Characterization of a Clinically and Biologically Defined Subgroup of Patients with Autism Spectrum Disorder and Identification of a Tailored Combination Treatment.

Autism spectrum disorder (ASD) is a heterogeneous group of neurodevelopmental disorders (NDDs) with a high unmet medical need. The diagnosis of ASD is currently based on behavior criteria, which overlooks the diversity of genetic, neurophysiological, and clinical manifestations. Failure to acknowledge such heterogeneity has hindered the development of efficient drug treatments for ASD and other NDDs. DEPI® (Databased Endophenotyping Patient Identification) is a systems biology, multi-omics, and machine learning-driven platform enabling the identification of subgroups of patients with NDDs and the development of patient-tailored treatments. In this study, we provide evidence for the validation of a first clinically and biologically defined subgroup of patients with ASD identified by DEPI, ASD Phenotype 1 (ASD-Phen1). Among 313 screened patients with idiopathic ASD, the prevalence of ASD-Phen1 was observed to be ~24% in 84 patients who qualified to be enrolled in the study. Metabolic and transcriptomic alterations differentiating patients with ASD-Phen1 were consistent with an over-activation of NF-κB and NRF2 transcription factors, as predicted by DEPI. Finally, the suitability of STP1 combination treatment to revert such observed molecular alterations in patients with ASD-Phen1 was determined. Overall, our results support the development of precision medicine-based treatments for patients diagnosed with ASD.

3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures.

MOTIVATION: The interpretation of genomic data is crucial to understand the molecular mechanisms of biological processes. Protein structures play a vital role in facilitating this interpretation by providing functional context to genetic coding variants. However, mapping genes to proteins is a tedious and error-prone task due to inconsistencies in data formats. Over the past two decades, numerous tools and databases have been developed to automatically map annotated positions and variants to protein structures. However, most of these tools are web-based and not well-suited for large-scale genomic data analysis. RESULTS: To address this issue, we introduce 3Dmapper, a stand-alone command-line tool developed in Python and R. It systematically maps annotated protein positions and variants to protein structures, providing a solution that is both efficient and reliable. AVAILABILITY AND IMPLEMENTATION: https://github.com/vicruiser/3Dmapper.

Germline determinants of aberrant signaling pathways in cancer.

Cancer is a complex disease influenced by a heterogeneous landscape of both germline genetic variants and somatic aberrations. While there is growing evidence suggesting an interplay between germline and somatic variants, and a substantial number of somatic aberrations in specific pathways are now recognized as hallmarks in many well-known forms of cancer, the interaction landscape between germline variants and the aberration of those pathways in cancer remains largely unexplored. Utilizing over 8500 human samples across 33 cancer types characterized by TCGA and considering binary traits defined using a large collection of somatic aberration profiles across ten well-known oncogenic signaling pathways, we conducted a series of GWAS and identified genome-wide and suggestive associations involving 276 SNPs. Among these, 94 SNPs revealed cis-eQTL links with cancer-related genes or with genes functionally correlated with the corresponding traits' oncogenic pathways. GWAS summary statistics for all tested traits were then used to construct a set of polygenic scores employing a customized computational strategy. Polygenic scores for 24 traits demonstrated significant performance and were validated using data from PCAWG and CCLE datasets. These scores showed prognostic value for clinical variables and exhibited significant effectiveness in classifying patients into specific cancer subtypes or stratifying patients with cancer-specific aggressive phenotypes. Overall, we demonstrate that germline genetics can describe patients' genetic liability to develop specific cancer molecular and clinical profiles.

YES1 and MYC Amplifications as Synergistic Resistance Mechanisms to Different Generation ALK Tyrosine Kinase Inhibitors in Advanced NSCLC: Brief Report of Clinical and Preclinical Proofs.

INTRODUCTION: ALK tyrosine kinase inhibitors (TKIs) are the standard treatment for advanced ALK-positive NSCLC. Nevertheless, drug resistance inevitably occurs. Here, we report a case of a patient with metastatic ALK-positive lung adenocarcinoma with an impressive resistance to sequential treatment with ALK TKIs mediated by YES1 and MYC amplification in a contest of epithelial-to-mesenchymal transition and high progressive chromosomal instability. METHODS: The patient received, after chemotherapy and 7 months of crizotinib, brigatinib and lorlatinib with no clinical benefit to both treatments. A study of resistance mechanisms was performed with whole exome sequencing on different biological samples; primary cell lines were established from pleural effusion after lorlatinib progression. RESULTS: At whole exome sequencing analysis, YES1 and MYC amplifications were observed both in the pericardial biopsy and the pleural effusion samples collected at brigatinib and lorlatinib progression, respectively. Increasing chromosomal instability from diagnostic biopsy to pleural effusion was also observed. The addition of dasatinib to brigatinib or lorlatinib restored the sensitivity in primary cell lines; data were confirmed also in H3122_ALK-positive model overexpressing both YES1 and MYC. CONCLUSIONS: In conclusion, YES1 and MYC amplifications are candidates to justify a rapid acquired resistance to crizotinib entailing primary brigatinib and lorlatinib resistance. In this context, a combination strategy of ALK TKI with dasatinib could be effective to overcome a rapid resistance.

Polympact: exploring functional relations among common human genetic variants.

In the last years, many studies were able to identify associations between common genetic variants and complex diseases. However, the mechanistic biological links explaining these associations are still mostly unknown. Common variants are usually associated with a relatively small effect size, suggesting that interactions among multiple variants might be a major genetic component of complex diseases. Hence, elucidating the presence of functional relations among variants may be fundamental to identify putative variants' interactions. To this aim, we developed Polympact, a web-based resource that allows to explore functional relations among human common variants by exploiting variants' functional element landscape, their impact on transcription factor binding motifs, and their effect on transcript levels of protein-coding genes. Polympact characterizes over 18 million common variants and allows to explore putative relations by combining clustering analysis and innovative similarity and interaction network models. The properties of the network models were studied and the utility of Polympact was demonstrated by analysing the rich sets of Breast Cancer and Alzheimer's GWAS variants. We identified relations among multiple variants, suggesting putative interactions. Polympact is freely available at bcglab.cibio.unitn.it/polympact.

The structural coverage of the human proteome before and after AlphaFold.

The protein structure field is experiencing a revolution. From the increased throughput of techniques to determine experimental structures, to developments such as cryo-EM that allow us to find the structures of large protein complexes or, more recently, the development of artificial intelligence tools, such as AlphaFold, that can predict with high accuracy the folding of proteins for which the availability of homology templates is limited. Here we quantify the effect of the recently released AlphaFold database of protein structural models in our knowledge on human proteins. Our results indicate that our current baseline for structural coverage of 48%, considering experimentally-derived or template-based homology models, elevates up to 76% when including AlphaFold predictions. At the same time the fraction of dark proteome is reduced from 26% to just 10% when AlphaFold models are considered. Furthermore, although the coverage of disease-associated genes and mutations was near complete before AlphaFold release (69% of Clinvar pathogenic mutations and 88% of oncogenic mutations), AlphaFold models still provide an additional coverage of 3% to 13% of these critically important sets of biomedical genes and mutations. Finally, we show how the contribution of AlphaFold models to the structural coverage of non-human organisms, including important pathogenic bacteria, is significantly larger than that of the human proteome. Overall, our results show that the sequence-structure gap of human proteins has almost disappeared, an outstanding success of direct consequences for the knowledge on the human genome and the derived medical applications.

TranSNPs: A class of functional SNPs affecting mRNA translation potential revealed by fraction-based allelic imbalance.

Few studies have explored the association between SNPs and alterations in mRNA translation potential. We developed an approach to identify SNPs that can mark allele-specific protein expression levels and could represent sources of inter-individual variation in disease risk. Using MCF7 cells under different treatments, we performed polysomal profiling followed by RNA sequencing of total or polysome-associated mRNA fractions and designed a computational approach to identify SNPs showing a significant change in the allelic balance between total and polysomal mRNA fractions. We identified 147 SNPs, 39 of which located in UTRs. Allele-specific differences at the translation level were confirmed in transfected MCF7 cells by reporter assays. Exploiting breast cancer data from TCGA we identified UTR SNPs demonstrating distinct prognosis features and altering binding sites of RNA-binding proteins. Our approach produced a catalog of tranSNPs, a class of functional SNPs associated with allele-specific translation and potentially endowed with prognostic value for disease risk.

Exploring functionally annotated transcriptional consensus regulatory elements with CONREL.

Understanding the interaction between human genome regulatory elements and transcription factors is fundamental to elucidate the structure of gene regulatory networks. Here we present CONREL, a web application that allows for the exploration of functionally annotated transcriptional 'consensus' regulatory elements at different levels of abstraction. CONREL provides an extensive collection of consensus promoters, enhancers and active enhancers for 198 cell-lines across 38 tissue types, which are also combined to provide global consensuses. In addition, 1000 Genomes Project genotype data and the 'total binding affinity' of thousands of transcription factor binding motifs at genomic regulatory elements is fully combined and exploited to characterize and annotate functional properties of our collection. Comparison with other available resources highlights the strengths and advantages of CONREL. CONREL can be used to explore genomic loci, specific genes or genomic regions of interest across different cell lines and tissue types. The resource is freely available at https://bcglab.cibio.unitn.it/conrel.

PaCBAM: fast and scalable processing of whole exome and targeted sequencing data.

BACKGROUND: Interrogation of whole exome and targeted sequencing NGS data is rapidly becoming a preferred approach for the exploration of large cohorts in the research setting and importantly in the context of precision medicine. Single-base and genomic region level data retrieval and processing still constitute major bottlenecks in NGS data analysis. Fast and scalable tools are hence needed. RESULTS: PaCBAM is a command line tool written in C and designed for the characterization of genomic regions and single nucleotide positions from whole exome and targeted sequencing data. PaCBAM computes depth of coverage and allele-specific pileup statistics, implements a fast and scalable multi-core computational engine, introduces an innovative and efficient on-the-fly read duplicates filtering strategy and provides comprehensive text output files and visual reports. We demonstrate that PaCBAM exploits parallel computation resources better than existing tools, resulting in important reductions of processing time and memory usage, hence enabling an efficient and fast exploration of large datasets. CONCLUSIONS: PaCBAM is a fast and scalable tool designed to process genomic regions from NGS data files and generate coverage and pileup comprehensive statistics for downstream analysis. The tool can be easily integrated in NGS processing pipelines and is available from Bitbucket and Docker/Singularity hubs.

Discovering Causal Relationships in Grapevine Expression Data to Expand Gene Networks. A Case Study: Four Networks Related to Climate Change.

In recent years the scientific community has been heavily engaged in studying the grapevine response to climate change. Final goal is the identification of key genetic traits to be used in grapevine breeding and the setting of agronomic practices to improve climatic resilience. The increasing availability of transcriptomic studies, describing gene expression in many tissues and developmental, or treatment conditions, have allowed the implementation of gene expression compendia, which enclose a huge amount of information. The mining of transcriptomic data represents an effective approach to expand a known local gene network (LGN) by finding new related genes. We recently published a pipeline based on the iterative application of the PC-algorithm, named NES2RA, to expand gene networks in Escherichia coli and Arabidopsis thaliana. Here, we propose the application of this method to the grapevine transcriptomic compendium Vespucci, in order to expand four LGNs related to the grapevine response to climate change. Two networks are related to the secondary metabolic pathways for anthocyanin and stilbenoid synthesis, involved in the response to solar radiation, whereas the other two are signaling networks, related to the hormones abscisic acid and ethylene, possibly involved in the regulation of cell water balance and cuticle transpiration. The expansion networks produced by NES2RA algorithm have been evaluated by comparison with experimental data and biological knowledge on the identified genes showing fairly good consistency of the results. In addition, the algorithm was effective in retaining only the most significant interactions among the genes providing a useful framework for experimental validation. The application of the NES2RA to Vitis vinifera expression data by means of the BOINC-based implementation is available upon request (valter.cavecchia@cnr.it).