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  1. Article ; Online: Analysis of Genetic Ancestry from NGS Data Using EthSEQ.

    Dalfovo, Davide / Romanel, Alessandro

    Current protocols

    2023  Volume 3, Issue 2, Page(s) e663

    Abstract: Next-generation sequencing (NGS) is widely utilized both in translational cancer genomics studies and in the setting of precision medicine. Identification and stratification of an individual's ancestry is fundamental for the correct interpretation of ... ...

    Abstract Next-generation sequencing (NGS) is widely utilized both in translational cancer genomics studies and in the setting of precision medicine. Identification and stratification of an individual's ancestry is fundamental for the correct interpretation of genetic and genomic profiling. EthSEQ provides an easy and effective computational workflow to determine the ancestry of individuals, exploiting single nucleotide polymorphism genotypes computed from NGS data of whole-exome and targeted sequencing experiments. Genotypes are determined by EthSEQ from sequencing alignment files (BAM files) or can be provided as input in Variant Call Format (VCF) or CoreArray Genomic Data Structure (GDS) format. Ancestry is determined and assigned to individuals by EthSEQ exploiting a reference model and a standard or multi-step refinement approach based on Principal Component Analysis (PCA). A complete and detailed set of textual and graphical output files are generated by EthSEQ as result. EthSEQ is easy to use and can be integrated into any NGS-based processing pipeline also exploiting multi-core capabilities. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Perform ancestry analysis using a pre-computed reference model Alternate Protocol: Perform ancestry analysis using a user-specified GDS file as reference model Basic Protocol 2: Perform ancestry analysis using multi-step refinement Support Protocol 1: Create a reference model from multiple VCF genotype data files Support Protocol 2: Create VCF genotype data files from a BAM file.
    MeSH term(s) Humans ; Software ; Genomics/methods ; Genotype ; Information Storage and Retrieval ; High-Throughput Nucleotide Sequencing/methods
    Language English
    Publishing date 2023-01-27
    Publishing country United States
    Document type Journal Article
    ISSN 2691-1299
    ISSN (online) 2691-1299
    DOI 10.1002/cpz1.663
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Germline determinants of aberrant signaling pathways in cancer.

    Dalfovo, Davide / Scandino, Riccardo / Paoli, Marta / Valentini, Samuel / Romanel, Alessandro

    NPJ precision oncology

    2024  Volume 8, Issue 1, Page(s) 57

    Abstract: 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 ... ...

    Abstract 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.
    Language English
    Publishing date 2024-03-01
    Publishing country England
    Document type Journal Article
    ISSN 2397-768X
    ISSN 2397-768X
    DOI 10.1038/s41698-024-00546-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Exploring functionally annotated transcriptional consensus regulatory elements with CONREL.

    Dalfovo, Davide / Valentini, Samuel / Romanel, Alessandro

    Database : the journal of biological databases and curation

    2020  Volume 2020

    Abstract: 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 ... ...

    Abstract 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.
    MeSH term(s) Consensus ; Gene Regulatory Networks ; Genome, Human/genetics ; Humans ; Promoter Regions, Genetic ; Transcription Factors/genetics
    Chemical Substances Transcription Factors
    Language English
    Publishing date 2020-11-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2496706-3
    ISSN 1758-0463 ; 1758-0463
    ISSN (online) 1758-0463
    ISSN 1758-0463
    DOI 10.1093/database/baaa071
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Polympact: exploring functional relations among common human genetic variants.

    Valentini, Samuel / Gandolfi, Francesco / Carolo, Mattia / Dalfovo, Davide / Pozza, Lara / Romanel, Alessandro

    Nucleic acids research

    2022  Volume 50, Issue 3, Page(s) 1335–1350

    Abstract: 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 ... ...

    Abstract 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.
    MeSH term(s) Cluster Analysis ; Genome-Wide Association Study ; Human Genetics ; Humans ; Polymorphism, Single Nucleotide
    Language English
    Publishing date 2022-01-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkac024
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  5. Article: Rarγ -Foxa1 signaling promotes luminal identity in prostate progenitors and is disrupted in prostate cancer.

    Felice, Dario De / Alaimo, Alessandro / Bressan, Davide / Genovesi, Sacha / Marmocchi, Elisa / Annesi, Nicole / Beccaceci, Giulia / Dalfovo, Davide / Cutrupi, Federico / Foletto, Veronica / Lorenzoni, Marco / Gandolfi, Francesco / Kannan, Srinivasaraghavan / Verma, Chandra S / Vasciaveo, Alessandro / Shen, Michael M / Romanel, Alessandro / Chiacchiera, Fulvio / Cambuli, Francesco /
    Lunardi, Andrea

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Retinoic acid (RA) signaling is a master regulator of vertebrate development with crucial roles in directing body axis orientation and tissue differentiation, including in the reproductive system. However, a mechanistic understanding of how RA signaling ... ...

    Abstract Retinoic acid (RA) signaling is a master regulator of vertebrate development with crucial roles in directing body axis orientation and tissue differentiation, including in the reproductive system. However, a mechanistic understanding of how RA signaling promotes cell lineage identity in different tissues is often missing. Here, leveraging prostate organoid technology, we demonstrated that RA signaling orchestrates the commitment of adult mouse prostate progenitors to glandular identity, epithelial barrier integrity, and ultimately, proper specification of the prostatic lumen. Mechanistically, RA-dependent RARγ activation promotes the expression of the pioneer factor Foxa1, which synergizes with the androgen pathway for proper luminal expansion, cytoarchitecture and function.
    Language English
    Publishing date 2024-03-08
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.06.583256
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common

    Lim, Wan Ching / Marques Da Costa, Maria Eugenia / Godefroy, Karine / Jacquet, Eric / Gragert, Loren / Rondof, Windy / Marchais, Antonin / Nhiri, Naima / Dalfovo, Davide / Viard, Mathias / Labaied, Nizar / Khan, Asif M / Dessen, Philippe / Romanel, Alessandro / Pasqualini, Claudia / Schleiermacher, Gudrun / Carrington, Mary / Zitvogel, Laurence / Scoazec, Jean-Yves /
    Geoerger, Birgit / Salmon, Jerome

    Frontiers in immunology

    2024  Volume 14, Page(s) 1265469

    Abstract: The human leukocyte antigen (HLA) system is a major factor controlling cancer immunosurveillance and response to immunotherapy, yet its status in pediatric cancers remains fragmentary. We determined high-confidence HLA genotypes in 576 children, ... ...

    Abstract The human leukocyte antigen (HLA) system is a major factor controlling cancer immunosurveillance and response to immunotherapy, yet its status in pediatric cancers remains fragmentary. We determined high-confidence HLA genotypes in 576 children, adolescents and young adults with recurrent/refractory solid tumors from the MOSCATO-01 and MAPPYACTS trials, using normal and tumor whole exome and RNA sequencing data and benchmarked algorithms. There was no evidence for narrowed HLA allelic diversity but discordant homozygosity and allele frequencies across tumor types and subtypes, such as in embryonal and alveolar rhabdomyosarcoma, neuroblastoma
    MeSH term(s) Adolescent ; Child ; Humans ; Antigen Presentation ; Glioma ; Histocompatibility Antigens Class I/genetics ; Histocompatibility Antigens Class II/genetics ; HLA Antigens/genetics ; HLA-B Antigens/genetics ; Sarcoma, Ewing/genetics ; Animals ; Young Adult
    Chemical Substances Histocompatibility Antigens Class I ; Histocompatibility Antigens Class II ; HLA Antigens ; HLA-B Antigens
    Language English
    Publishing date 2024-01-22
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2023.1265469
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: LSD1/PRMT6-targeting gene therapy to attenuate androgen receptor toxic gain-of-function ameliorates spinobulbar muscular atrophy phenotypes in flies and mice.

    Prakasam, Ramachandran / Bonadiman, Angela / Andreotti, Roberta / Zuccaro, Emanuela / Dalfovo, Davide / Marchioretti, Caterina / Tripathy, Debasmita / Petris, Gianluca / Anderson, Eric N / Migazzi, Alice / Tosatto, Laura / Cereseto, Anna / Battaglioli, Elena / Sorarù, Gianni / Lim, Wooi Fang / Rinaldi, Carlo / Sambataro, Fabio / Pourshafie, Naemeh / Grunseich, Christopher /
    Romanel, Alessandro / Pandey, Udai Bhan / Contestabile, Andrea / Ronzitti, Giuseppe / Basso, Manuela / Pennuto, Maria

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 603

    Abstract: Spinobulbar muscular atrophy (SBMA) is caused by CAG expansions in the androgen receptor gene. Androgen binding to polyQ-expanded androgen receptor triggers SBMA through a combination of toxic gain-of-function and loss-of-function mechanisms. Leveraging ... ...

    Abstract Spinobulbar muscular atrophy (SBMA) is caused by CAG expansions in the androgen receptor gene. Androgen binding to polyQ-expanded androgen receptor triggers SBMA through a combination of toxic gain-of-function and loss-of-function mechanisms. Leveraging cell lines, mice, and patient-derived specimens, we show that androgen receptor co-regulators lysine-specific demethylase 1 (LSD1) and protein arginine methyltransferase 6 (PRMT6) are overexpressed in an androgen-dependent manner specifically in the skeletal muscle of SBMA patients and mice. LSD1 and PRMT6 cooperatively and synergistically transactivate androgen receptor, and their effect is enhanced by expanded polyQ. Pharmacological and genetic silencing of LSD1 and PRMT6 attenuates polyQ-expanded androgen receptor transactivation in SBMA cells and suppresses toxicity in SBMA flies, and a preclinical approach based on miRNA-mediated silencing of LSD1 and PRMT6 attenuates disease manifestations in SBMA mice. These observations suggest that targeting overexpressed co-regulators can attenuate androgen receptor toxic gain-of-function without exacerbating loss-of-function, highlighting a potential therapeutic strategy for patients with SBMA.
    MeSH term(s) Mice ; Animals ; Receptors, Androgen/genetics ; Receptors, Androgen/metabolism ; Bulbo-Spinal Atrophy, X-Linked/genetics ; Androgens ; Diptera ; Gain of Function Mutation ; Phenotype ; Histone Demethylases/genetics ; Muscular Disorders, Atrophic/genetics ; Muscular Disorders, Atrophic/metabolism
    Chemical Substances Receptors, Androgen ; Androgens ; Histone Demethylases (EC 1.14.11.-)
    Language English
    Publishing date 2023-02-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-36186-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Inherited determinants of early recurrent somatic mutations in prostate cancer.

    Romanel, Alessandro / Garritano, Sonia / Stringa, Blerta / Blattner, Mirjam / Dalfovo, Davide / Chakravarty, Dimple / Soong, David / Cotter, Kellie A / Petris, Gianluca / Dhingra, Priyanka / Gasperini, Paola / Cereseto, Anna / Elemento, Olivier / Sboner, Andrea / Khurana, Ekta / Inga, Alberto / Rubin, Mark A / Demichelis, Francesca

    Nature communications

    2017  Volume 8, Issue 1, Page(s) 48

    Abstract: Prostate cancer is a highly heritable molecularly and clinically heterogeneous disease. To discover germline events involved in prostate cancer predisposition, we develop a computational approach to nominate heritable facilitators of somatic genomic ... ...

    Abstract Prostate cancer is a highly heritable molecularly and clinically heterogeneous disease. To discover germline events involved in prostate cancer predisposition, we develop a computational approach to nominate heritable facilitators of somatic genomic events in the context of the androgen receptor signaling. Here, we use a ranking score and benign prostate transcriptomes to identify a non-coding polymorphic regulatory element at 7p14.3 that associates with DNA repair and hormone-regulated transcript levels and with an early recurrent prostate cancer-specific somatic mutation in the Speckle-Type POZ protein (SPOP) gene. The locus shows allele-specific activity that is concomitantly modulated by androgen receptor and by CCAAT/enhancer-binding protein (C/EBP) beta (CEBPB). Deletion of this locus via CRISPR-Cas9 leads to deregulation of the genes predicted to interact with the 7p14.3 locus by Hi-C chromosome conformation capture data. This study suggests that a polymorphism at 7p14.3 may predispose to SPOP mutant prostate cancer subclass through a hormone-dependent DNA damage response.Prostate cancer is a heterogeneous disease, and many cases show somatic mutations of SPOP. Here, the authors show that a non-coding polymorphic regulatory element at 7p14.3 may predispose to SPOP mutant prostate cancer subclass through a hormone dependent DNA damage response.
    MeSH term(s) Cell Line, Tumor ; Gene Expression Regulation, Neoplastic/physiology ; Genotype ; Humans ; Male ; Mutation ; Neoplasm Recurrence, Local ; Prostatic Neoplasms/genetics ; Transcriptome
    Language English
    Publishing date 2017-06-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-017-00046-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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