SnapShot: APC/T Cell Immune Checkpoints.

Immune checkpoints are key regulatory mechanisms integral to the maintenance of self-tolerance and execution of antigen-specific immune responses. In recent years, they have been leveraged to treat both autoimmune disease and various forms of cancer with much success. This SnapShot illustrates known immune checkpoint interactions in APC-mediated T cell modulation. To view this SnapShot, open or download the PDF.

Engineering signal transduction pathways.

Cells respond to their environment by sensing signals and translating them into changes in gene expression. In recent years, synthetic networks have been designed in both prokaryotic and eukaryotic systems to create new functionalities and for specific applications. In this review, we discuss the challenges associated with engineering signal transduction pathways. Furthermore, we address advantages and disadvantages of engineering signaling pathways in prokaryotic and eukaryotic cells, highlighting recent examples, and discuss how progress in synthetic biology might impact biotechnology and biomedicine.

Seed sequence polymorphism rs2168518 and allele-specific target gene regulation of hsa-miR-4513.

MicroRNAs (miRNAs) are small post-transcriptional regulators that offer promising targets for treating complex diseases. To this end, hsa-miR-4513 is an excellent candidate as this gene harbors within its conserved heptametrical seed sequence a frequent polymorphism (rs2168518), which has previously been associated with several complex phenotypes. So far, little is known about the biological mechanism(s) underlying these associations. In an initial step, we now aimed to identify allele-specific target genes of hsa-miR-4513. We performed RNA sequencing in a miRNA overexpression model in human umbilical vein endothelial cells transfected with separated hsa-miR-4513 alleles at rs2168518, namely hsa-miR-4513-G and hsa-miR-4513-A. Genes specifically regulated by the rs2168518 alleles were independently verified by quantitative reverse transcription PCR (qRT-PCR), western blot analysis and allele-specific miRNA binding via a luciferase reporter assay. By a text-based search publicly available databases such as Online Mendelian Inheritance in Man and Mouse Genome Informatics were utilized to link target genes of hsa-miR-4513 to previously described phenotypes. Overall, we identified 23 allele-specific hsa-miR-4513 target genes and replicated 19 of those independently via qRT-PCR. Western blot analysis and luciferase reporter assays conducted for an exemplary subsample further confirmed the allele-specific regulation of these genes by hsa-miR-4513. Remarkably, multiple allele-specific target genes identified are linked via text retrieval to several phenotypes previously reported to be associated with hsa-miR-4513. These genes offer promising candidates for ongoing research on the functional pathobiological impact of hsa-miR-4513 and its seed polymorphism rs2168518. This could give rise to therapeutic applications targeting this miRNA.

HOMELETTE: a unified interface to homology modelling software.

SUMMARY: Homology modelling, the technique of generating models of 3D protein structures based on experimental structures from related proteins, has become increasingly popular over the years. An abundance of different tools for model generation and model evaluation is available from various research groups. We present HOMELETTE, an interface which implements a unified programmatic access to these tools. This allows for the assemble of custom pipelines from pre- or self-implemented building blocks. AVAILABILITY AND IMPLEMENTATION: HOMELETTE is implemented in Python, compatible with version 3.6 and newer. It is distributed under the MIT license. Documentation and tutorials are available at Read the Docs (https://homelette.readthedocs.io/). The latest version of HOMELETTE is available on PyPI (https://pypi.org/project/homelette/) and GitHub (https://github.com/PhilippJunk/homelette). A full installation of the latest version of HOMELETTE with all dependencies is also available as a Docker container (https://hub.docker.com/r/philippjunk/homelette_template). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Classification of GTP-dependent K-Ras4B active and inactive conformational states.

Classifying reliably active and inactive molecular conformations of wildtype (WT) and mutated oncogenic proteins is a key, ongoing challenge in molecular cancer studies. Here, we probe the GTP-bound K-Ras4B conformational dynamics using long-time atomistic molecular dynamics (MD) simulations. We extract and analyze the detailed underlying free energy landscape of WT K-Ras4B. We use two key reaction coordinates, labeled d1 and d2 (i.e., distances coordinating the Pß atom of the GTP ligand with two key residues, T35 and G60), shown to correlate closely with activities of WT and mutated K-Ras4B. However, our new K-Ras4B conformational kinetics study reveals a more complex network of equilibrium Markovian states. We show that a new reaction coordinate is required to account for the orientation of acidic K-Ras4B sidechains such as D38 with respect to the interface with binding effector RAF1 and rationalize the activation/inactivation propensities and the corresponding molecular binding mechanisms. We use this understanding to unveil how a relatively conservative mutation (i.e., D33E, in the switch I region) can lead to significantly different activation propensities compared with WT K-Ras4B. Our study sheds new light on the ability of residues near the K-Ras4B-RAF1 interface to modulate the network of salt bridges at the binding interface with the RAF1 downstream effector and, thus, to influence the underlying GTP-dependent activation/inactivation mechanism. Altogether, our hybrid MD-docking modeling approach enables the development of new in silico methods for quantitative assessment of activation propensity changes (e.g., due to mutations or local binding environment). It also unveils the underlying molecular mechanisms and facilitates the rational design of new cancer drugs.

A mega-analysis of expression quantitative trait loci in retinal tissue.

Significant association signals from genome-wide association studies (GWAS) point to genomic regions of interest. However, for most loci the causative genetic variant remains undefined. Determining expression quantitative trait loci (eQTL) in a disease relevant tissue is an excellent approach to zoom in on disease- or trait-associated association signals and hitherto on relevant disease mechanisms. To this end, we explored regulation of gene expression in healthy retina (n = 311) and generated the largest cis-eQTL data set available to date. Genotype- and RNA-Seq data underwent rigorous quality control protocols before FastQTL was applied to assess the influence of genetic markers on local (cis) gene expression. Our analysis identified 403,151 significant eQTL variants (eVariants) that regulate 3,007 genes (eGenes) (Q-Value < 0.05). A conditional analysis revealed 744 independent secondary eQTL signals for 598 of the 3,007 eGenes. Interestingly, 99,165 (24.71%) of all unique eVariants regulate the expression of more than one eGene. Filtering the dataset for eVariants regulating three or more eGenes revealed 96 potential regulatory clusters. Of these, 31 harbour 130 genes which are partially regulated by the same genetic signal. To correlate eQTL and association signals, GWAS data from twelve complex eye diseases or traits were included and resulted in identification of 80 eGenes with potential association. Remarkably, expression of 10 genes is regulated by eVariants associated with multiple eye diseases or traits. In conclusion, we generated a unique catalogue of gene expression regulation in healthy retinal tissue and applied this resource to identify potentially pleiotropic effects in highly prevalent human eye diseases. Our study provides an excellent basis to further explore mechanisms of various retinal disease etiologies.

Reconstruction and analysis of a large-scale binary Ras-effector signaling network.

BACKGROUND: Ras is a key cellular signaling hub that controls numerous cell fates via multiple downstream effector pathways. While pathways downstream of effectors such as Raf, PI3K and RalGDS are extensively described in the literature, how other effectors signal downstream of Ras is often still enigmatic. METHODS: A comprehensive and unbiased Ras-effector network was reconstructed downstream of 43 effector proteins (converging onto 12 effector classes) using public pathway and protein-protein interaction (PPI) databases. The output is an oriented graph of pairwise interactions defining a 3-layer signaling network downstream of Ras. The 2290 proteins comprising the network were studied for their implication in signaling crosstalk and feedbacks, their subcellular localizations, and their cellular functions. RESULTS: The final Ras-effector network consists of 2290 proteins that are connected via 19,080 binary PPIs, increasingly distributed across the downstream layers, with 441 PPIs in layer 1, 1660 in layer 2, and 16,979 in layer 3. We identified a high level of crosstalk among proteins of the 12 effector classes. A class-specific Ras sub-network was generated in CellDesigner (.xml file) and a functional enrichment analysis thereof shows that 58% of the processes have previously been associated to a respective effector pathway, with the remaining providing insights into novel and unexplored functions of specific effector pathways. CONCLUSIONS: Our large-scale and cell general Ras-effector network is a crucial steppingstone towards defining the network boundaries. It constitutes a 'reference interactome' and can be contextualized for specific conditions, e.g. different cell types or biopsy material obtained from cancer patients. Further, it can serve as a basis for elucidating systems properties, such as input-output relationships, crosstalk, and pathway redundancy. Video Abstract.

Signaling pathways in intestinal homeostasis and colorectal cancer: KRAS at centre stage.

The intestinal epithelium acts as a physical barrier that separates the intestinal microbiota from the host and is critical for preserving intestinal homeostasis. The barrier is formed by tightly linked intestinal epithelial cells (IECs) (i.e. enterocytes, goblet cells, neuroendocrine cells, tuft cells, Paneth cells, and M cells), which constantly self-renew and shed. IECs also communicate with microbiota, coordinate innate and adaptive effector cell functions. In this review, we summarize the signaling pathways contributing to intestinal cell fates and homeostasis functions. We focus especially on intestinal stem cell proliferation, cell junction formation, remodelling, hypoxia, the impact of intestinal microbiota, the immune system, inflammation, and metabolism. Recognizing the critical role of KRAS mutants in colorectal cancer, we highlight the connections of KRAS signaling pathways in coordinating these functions. Furthermore, we review the impact of KRAS colorectal cancer mutants on pathway rewiring associated with disruption and dysfunction of the normal intestinal homeostasis. Given that KRAS is still considered undruggable and the development of treatments that directly target KRAS are unlikely, we discuss the suitability of targeting pathways downstream of KRAS as well as alterations of cell extrinsic/microenvironmental factors as possible targets for modulating signaling pathways in colorectal cancer. Video Abstract.

A Circulating MicroRNA Profile in a Laser-Induced Mouse Model of Choroidal Neovascularization.

Choroidal neovascularization (CNV) is a pathological process in which aberrant blood vessels invade the subretinal space of the mammalian eye. It is a characteristic feature of the prevalent neovascular age-related macular degeneration (nAMD). Circulating microRNAs (cmiRNAs) are regarded as potentially valuable biomarkers for various age-related diseases, including nAMD. Here, we investigated cmiRNA expression in an established laser-induced CNV mouse model. Upon CNV induction in C57Bl/6 mice, blood-derived cmiRNAs were initially determined globally by RNA next generation sequencing, and the most strongly dysregulated cmiRNAs were independently replicated by quantitative reverse transcription PCR (RT-qPCR) in blood, retinal, and retinal pigment epithelium (RPE)/choroidal tissue. Our findings suggest that two miRNAs, mmu-mir-486a-5p and mmur-mir-92a-3p, are consistently dysregulated during CNV formation. Furthermore, in functional in vitro assays, a significant impact of mmu-mir-486a-5p and mmu-mir-92a-3p on murine microglial cell viability was observed, while mmu-mir-92a-3p also showed an impact on microglial mobility. Taken together, we report a robust dysregulation of two miRNAs in blood and RPE/choroid after laser-induced initiation of CNV lesions in mice, highlighting their potential role in pathology and eventual therapy of CNV-associated complications.

Phylogeographic and evolutionary history analyses of the warty crab Eriphia verrucosa (Decapoda, Brachyura, Eriphiidae) unveil genetic imprints of a late Pleistocene vicariant event across the Gibraltar Strait, erased by postglacial expansion and admixture among refugial lineages.

BACKGROUND: The Pleistocene cyclic sea-level fluctuations are thought to have markedly affected the distribution and genetic architecture of Atlanto-Mediterranean biota. Despite the acknowledged key role played by these historical events in shaping population genetic structure of marine species, little is still known about the processes involved in shaping the spatial distribution of genetic variation within intertidal species. We intended in this study to reconstruct the phylogeography of a common and widely distributed coastal species across the East Atlantic and Mediterranean Sea (the warty crab Eriphia verrucosa), aiming to unravel potential microevolutionary processes likely involved in shaping its genetic polymorphism. For this purpose, a total of 155 specimens of E. verrucosa from 35 locations across the entire distribution range were analyzed by comparing a 453 basepairs region of the mitochondrial gene cytochrome oxidase subunit 1 (Cox1). RESULTS: Our results unveiled the prevalence of high genetic connectivity among East Atlantic and Mediterranean populations, with noticeable genetic distinctiveness of the peripheral population from the Azores. Spatio-temporal patterns of genetic diversification and demographic history allowed retrieving genetic imprints of late Pleistocene vicariant event across the Gibraltar Strait followed by subsequent postglacial expansion events for both the East Atlantic and Mediterranean regions. Integrative evidences from the outcomes of comparison of regional genetic diversification, as well as evolutionary and biogeographic histories reconstructions, support the existence of potential glacial refugia for E. verrucosa in the East Atlantic and western Mediterranean. Our results also revealed low levels of genetic variability along with recent demographic and spatial expansion events for eastern Mediterranean warty crabs, suggesting that the eastern areas within the distribution range of the species might have been recently colonized from putative glacial refugia. CONCLUSIONS: These findings provide new insights into the phylogeography and evolutionary history of a common but poorly studied Atlanto-Mediterranean decapod species. Specifically, they contribute to the understanding of the impact of historical processes on shaping contemporary population genetic structure and diversity in intertidal marine species.

Systems level expression correlation of Ras GTPase regulators.

BACKGROUND: Proteins of the ubiquitously expressed core proteome are quantitatively correlated across multiple eukaryotic species. In addition, it was found that many protein paralogues exhibit expression anticorrelation, suggesting that the total level of protein with a given functionality must be kept constant. METHODS: We performed Spearman's rank correlation analyses of gene expression levels for the RAS GTPase subfamily and their regulatory GEF and GAP proteins across tissues and across individuals for each tissue. A large set of published data for normal tissues from a wide range of species, human cancer tissues and human cell lines was analysed. RESULTS: We show that although the multidomain regulatory proteins of Ras GTPases exhibit considerable tissue and individual gene expression variability, their total amounts are balanced in normal tissues. In a given tissue, the sum of activating (GEFs) and deactivating (GAPs) domains of Ras GTPases can vary considerably, but each person has balanced GEF and GAP levels. This balance is impaired in cell lines and in cancer tissues for some individuals. CONCLUSIONS: Our results are relevant for critical considerations of knock out experiments, where functionally related homologs may compensate for the down regulation of a protein.

Pleiotropic Effects of Risk Factors in Age-Related Macular Degeneration and Seemingly Unrelated Complex Diseases.

Age-related macular degeneration (AMD) is a complex disease with both environmental and genetic factors influencing disease risk. Genome-wide case-control association studies, candidate gene analyses, and epidemiological studies reinforced the notion that AMD is predominantly a disease of an impaired complement system and an altered high-density lipoprotein (HDL) metabolism. Recent reports demonstrated the pleiotropic role of the complement system and HDL in complex diseases such as cardiovascular disease, autoimmune disorders, cancer, and Alzheimer's disease. In light of these findings, we explore current evidence for a shared genetic and environmental risk of AMD and unrelated complex diseases based on epidemiological studies. Shared risk factors may indicate common pathways in disease pathology and thus may have implications for novel treatment options of AMD pathology.

Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses.

The molecular details underlying the time-dependent assembly of protein complexes in cellular networks, such as those that occur during differentiation, are largely unexplored. Focusing on the calcium-induced differentiation of primary human keratinocytes as a model system for a major cellular reorganization process, we look at the expression of genes whose products are involved in manually-annotated protein complexes. Clustering analyses revealed only moderate co-expression of functionally related proteins during differentiation. However, when we looked at protein complexes, we found that the majority (55%) are composed of non-dynamic and dynamic gene products ('di-chromatic'), 19% are non-dynamic, and 26% only dynamic. Considering three-dimensional protein structures to predict steric interactions, we found that proteins encoded by dynamic genes frequently interact with a common non-dynamic protein in a mutually exclusive fashion. This suggests that during differentiation, complex assemblies may also change through variation in the abundance of proteins that compete for binding to common proteins as found in some cases for paralogous proteins. Considering the example of the TNF-α/NFκB signaling complex, we suggest that the same core complex can guide signals into diverse context-specific outputs by addition of time specific expressed subunits, while keeping other cellular functions constant. Thus, our analysis provides evidence that complex assembly with stable core components and competition could contribute to cell differentiation.

TAPAS: tools to assist the targeted protein quantification of human alternative splice variants.

MOTIVATION: In proteomes of higher eukaryotes, many alternative splice variants can only be detected by their shared peptides. This makes it highly challenging to use peptide-centric mass spectrometry to distinguish and to quantify protein isoforms resulting from alternative splicing events. RESULTS: We have developed two complementary algorithms based on linear mathematical models to efficiently compute a minimal set of shared and unique peptides needed to quantify a set of isoforms and splice variants. Further, we developed a statistical method to estimate the splice variant abundances based on stable isotope labeled peptide quantities. The algorithms and databases are integrated in a web-based tool, and we have experimentally tested the limits of our quantification method using spiked proteins and cell extracts. AVAILABILITY AND IMPLEMENTATION: The TAPAS server is available at URL http://davinci.crg.es/tapas/. CONTACT: luis.serrano@crg.eu or christina.kiel@crg.eu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Structure-energy-based predictions and network modelling of RASopathy and cancer missense mutations.

The Ras/MAPK syndromes ('RASopathies') are a class of developmental disorders caused by germline mutations in 15 genes encoding proteins of the Ras/mitogen-activated protein kinase (MAPK) pathway frequently involved in cancer. Little is known about the molecular mechanisms underlying the differences in mutations of the same protein causing either cancer or RASopathies. Here, we shed light on 956 RASopathy and cancer missense mutations by combining protein network data with mutational analyses based on 3D structures. Using the protein design algorithm FoldX, we predict that most of the missense mutations with destabilising energies are in structural regions that control the activation of proteins, and only a few are predicted to compromise protein folding. We find a trend that energy changes are higher for cancer compared to RASopathy mutations. Through network modelling, we show that partly compensatory mutations in RASopathies result in only minor downstream pathway deregulation. In summary, we suggest that quantitative rather than qualitative network differences determine the phenotypic outcome of RASopathy compared to cancer mutations.

Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways.

Many proteins and signaling pathways are present in most cell types and tissues and yet perform specialized functions. To elucidate mechanisms by which these ubiquitous pathways are modulated, we overlaid information about cross-cell line protein abundance and variability, and evolutionary conservation onto functional pathway components and topological layers in the pathway hierarchy. We found that the input (receptors) and the output (transcription factors) layers evolve more rapidly than proteins in the intermediary transmission layer. In contrast, protein expression variability decreases from the input to the output layer. We observed that the differences in protein variability between the input and transmission layer can be attributed to both the network position and the tendency of variable proteins to physically interact with constitutively expressed proteins. Differences in protein expression variability and conservation are also accompanied by the tendency of conserved and constitutively expressed proteins to acquire somatic mutations, while germline mutations tend to occur in cell type-specific proteins. Thus, conserved core proteins in the transmission layer could perform a fundamental role in most cell types and are therefore less tolerant to germline mutations. In summary, we propose that the core signal transmission machinery is largely modulated by a variable input layer through physical protein interactions. We hypothesize that the bow-tie organization of cellular signaling on the level of protein abundance variability contributes to the specificity of the signal response in different cell types.

Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell-general and cell-type-specific signaling proteins.

Relating protein concentration to cell-type-specific responses is one of the remaining challenges for obtaining a quantitative systems level understanding of mammalian signaling. Here we used mass-spectrometry (MS)- and antibody-based quantitative proteomic approaches to measure protein abundances for 75% of a hand-curated reconstructed ErbB network of 198 proteins, in two established cell types (HEK293 and MCF-7) and in primary keratinocyte cells. Comparison with other quantitative studies allowed building a set of ErbB network proteins expressed in all cells and another which are cell-specific and could impart specific properties to the network. As a proof-of-concept of the importance of protein concentration, we generated a small simplified mathematical model encompassing ligand binding, followed by receptor dimerization, activation, and degradation. The model predicts ErbB phosphorylation in HEK293, MCF-7, and keratinocyte cells simply by incorporating cell-type-specific ErbB1, ErbB2, and caveolin-1 abundances but otherwise contains similar rate constants. Altogether, the data provide a resource for protein abundances and localization to be included in larger mathematical models, enabling the generation of cell-type-specific computational models. MS data have been deposited to the ProteomeXchange via PRIDE (with identifier PXD000623) and PASSEL (with identifier PASS00372).

Assessing the correlation between mutant rhodopsin stability and the severity of retinitis pigmentosa.

PURPOSE: Following a previous study that demonstrated a correlation between rhodopsin stability and the severity of retinitis pigmentosa (RP), we investigated whether predictions of severity can be improved with a regional analysis of this correlation. The association between changes to the stability of the protein and the relative amount of rhodopsin reaching the plasma membrane was assessed. METHODS: Crystallography-based estimations of mutant rhodopsin stability were compared with descriptions in the scientific literature of the visual function of mutation carriers to determine the extent of associations between rhodopsin stability and clinical phenotype. To test the findings of this analysis, three residues of a green fluorescent protein (GFP) tagged rhodopsin plasmid were targeted with site-directed random mutagenesis to generate mutant variants with a range of stability changes. These plasmids were transfected into HEK-293 cells, and then flow cytometry was used to measure rhodopsin on the cells' plasma membrane. The GFP signal was used to measure the ratio between this membrane-bound rhodopsin and total cellular rhodopsin. FoldX stability predictions were then compared with the surface staining data and clinical data from the database to characterize the relationship between rhodopsin stability, the severity of RP, and the expression of rhodopsin at the cell surface. RESULTS: There was a strong linear correlation between the scale of the destabilization of mutant variants and the severity of retinal disease. A correlation was also seen in vitro between stability and the amount of rhodopsin at the plasma membrane. Rhodopsin is drastically reduced on the surface of cells transfected with variants that differ in their inherent stability from the wild-type by more than 2 kcal/mol. Below this threshold, surface levels are closer to those of the wild-type. CONCLUSIONS: There is a correlation between the stability of rhodopsin mutations and disease severity and levels of membrane-bound rhodopsin. Measuring membrane-bound rhodopsin with flow cytometry could improve prognoses for poorly characterized mutations and could provide a platform for measuring the effectiveness of treatments.

QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration.

DNA methylation provides a crucial epigenetic mark linking genetic variations to environmental influence. We have analyzed array-based DNA methylation profiles of 160 human retinas with co-measured RNA-seq and >8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 methylation quantitative trait loci and 12,505 expression quantitative trait loci) and 13,747 DNA methylation loci affecting gene expression, with over one-third specific to the retina. Methylation and expression quantitative trait loci show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration. Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of macular degeneration pathology by genotype-environment interaction in retina.

SAPIN: a framework for the structural analysis of protein interaction networks.

SUMMARY: Protein interaction networks are widely used to depict the relationships between proteins. These networks often lack the information on physical binary interactions, and they do not inform whether there is incompatibility of structure between binding partners. Here, we introduce SAPIN, a framework dedicated to the structural analysis of protein interaction networks. SAPIN first identifies the protein parts that could be involved in the interaction and provides template structures. Next, SAPIN performs structural superimpositions to identify compatible and mutually exclusive interactions. Finally, the results are displayed using Cytoscape Web. AVAILABILITY: The SAPIN server is available at http://sapin.crg.es. CONTACT: jae-seong.yang@crg.eu or christina.kiel@crg.eu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.