled, Preventive Health Program on Blood Pressure in an Adult, Dutch General Population Cohort: An Observational Pilot Study.

Worldwide, it is estimated that at least one in four adults suffers from hypertension, and this number is expected to increase as populations grow and age. Blood pressure (BP) possesses substantial heritability, but is also heavily modulated by lifestyle factors. As such, digital, lifestyle-based interventions are a promising alternative to standard care for hypertension prevention and management. In this study, we assessed the prevalence of elevated and high BP in a Dutch general population cohort undergoing a health screening, and observed the effects of a subsequent self-initiated, digitally-enabled lifestyle program on BP regulation. Baseline data were available for 348 participants, of which 56 had partaken in a BP-focused lifestyle program and got remeasured 10 months after the intervention. Participants with elevated SBP and DBP at baseline showed a mean decrease of 7.2 mmHg and 5.4 mmHg, respectively. Additionally, 70% and 72.5% of participants showed an improvement in systolic and diastolic BP at remeasurement. These improvements in BP are superior to those seen in other recent studies. The long-term sustainability and the efficacy of this and similar digital lifestyle interventions will need to be established in additional, larger studies.

Changes in Blood Lipid Levels After a Digitally Enabled Cardiometabolic Preventive Health Program: Pre-Post Study in an Adult Dutch General Population Cohort.

BACKGROUND: Despite widespread education, many individuals fail to follow basic health behaviors such as consuming a healthy diet and exercising. Positive changes in lifestyle habits are associated with improvements in multiple cardiometabolic health risk factors, including lipid levels. Digital lifestyle interventions have been suggested as a viable complement or potential alternative to conventional health behavior change strategies. However, the benefit of digital preventive interventions for lipid levels in a preventive health context remains unclear. OBJECTIVE: This observational study aimed to determine how the levels of lipids, namely total cholesterol, high-density lipoprotein (HDL) cholesterol, low-density lipoprotein (LDL) cholesterol, non-HDL cholesterol, and triglycerides, changed over time in a Dutch general population cohort undergoing a digital preventive health program. Moreover, we looked to establish associations between lifestyle factors at baseline and lipid levels. METHODS: We included 348 adults from the Dutch general population who underwent a digitally enabled preventive health program at Ancora Health between January 2020 and October 2021. Upon enrollment, participants underwent a baseline assessment involving a comprehensive lifestyle questionnaire, a blood biochemistry panel, physical measurements, and cardiopulmonary fitness measurements. Thereafter, users underwent a lifestyle coaching program and could access the digital application to register and track health behaviors, weight, and anthropometric data at any time. Lipid levels were categorized as normal, elevated, high, and clinical dyslipidemia according to accepted international standards. If at least one lipid marker was high or HDL was low, participants received specific coaching and advice for cardiometabolic health. We retrospectively analyzed the mean and percentage changes in lipid markers in users who were remeasured after a cardiometabolic health-focused intervention, and studied the association between baseline user lifestyle characteristics and having normal lipid levels. RESULTS: In our cohort, 199 (57.2%) participants had dyslipidemia at baseline, of which 104 participants were advised to follow a cardiometabolic health-focused intervention. Eating more amounts of favorable food groups and being more active were associated with normal lipid profiles. Among the participants who underwent remeasurement 9 months after intervention completion, 57% (17/30), 61% (19/31), 56% (15/27), 82% (9/11), and 100% (8/8) showed improvements at remeasurement for total, LDL, HDL, and non-HDL cholesterol, and triglycerides, respectively. Moreover, between 35.3% and 77.8% showed a return to normal levels. In those with high lipid levels at baseline, total cholesterol decreased by 0.5 mmol/L (7.5%), LDL cholesterol decreased by 0.39 mmol/L (10.0%), non-HDL cholesterol decreased by 0.44 mmol/L (8.3%), triglycerides decreased by 0.97 mmol/L (32.0%), and HDL increased by 0.17 mmol/L (15.6%), after the intervention. CONCLUSIONS: A cardiometabolic screening program in a general population cohort identified a significant portion of individuals with subclinical and clinical lipid levels. Individuals who, after screening, actively engaged in a cardiometabolic health-focused lifestyle program improved their lipid levels.

A Pilot Study on the Prevalence of Micronutrient Imbalances in a Dutch General Population Cohort and the Effects of a Digital Lifestyle Program.

Maintaining an adequate micronutrient status can be achieved by following a complete, diverse diet. Yet, food trends in Western countries show suboptimal consumption of healthy nutrients. In this study, we explored the prevalence of vitamin and mineral imbalances in a general population cohort of Dutch adults and evaluated the effect of a digital lifestyle program on the nutritional status and nutrition health behaviors of these individuals. A micronutrient panel was measured in 348 participants, alongside a dietary assessment. One hundred users subsequently underwent a remeasurement. We identified at least one nutritional imbalance in 301 individuals (86.5%). A total of 80% improved and normalized B6, 67% improved folate, 70% improved B12, and 86% improved vitamin D. Iron abnormalities were corrected in 75% of the participants. In conclusion, this study found that micronutrient deficiencies of easily obtainable vitamins through diet or supplementation such as B vitamins and vitamin D were more prevalent than expected in a Dutch population. This can partly be explained by insufficient consumption of food groups rich in B vitamins. Our preliminary results in those remeasured after a digitally enabled lifestyle intervention show these imbalances can be corrected with adequate behavioral support complemented with supplementation where needed.

Development and Validation of Decision Rules Models to Stratify Coronary Artery Disease, Diabetes, and Hypertension Risk in Preventive Care: Cohort Study of Returning UK Biobank Participants.

Many predictive models exist that predict risk of common cardiometabolic conditions. However, a vast majority of these models do not include genetic risk scores and do not distinguish between clinical risk requiring medical or pharmacological interventions and pre-clinical risk, where lifestyle interventions could be first-choice therapy. In this study, we developed, validated, and compared the performance of three decision rule algorithms including biomarkers, physical measurements, and genetic risk scores for incident coronary artery disease (CAD), diabetes (T2D), and hypertension against commonly used clinical risk scores in 60,782 UK Biobank participants. The rules models were tested for an association with incident CAD, T2D, and hypertension, and hazard ratios (with 95% confidence interval) were calculated from survival models. Model performance was assessed using the area under the receiver operating characteristic curve (AUROC), and Net Reclassification Index (NRI). The higher risk group in the decision rules model had a 40-, 40.9-, and 21.6-fold increased risk of CAD, T2D, and hypertension, respectively (p < 0.001 for all). Risk increased significantly between the three strata for all three conditions (p < 0.05). Based on genetic risk alone, we identified not only a high-risk group, but also a group at elevated risk for all health conditions. These decision rule models comprising blood biomarkers, physical measurements, and polygenic risk scores moderately improve commonly used clinical risk scores at identifying individuals likely to benefit from lifestyle intervention for three of the most common lifestyle-related chronic health conditions. Their utility as part of digital data or digital therapeutics platforms to support the implementation of lifestyle interventions in preventive and primary care should be further validated.

Improving the diagnostic yield of exome- sequencing by predicting gene-phenotype associations using large-scale gene expression analysis.

The diagnostic yield of exome and genome sequencing remains low (8-70%), due to incomplete knowledge on the genes that cause disease. To improve this, we use RNA-seq data from 31,499 samples to predict which genes cause specific disease phenotypes, and develop GeneNetwork Assisted Diagnostic Optimization (GADO). We show that this unbiased method, which does not rely upon specific knowledge on individual genes, is effective in both identifying previously unknown disease gene associations, and flagging genes that have previously been incorrectly implicated in disease. GADO can be run on www.genenetwork.nl by supplying HPO-terms and a list of genes that contain candidate variants. Finally, applying GADO to a cohort of 61 patients for whom exome-sequencing analysis had not resulted in a genetic diagnosis, yields likely causative genes for ten cases.

Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging.

BACKGROUND: Caloric restriction (CR) can increase longevity in rodents and improve memory function in humans. α-Lipoic acid (LA) has been shown to improve memory function in rats, but not longevity. While studies have looked at survival in rodents after switching from one diet to another, the underlying mechanisms of the beneficial effects of CR and LA supplementation are unknown. Here, we use RNA-seq in cerebral cortex from rats subjected to CR and LA-supplemented rats to understand how changes in diet can affect aging, neurodegeneration and longevity. RESULTS: Gene expression changes during aging in ad libitum-fed rats are largely prevented by CR, and neuroprotective genes are overexpressed in response to both CR and LA diets with a strong overlap of differentially expressed genes between the two diets. Moreover, a number of genes are differentially expressed specifically in rat cohorts exhibiting diet-induced life extension. Finally, we observe that LA supplementation inhibits histone deacetylase (HDAC) protein activity in vitro in rat astrocytes. We find a single microRNA, miR-98-3p, that is overexpressed during CR feeding and LA dietary supplementation; this microRNA alters HDAC and histone acetyltransferase (HAT) activity, which suggests a role for HAT/HDAC homeostasis in neuroprotection. CONCLUSIONS: This study presents extensive data on the effects of diet and aging on the cerebral cortex transcriptome, and also emphasises the importance of epigenetics and post-translational modifications in longevity and neuroprotection.

Insights into the evolution of longevity from the bowhead whale genome.

The bowhead whale (Balaena mysticetus) is estimated to live over 200 years and is possibly the longest-living mammal. These animals should possess protective molecular adaptations relevant to age-related diseases, particularly cancer. Here, we report the sequencing and comparative analysis of the bowhead whale genome and two transcriptomes from different populations. Our analysis identifies genes under positive selection and bowhead-specific mutations in genes linked to cancer and aging. In addition, we identify gene gain and loss involving genes associated with DNA repair, cell-cycle regulation, cancer, and aging. Our results expand our understanding of the evolution of mammalian longevity and suggest possible players involved in adaptive genetic changes conferring cancer resistance. We also found potentially relevant changes in genes related to additional processes, including thermoregulation, sensory perception, dietary adaptations, and immune response. Our data are made available online (http://www.bowhead-whale.org) to facilitate research in this long-lived species.

A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms.

Caloric restriction, a reduction in calorie intake without malnutrition, retards age-related degeneration and extends lifespan in several organisms. CR induces multiple changes, yet its underlying mechanisms remain poorly understood. In this work, we first performed a meta-analysis of microarray CR studies in mammals and identified genes and processes robustly altered due to CR. Our results reveal a complex array of CR-induced changes and we re-identified several genes and processes previously associated with CR, such as growth hormone signalling, lipid metabolism and immune response. Moreover, our results highlight novel associations with CR, such as retinol metabolism and copper ion detoxification, as well as hint of a strong effect of CR on circadian rhythms that in turn may contribute to metabolic changes. Analyses of our signatures by integrating co-expression data, information on genetic mutants, and transcription factor binding site analysis revealed candidate regulators of transcriptional modules in CR. Our results hint at a transcriptional module involved in sterol metabolism regulated by Srebf1. A putative regulatory role of Ppara was also identified. Overall, our conserved molecular signatures of CR provide a comprehensive picture of CR-induced changes and help understand its regulatory mechanisms.