Interaction of the La-related protein Slf1 with colliding ribosomes maintains translation of oxidative-stress responsive mRNAs.

In response to oxidative stress cells reprogram gene expression to enhance levels of antioxidant enzymes and promote survival. In Saccharomyces cerevisiae the polysome-interacting La-related proteins (LARPs) Slf1 and Sro9 aid adaptation of protein synthesis during stress by undetermined means. To gain insight in their mechanisms of action in stress responses, we determined LARP mRNA binding positions in stressed and unstressed cells. Both proteins bind within coding regions of stress-regulated antioxidant enzyme and other highly translated mRNAs in both optimal and stressed conditions. LARP interaction sites are framed and enriched with ribosome footprints suggesting ribosome-LARP-mRNA complexes are identified. Although stress-induced translation of antioxidant enzyme mRNAs is attenuated in slf1Δ, these mRNAs remain on polysomes. Focusing further on Slf1, we find it binds to both monosomes and disomes following RNase treatment. slf1Δ reduces disome enrichment during stress and alters programmed ribosome frameshifting rates. We propose that Slf1 is a ribosome-associated translational modulator that stabilises stalled/collided ribosomes, prevents ribosome frameshifting and so promotes translation of a set of highly-translated mRNAs that together facilitate cell survival and adaptation to stress.

Translation factor and RNA binding protein mRNA interactomes support broader RNA regulons for posttranscriptional control.

The regulation of translation provides a rapid and direct mechanism to modulate the cellular proteome. In eukaryotes, an established model for the recruitment of ribosomes to mRNA depends upon a set of conserved translation initiation factors. Nevertheless, how cells orchestrate and define the selection of individual mRNAs for translation, as opposed to other potential cytosolic fates, is poorly understood. We have previously found significant variation in the interaction between individual mRNAs and an array of translation initiation factors. Indeed, mRNAs can be separated into different classes based upon these interactions to provide a framework for understanding different modes of translation initiation. Here, we extend this approach to include new mRNA interaction profiles for additional proteins involved in shaping the cytoplasmic fate of mRNAs. This work defines a set of seven mRNA clusters, based on their interaction profiles with 12 factors involved in translation and/or RNA binding. The mRNA clusters share both physical and functional characteristics to provide a rationale for the interaction profiles. Moreover, a comparison with mRNA interaction profiles from a host of RNA binding proteins suggests that there are defined patterns in the interactions of functionally related mRNAs. Therefore, this work defines global cytoplasmic mRNA binding modules that likely coordinate the synthesis of functionally related proteins.

Joint analysis of functionally related genes yields further candidates associated with Tetralogy of Fallot.

Although several genes involved in the development of Tetralogy of Fallot have been identified, no genetic diagnosis is available for the majority of patients. Low statistical power may have prevented the identification of further causative genes in gene-by-gene survey analyses. Thus, bigger samples and/or novel analytic approaches may be necessary. We studied if a joint analysis of groups of functionally related genes might be a useful alternative approach. Our reanalysis of whole-exome sequencing data identified 12 groups of genes that exceedingly contribute to the burden of Tetralogy of Fallot. Further analysis of those groups showed that genes with high-impact variants tend to interact with each other. Thus, our results strongly suggest that additional candidate genes may be found by studying the protein interaction network of known causative genes. Moreover, our results show that the joint analysis of functionally related genes can be a useful complementary approach to classical single-gene analyses.

Deciphering Protein Glycosylation by Computational Integration of On-chip Profiling, Glycan-array Data, and Mass Spectrometry.

The difficulty in uncovering detailed information about protein glycosylation stems from the complexity of glycans and the large amount of material needed for the experiments. Here we report a method that gives information on the isomeric variants of glycans in a format compatible with analyzing low-abundance proteins. On-chip glycan modification and probing (on-chip gmap) uses sequential and parallel rounds of exoglycosidase cleavage and lectin profiling of microspots of proteins, together with algorithms that incorporate glycan-array analyses and information from mass spectrometry, when available, to computationally interpret the data. In tests on control proteins with simple or complex glycosylation, on-chip gmap accurately characterized the relative proportions of core types and terminal features of glycans. Subterminal features (monosaccharides and linkages under a terminal monosaccharide) were accurately probed using a rationally designed sequence of lectin and exoglycosidase incubations. The integration of mass information further improved accuracy in each case. An alternative use of on-chip gmap was to complement the mass spectrometry analysis of detached glycans by specifying the isomers that comprise the glycans identified by mass spectrometry. On-chip gmap provides the potential for detailed studies of glycosylation in a format compatible with clinical specimens or other low-abundance sources.

Sleep-related problems and suicide behavior and ideation among Black and White trauma-exposed psychiatric inpatients.

OBJECTIVE: Sleep-related problems (SRPs) are associated with increased risk for suicide-related behavior and death. Given that Black adults report greater SRPs as compared to White adults, the purpose of the current study was to examine sleep problems, suicide-related psychiatric admission, and suicide ideation, in Black and White trauma-exposed adults. METHOD: Suicide-related behavior (i.e., intent, plan, and/or behavior) as reason for hospital admission was obtained via medical records review for 172 Black and White adults who were admitted to an acute-care psychiatric facility; all participants completed validated measures of sleep quality and suicide ideation. RESULTS: Adjusted logistic regression analyses revealed that sleep-related daytime dysfunction (AOR = 4.32, p < .05) and poor sleep quality (AOR = 3.64, p < .05) were associated with significantly increased odds that Black participants were admitted for suicide-related psychiatric care. Poorer sleep quality (AOR = 2.10, p < .05) was also associated with increased odds of suicide-related admission among White participants. However, shorter sleep duration was marginally associated with suicide ideation in Black participants only. CONCLUSIONS: SRPs may be related to suicide-related behavior and ideation differently for vulnerable Black and White adults. More research is needed to understand potential race group differences and mechanisms by which SRPs increase risk for suicide crisis across racial groups.

The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response.

The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p and Sro9p are atypical-La motif containing proteins which are members of a superfamily of RNA-binding proteins conserved in eukaryotes. RIP-Seq analysis of these two yeast proteins identified overlapping and distinct sets of mRNA targets, including highly translated mRNAs such as those encoding ribosomal proteins. In paralell, transcriptome analysis of slf1Δ and sro9Δ mutant strains indicated altered gene expression in similar functional classes of mRNAs following loss of each factor. The loss of SLF1 had a greater impact on the transcriptome, and in particular, revealed changes in genes involved in the oxidative stress response. slf1Δ cells are more sensitive to oxidants and RIP-Seq analysis of oxidatively stressed cells enriched Slf1p targets encoding antioxidants and other proteins required for oxidant tolerance. To quantify these effects at the protein level, we used label-free mass spectrometry to compare the proteomes of wild-type and slf1Δ strains following oxidative stress. This analysis identified several proteins which are normally induced in response to hydrogen peroxide, but where this increase is attenuated in the slf1Δ mutant. Importantly, a significant number of the mRNAs encoding these targets were also identified as Slf1p-mRNA targets. We show that Slf1p remains associated with the few translating ribosomes following hydrogen peroxide stress and that Slf1p co-immunoprecipitates ribosomes and members of the eIF4E/eIF4G/Pab1p 'closed loop' complex suggesting that Slf1p interacts with actively translated mRNAs following stress. Finally, mutational analysis of SLF1 revealed a novel ribosome interacting domain in Slf1p, independent of its RNA binding La-motif. Together, our results indicate that Slf1p mediates a translational response to oxidative stress via mRNA-specific translational control.

The 4E-BP Caf20p Mediates Both eIF4E-Dependent and Independent Repression of Translation.

Translation initiation factor eIF4E mediates mRNA selection for protein synthesis via the mRNA 5'cap. A family of binding proteins, termed the 4E-BPs, interact with eIF4E to hinder ribosome recruitment. Mechanisms underlying mRNA specificity for 4E-BP control remain poorly understood. Saccharomyces cerevisiae 4E-BPs, Caf20p and Eap1p, each regulate an overlapping set of mRNAs. We undertook global approaches to identify protein and RNA partners of both 4E-BPs by immunoprecipitation of tagged proteins combined with mass spectrometry or next-generation sequencing. Unexpectedly, mass spectrometry indicated that the 4E-BPs associate with many ribosomal proteins. 80S ribosome and polysome association was independently confirmed and was not dependent upon interaction with eIF4E, as mutated forms of both Caf20p and Eap1p with disrupted eIF4E-binding motifs retain ribosome interaction. Whole-cell proteomics revealed Caf20p mutations cause both up and down-regulation of proteins and that many changes were independent of the 4E-binding motif. Investigations into Caf20p mRNA targets by immunoprecipitation followed by RNA sequencing revealed a strong association between Caf20p and mRNAs involved in transcription and cell cycle processes, consistent with observed cell cycle phenotypes of mutant strains. A core set of over 500 Caf20p-interacting mRNAs comprised of both eIF4E-dependent (75%) and eIF4E-independent targets (25%), which differ in sequence attributes. eIF4E-independent mRNAs share a 3' UTR motif. Caf20p binds all tested motif-containing 3' UTRs. Caf20p and the 3'UTR combine to influence ERS1 mRNA polysome association consistent with Caf20p contributing to translational control. Finally ERS1 3'UTR confers Caf20-dependent repression of expression to a heterologous reporter gene. Taken together, these data reveal conserved features of eIF4E-dependent Caf20p mRNA targets and uncover a novel eIF4E-independent mode of Caf20p binding to mRNAs that extends the regulatory role of Caf20p in the mRNA-specific repression of protein synthesis beyond its interaction with eIF4E.

Does purpose in life or ethnic identity moderate the association for racial discrimination and suicide ideation in racial/ethnic minority emerging adults?

OBJECTIVE: To examine purpose in life (PIL) and ethnic identity (EI) as buffers to suicide ideation for Asian American, Hispanic, and Black emerging adults who perceive racial discrimination. METHOD: Two-hundred eighty-nine undergraduate students enrolled at a large university in the southwestern region of the United States (40.8% Asian American, 32.5% Hispanic, 26.6% Black; 61.2% women; mean age = 20.47, SD = 1.83) reported on experiences of racial discrimination, PIL, EI, and suicidal thoughts. Covariates were intrinsic religiosity, gender, and age. RESULTS: Regression analysis showed that EI was not a significant moderator for the association between perceived racial discrimination (PRD) and suicidal ideation (ß = -.08, p = .13; 95% confidence interval (CI) [-.19, .03]). However, PIL was a significant moderator (ß = -.11, p = .025; CI [-.20, -.01]). A hierarchical regression showed that PIL as a moderator explained additional variance (ΔR2 = 0.11, p < .001) in suicide ideation above and beyond EI. CONCLUSIONS: These findings provide some insight into how life purpose might ameliorate the impact of social stressors above and beyond a positive cultural identity for young racial/ethnic minority adults. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Binding interface change and cryptic variation in the evolution of protein-protein interactions.

BACKGROUND: Physical interactions between proteins are essential for almost all biological functions and systems. To understand the evolution of function it is therefore important to understand the evolution of molecular interactions. Of key importance is the evolution of binding specificity, the set of interactions made by a protein, since change in specificity can lead to "rewiring" of interaction networks. Unfortunately, the interfaces through which proteins interact are complex, typically containing many amino-acid residues that collectively must contribute to binding specificity as well as binding affinity, structural integrity of the interface and solubility in the unbound state. RESULTS: In order to study the relationship between interface composition and binding specificity, we make use of paralogous pairs of yeast proteins. Immediately after duplication these paralogues will have identical sequences and protein products that make an identical set of interactions. As the sequences diverge, we can correlate amino-acid change in the interface with any change in the specificity of binding. We show that change in interface regions correlates only weakly with change in specificity, and many variants in interfaces are functionally equivalent. We show that many of the residue replacements within interfaces are silent with respect to their contribution to binding specificity. CONCLUSIONS: We conclude that such functionally-equivalent change has the potential to contribute to evolutionary plasticity in interfaces by creating cryptic variation, which in turn may provide the raw material for functional innovation and coevolution.

Covariation Is a Poor Measure of Molecular Coevolution.

Recent developments in the analysis of amino acid covariation are leading to breakthroughs in protein structure prediction, protein design, and prediction of the interactome. It is assumed that observed patterns of covariation are caused by molecular coevolution, where substitutions at one site affect the evolutionary forces acting at neighboring sites. Our theoretical and empirical results cast doubt on this assumption. We demonstrate that the strongest coevolutionary signal is a decrease in evolutionary rate and that unfeasibly long times are required to produce coordinated substitutions. We find that covarying substitutions are mostly found on different branches of the phylogenetic tree, indicating that they are independent events that may or may not be attributable to coevolution. These observations undermine the hypothesis that molecular coevolution is the primary cause of the covariation signal. In contrast, we find that the pairs of residues with the strongest covariation signal tend to have low evolutionary rates, and that it is this low rate that gives rise to the covariation signal. Slowly evolving residue pairs are disproportionately located in the protein's core, which explains covariation methods' ability to detect pairs of residues that are close in three dimensions. These observations lead us to propose the "coevolution paradox": The strength of coevolution required to cause coordinated changes means the evolutionary rate is so low that such changes are highly unlikely to occur. As modern covariation methods may lead to breakthroughs in structural genomics, it is critical to recognize their biases and limitations.

ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models.

Molecular phylogenetics is a powerful tool for inferring both the process and pattern of evolution from genomic sequence data. Statistical approaches, such as maximum likelihood and Bayesian inference, are now established as the preferred methods of inference. The choice of models that a researcher uses for inference is of critical importance, and there are established methods for model selection conditioned on a particular type of data, such as nucleotides, amino acids, or codons. A major limitation of existing model selection approaches is that they can only compare models acting upon a single type of data. Here, we extend model selection to allow comparisons between models describing different types of data by introducing the idea of adapter functions, which project aggregated models onto the originally observed sequence data. These projections are implemented in the program ModelOMatic and used to perform model selection on 3722 families from the PANDIT database, 68 genes from an arthropod phylogenomic data set, and 248 genes from a vertebrate phylogenomic data set. For the PANDIT and arthropod data, we find that amino acid models are selected for the overwhelming majority of alignments; with progressively smaller numbers of alignments selecting codon and nucleotide models, and no families selecting RY-based models. In contrast, nearly all alignments from the vertebrate data set select codon-based models. The sequence divergence, the number of sequences, and the degree of selection acting upon the protein sequences may contribute to explaining this variation in model selection. Our ModelOMatic program is fast, with most families from PANDIT taking fewer than 150 s to complete, and should therefore be easily incorporated into existing phylogenetic pipelines. ModelOMatic is available at https://code.google.com/p/modelomatic/.

Mcam stabilizes luminal progenitor breast cancer phenotypes via Ck2 control and Src/Akt/Stat3 attenuation.

Breast cancers are categorized into subtypes with distinctive therapeutic vulnerabilities and prognoses based on their expression of clinically targetable receptors and gene expression patterns mimicking different cell types of the normal gland. Here, we tested the role of Mcam in breast cancer cell state control and tumorigenicity in a luminal progenitor-like murine tumor cell line (Py230) that exhibits lineage and tumor subtype plasticity. Mcam knockdown Py230 cells show augmented Stat3 and Pi3K/Akt activation associated with a lineage state switch away from a hormone-sensing/luminal progenitor state toward alveolar and basal cell related phenotypes that were refractory to growth inhibition by the anti-estrogen therapeutic, tamoxifen. Inhibition of Stat3, or the upstream activator Ck2, reversed these cell state changes. Mcam binds Ck2 and acts as a regulator of Ck2 substrate utilization across multiple mammary tumor cell lines. In Py230 cells this activity manifests as increased mesenchymal morphology, migration, and Src/Fak/Mapk/Paxillin adhesion complex signaling in vitro, in contrast to Mcam's reported roles in promoting mesenchymal phenotypes. In vivo, Mcam knockdown reduced tumor growth and take rate and inhibited cell state transition to Sox10+/neural crest like cells previously been associated with tumor aggressiveness. This contrasts with human luminal breast cancers where MCAM copy number loss is highly coupled to Cyclin D amplification, increased proliferation, and the more aggressive Luminal B subtype. Together these data indicate a critical role for Mcam and its regulation of Ck2 in control of breast cancer cell state plasticity with implications for progression, evasion of targeted therapies and combination therapy design.

Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets.

Genetic mechanisms of blood pressure (BP) regulation remain poorly defined. Using kidney-specific epigenomic annotations and 3D genome information we generated and validated gene expression prediction models for the purpose of transcriptome-wide association studies in 700 human kidneys. We identified 889 kidney genes associated with BP of which 399 were prioritised as contributors to BP regulation. Imputation of kidney proteome and microRNAome uncovered 97 renal proteins and 11 miRNAs associated with BP. Integration with plasma proteomics and metabolomics illuminated circulating levels of myo-inositol, 4-guanidinobutanoate and angiotensinogen as downstream effectors of several kidney BP genes (SLC5A11, AGMAT, AGT, respectively). We showed that genetically determined reduction in renal expression may mimic the effects of rare loss-of-function variants on kidney mRNA/protein and lead to an increase in BP (e.g., ENPEP). We demonstrated a strong correlation (r = 0.81) in expression of protein-coding genes between cells harvested from urine and the kidney highlighting a diagnostic potential of urinary cell transcriptomics. We uncovered adenylyl cyclase activators as a repurposing opportunity for hypertension and illustrated examples of BP-elevating effects of anticancer drugs (e.g. tubulin polymerisation inhibitors). Collectively, our studies provide new biological insights into genetic regulation of BP with potential to drive clinical translation in hypertension.

A Cell Membrane Fusion Assay for the Fish Pathogen Spring Viremia of Carp Virus (SVCV).

Fusion of the infected cell membranes is a characteristic effect of a wide number of viral infections. Spring viremia of carp virus (SVCV), a rhabdovirus causing disease in farmed carp, can induce membrane fusion of the infected cells by shifting the pH of the culture medium to slightly acidic. Membrane fusion leads to the formation of clusters of cell nuclei enclosed in a cell membrane, the so-called syncytia, that can be easily visualized by cell staining and light microscope inspection. In the present work, we report a protocol to induce syncytia formation in EPC cells infected with SVCV, where membrane fusion is triggered by a low-pH incubation step. Appearance of syncytia can be observed at 18 hours post infection. The syncytia formation assay described here may serve as an experimental platform to quantitate SVCV, to determine virus infectivity, and a useful tool to study virus entry into the cell as well as to test candidate antiviral compounds that could block the entry of SVCV into cells by inhibiting membrane fusion.

Application of multidisciplinary team conference for neuromodulation candidates facilitates patient selection and optimization.

Introduction: Psychological evaluation is required by insurance companies in the United States prior to proceeding with a spinal cord stimulation or a dorsal root ganglion stimulation trial. Since January 2017, we implemented a Multidisciplinary Team Conference for Neuromodulation in our center to facilitate the collaboration between pain physicians and psychologists and to optimize screening of neuromodulation candidates. This study aims to report the impact of this team conference on improvement of neuromodulation outcome in our center. Methods: Appropriateness of neuromodulation were discussed in the team conference after initial visit with the pain specialist and psychological evaluation. For this study, we prospectively and retrospectively collected data on neuromodulation candidates who went through the team conference and those who did not as controls. Results: We discussed 461 patients in the team conference sessions from January 2017 to July 2023. Out of these, a spinal cord stimulator or a dorsal root ganglion stimulator trial was performed in 164 patients with 80.5% (132 cases) trial success rate leading to 140 implants. Out of these implants, 26 (18.6%) explanted and 21 (15%) required revision in 41 (29.3%) patients. We performed neuraxial neuromodulation trial for 70 patients without going through the team conference from January 2016 to July 2023 with a trial success rate of 45.7% (32 cases). In this group, 7 (21.9%) and 6 (18.8%) patients underwent explant and revision. The differences between the groups were statistically significant for trial success rate (odds ratio of 4.9 with p-value of <0.01) but not for explant (odds ratio of 0.8 with p-value of 0.627) or revision (odds ratio of 0.8 with p-value of 0.595). Conclusion: Implementing Multidisciplinary Team Conference increased trial success rate in our center. Team conference provides therapeutic benefit for patients, and also provides the opportunity for an educational discussion for trainees.

Significantly increased risk of chronic obstructive pulmonary disease amongst adults with predominantly mild congenital heart disease.

Adults with congenital heart disease (CHD) face increased risk of various comorbid diseases. Previous work on lung dysfunction in this population has mainly focused on restrictive lung disease, in patients with severe CHD phenotypes. We examined the association of mild CHD with chronic obstructive pulmonary disease (COPD) in the UK Biobank (UKB). Electronic health records (EHR) were used to identify 3385 CHD cases and 479,765 healthy controls in UKB, before performing a case-control analysis over a 20-year study period for a total of > 9.5 M person-years of follow-up. Our analysis showed that UKB participants with CHD are at substantially greater risk of developing COPD than healthy controls (8.7% vs 3.1% prevalence, unadjusted OR 2.98, 95% CI 2.63, 3.36, P = 1.40e-53). Slightly increased rates of smoking were observed amongst CHD cases, however the association with COPD was shown to be robust to adjustment for smoking and other factors known to modulate COPD risk within a multivariable-adjusted Cox regression framework (fully adjusted HR 2.21, 95% CI 1.97, 2.48, P = 5.5e-41). Care for adults with CHD should aim to mitigate their increased risk of COPD, possibly via increased smoking cessation support.

Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking.

A detailed and complete structural knowledge of the interactome is one of the grand challenges in Biology, and a variety of computational docking approaches have been developed to complement experimental efforts and help in the characterization of protein-protein interactions. Among the different docking scoring methods, those based on physicochemical considerations can give the maximum accuracy at the atomic level, but they are usually computationally demanding and necessarily noisy when implemented in rigid-body approaches. Coarser-grained knowledge-based potentials are less sensitive to details of atomic arrangements, thus providing an efficient alternative for scoring of rigid-body docking poses. In this study, we have extracted new statistical potentials from intermolecular pairs of exposed residues in known complex structures, which were then used to score protein-protein docking poses. The new method, called SIPPER (scoring by intermolecular pairwise propensities of exposed residues), combines the value of residue desolvation based on solvent-exposed area with the propensity-based contribution of intermolecular residue pairs. This new scoring function found a near-native orientation within the top 10 predictions in nearly one-third of the cases of a standard docking benchmark and proved to be also useful as a filtering step, drastically reducing the number of docking candidates needed by energy-based methods like pyDock.

Effectiveness of a multidisciplinary rehabilitation program in real-world patients with chronic back pain: A pilot cohort data analysis.

BACKGROUND: Randomized clinical trials (RCT) suggest a multidisciplinary approach to pain rehabilitation is superior to other active treatments in improving pain intensity, function, disability, and pain interference for patients with chronic pain, with small effect size (ds= 0.20-0.36) but its effectiveness remains unknown in real-world practice. OBJECTIVE: The current study examined the effectiveness of a multidisciplinary program to a cognitive and behavioral therapy (pain-CBT) in real-world patients with chronic back pain. METHODS: Twenty-eight patients (M𝑎𝑔𝑒= 57.6, 82.1% Female) completed a multidisciplinary program that included pain psychology and physical therapy. Eighteen patients (M𝑎𝑔𝑒= 58.9, 77.8% Female) completed a CBT-alone program. Using a learning healthcare system, the Pain Catastrophizing Scale, 0-10 Numerical Pain Rating Scale, and Patient-Reported Outcomes Measurement Information System® measures were administered before and after the programs. RESULTS: We found significant improvement in mobility and pain behavior only after a multidisciplinary program (p's < 0.031; d= 0.69 and 0.55). We also found significant improvement in pain interference, fatigue, depression, anxiety, social role satisfaction, and pain catastrophizing after pain-CBT or multidisciplinary programs (p's < 0.037; ds = 0.29-0.73). Pain ratings were not significantly changed by either program (p's > 0.207). CONCLUSIONS: The effect of a multidisciplinary rehabilitation program observed in RCT would be generalizable to real-world practice.

Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney.

The kidney is an organ of key relevance to blood pressure (BP) regulation, hypertension and antihypertensive treatment. However, genetically mediated renal mechanisms underlying susceptibility to hypertension remain poorly understood. We integrated genotype, gene expression, alternative splicing and DNA methylation profiles of up to 430 human kidneys to characterize the effects of BP index variants from genome-wide association studies (GWASs) on renal transcriptome and epigenome. We uncovered kidney targets for 479 (58.3%) BP-GWAS variants and paired 49 BP-GWAS kidney genes with 210 licensed drugs. Our colocalization and Mendelian randomization analyses identified 179 unique kidney genes with evidence of putatively causal effects on BP. Through Mendelian randomization, we also uncovered effects of BP on renal outcomes commonly affecting patients with hypertension. Collectively, our studies identified genetic variants, kidney genes, molecular mechanisms and biological pathways of key relevance to the genetic regulation of BP and inherited susceptibility to hypertension.

The (non)malignancy of cancerous amino acidic substitutions.

The process of natural selection acts both on individual organisms within a population and on individual cells within an organism as they develop into cancer. In this work, we have taken a first step toward understanding the differences in selection pressures exerted on the human genome under these disparate circumstances. Focusing on single amino acid substitutions, we have found that cancer-related mutations (CRMs) are frequent in evolutionarily conserved sites, whereas single amino acid polymorphisms (SAPs) tend to appear in sites having a more relaxed evolutionary pressure. Those CRMs classed as cancer driver mutations show greater enrichment for conserved sites than passenger mutations. Consistent with this, driver mutations are enriched for sites annotated as key functional residues and their neighbors, and are more likely to be located on the surface of proteins than expected by chance. Overall the pattern of CRM and polymorphism is remarkably similar, but we do see a clear signal indicative of diversifying selection for disruptive amino acid substitutions in the cancer driver mutations. The ultimate consequence of the appearance of those mutations must be advantageous for the tumor cell, leading to cell population-growth and migration events similar to those seen in natural ecosystems.