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  • 1
    In: Human Genetics, Springer Science and Business Media LLC, Vol. 141, No. 1 ( 2022-01), p. 147-173
    Abstract: The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management.
    Type of Medium: Online Resource
    ISSN: 0340-6717 , 1432-1203
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 1459188-1
    SSG: 12
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  • 2
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2024-02-06)
    Abstract: The clinical manifestations of SARS-CoV-2 infection vary widely among patients, from asymptomatic to life-threatening. Host genetics is one of the factors that contributes to this variability as previously reported by the COVID-19 Host Genetics Initiative (HGI), which identified sixteen loci associated with COVID-19 severity. Herein, we investigated the genetic determinants of COVID-19 mortality, by performing a case-only genome-wide survival analysis, 60 days after infection, of 3904 COVID-19 patients from the GEN-COVID and other European series (EGAS00001005304 study of the COVID-19 HGI). Using imputed genotype data, we carried out a survival analysis using the Cox model adjusted for age, age2, sex, series, time of infection, and the first ten principal components. We observed a genome-wide significant ( P -value 〈 5.0 × 10 −8 ) association of the rs117011822 variant, on chromosome 11, of rs7208524 on chromosome 17, approaching the genome-wide threshold ( P -value = 5.19 × 10 −8 ). A total of 113 variants were associated with survival at P -value 〈 1.0 × 10 −5 and most of them regulated the expression of genes involved in immune response (e.g., CD300 and KLR genes), or in lung repair and function (e.g., FGF19 and CDH13). Overall, our results suggest that germline variants may modulate COVID-19 risk of death, possibly through the regulation of gene expression in immune response and lung function pathways.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2024
    detail.hit.zdb_id: 2615211-3
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  • 3
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 41, No. 16_suppl ( 2023-06-01), p. e17043-e17043
    Abstract: e17043 Background: The cellular transmembrane protease serine 2 (TMPRSS2) cleaves the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to let viral cell entry. Patients (pts) with prostate carcinoma (PCa) are expected to be at higher risk for coronavirus disease 2019 (COVID-19). However, TMPRSS2 transcription is significantly down-regulated by luteinizing hormone releasing hormone agonists (LHRH-a) and enzalutamide used to treat different PCa stages and this could alter the ability of SARS-CoV-2 to enter target cells. This study aims to evaluate if Single Nucleotide Polymorphisms (SNPs) in the TMPRSS2 gene are associated to a different risk for developing severe COVID-19. Methods: This is the translational part of a large retrospective-prospective real world study designed to estimate whether anti-androgen therapy for PCa is associated to a lower severity of COVID-19. Blood samples were collected from volunteer pts affected with PCa treated at our Institution who developed COVID-19. To be included, pts should receive at least LHRH-a for locally advanced o metastatic hormone sensitive or resistant disease. Genomic DNA of PCa pts was genotyped with the Axiom Human Genotyping SARS-CoV-2 array. Raw genotyping data were analyzed using the Axiom Analysis Suite and genotypes of 219 TMPRSS2 variants were extracted. Identified SNPs were used to compare reference and alternative allele counts between PCa pts and a control cohort of healthy European subjects (n = 2848; DOI:10.1056/NEJMoa2020283) collected in the Milan area (Italy) with chi squared test. Uni- and multivariate logistic regressions were performed to investigate associations between such identified SNPs and severe COVID-19, defined as any between the need for hospitalization or access to an intensive care unit or oxygen therapy. Results: 45 pts were enrolled from November 2020 to May 2022. Median age at COVID-19 detection was 77 years (range 51-94). 10/45 (22%) pts had severe COVID-19, but none died. At COVID-19 diagnosis, 4/45 pts (9%) were receiving chemotherapy for PCa, 13/45 (29%) new generation hormonal agents, 24/45 (53%) LHRH-a, the remaining 4/45 (9%) other therapies. Compared to the control cohort, we identified 52 TMPRSS2 variants associated with the susceptibility to SARS-CoV-2 infection in the cohort of PCa pts (P-value 〈 0.05). Among them, 3 SNPs were associated with severity in univariable logistic regression models: 2 resulted to be protective (rs9974589, p 0.01, OR 0.26; rs28442123, p 0.04, OR 0.30), and one was associated with increased risk of severe COVID-19 (rs2070788, p 0.01, OR 3.8). A multivariate logistic model (p = 0.0004, AUC = 0.88) was performed considering rs11908828 (p = 0,0109, OR = 32.25), rs28442123 (p = 0.03, OR = 0.11) and rs2070788 (p = 0.02, OR = 6.33). Conclusions: These preliminary findings point to a possible role of TMPRSS2 SNPs in modulating the severity of COVID-19 in PCa pts. Validation in wider series is needed.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2023
    detail.hit.zdb_id: 2005181-5
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  • 4
    In: Cancer Science, Wiley, Vol. 114, No. 1 ( 2023-01), p. 281-294
    Abstract: Emerging evidence suggests that the prognosis of patients with lung adenocarcinoma can be determined from germline variants and transcript levels in nontumoral lung tissue. Gene expression data from noninvolved lung tissue of 483 lung adenocarcinoma patients were tested for correlation with overall survival using multivariable Cox proportional hazard and multivariate machine learning models. For genes whose transcript levels are associated with survival, we used genotype data from 414 patients to identify germline variants acting as cis ‐expression quantitative trait loci (eQTLs). Associations of eQTL variant genotypes with gene expression and survival were tested. Levels of four transcripts were inversely associated with survival by Cox analysis ( CLCF1 , hazard ratio [HR] = 1.53; CNTNAP1 , HR = 2.17; DUSP14 , HR = 1.78; and MT1F : HR = 1.40). Machine learning analysis identified a signature of transcripts associated with lung adenocarcinoma outcome that was largely overlapping with the transcripts identified by Cox analysis, including the three most significant genes ( CLCF1 , CNTNAP1 , and DUSP14 ). Pathway analysis indicated that the signature is enriched for ECM components. We identified 32 cis ‐eQTLs for CNTNAP1 , including 6 with an inverse correlation and 26 with a direct correlation between the number of minor alleles and transcript levels. Of these, all but one were prognostic: the six with an inverse correlation were associated with better prognosis (HR  〈  1) while the others were associated with worse prognosis. Our findings provide supportive evidence that genetic predisposition to lung adenocarcinoma outcome is a feature already present in patients' noninvolved lung tissue.
    Type of Medium: Online Resource
    ISSN: 1347-9032 , 1349-7006
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2115647-5
    detail.hit.zdb_id: 2111204-6
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  • 5
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2022
    In:  Scientific Reports Vol. 12, No. 1 ( 2022-03-17)
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2022-03-17)
    Abstract: SARS-CoV-2 has caused a worldwide epidemic of enormous proportions, which resulted in different mortality rates in different countries for unknown reasons. We analyzed factors associated with mortality using data from the Italian national database of more than 4 million SARS-CoV-2-positive cases diagnosed between January 2020 and July 2021, including  〉  415 thousand hospitalized for coronavirus disease-19 (COVID-19) and  〉  127 thousand deceased. For patients for whom age, sex and date of infection detection were available, we determined the impact of these variables on mortality 30 days after the date of diagnosis or hospitalization. Multivariable weighted Cox analysis showed that each of the analyzed variables independently affected COVID-19 mortality. Specifically, in the overall series, age was the main risk factor for mortality, with HR  〉  100 in the age groups older than 65 years compared with a reference group of 15–44 years. Male sex presented a two-fold higher risk of death than female sex. Patients infected after the first pandemic wave (i.e. after 30 June 2020) had an approximately threefold lower risk of death than those infected during the first wave. Thus, in a series of all confirmed SARS-CoV-2-infected cases in an entire European nation, elderly age was by far the most significant risk factor for COVID-19 mortality, confirming that protecting the elderly should be a priority in pandemic management. Male sex and being infected during the first wave were additional risk factors associated with COVID-19 mortality.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2615211-3
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  • 6
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2022-07-06)
    Abstract: The risk of colorectal cancer (CRC) depends on environmental and genetic factors. Among environmental factors, an imbalance in the gut microbiota can increase CRC risk. Also, microbiota is influenced by host genetics. However, it is not known if germline variants influence CRC development by modulating microbiota composition. We investigated germline variants associated with the abundance of bacterial populations in the normal (non-involved) colorectal mucosa of 93 CRC patients and evaluated their possible role in disease. Using a multivariable linear regression, we assessed the association between germline variants identified by genome wide genotyping and bacteria abundances determined by 16S rRNA gene sequencing. We identified 37 germline variants associated with the abundance of the genera Bacteroides, Ruminococcus, Akkermansia, Faecalibacterium and Gemmiger and with alpha diversity. These variants are correlated with the expression of 58 genes involved in inflammatory responses, cell adhesion, apoptosis and barrier integrity. Genes and bacteria appear to be involved in the same processes. In fact, expression of the pro-inflammatory genes GAL , GSDMD and LY6H was correlated with the abundance of Bacteroides , which has pro-inflammatory properties; abundance of the anti-inflammatory genus Faecalibacterium correlated with expression of KAZN, with barrier-enhancing functions. Both the microbiota composition and local inflammation are regulated, at least partially, by the same germline variants. These variants may regulate the microenvironment in which bacteria grow and predispose to the development of cancer. Identification of these variants is the first step to identifying higher-risk individuals and proposing tailored preventive treatments that increase beneficial bacterial populations.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2615211-3
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  • 7
    In: Pediatric Blood & Cancer, Wiley, Vol. 70, No. 9 ( 2023-09)
    Abstract: Osteosarcoma (OS) is a rare pediatric cancer for which therapeutic approaches, including chemotherapy and surgery, show a wide interindividual variability in patient response, both in terms of adverse events and therapy efficacy. There is growing evidence that this individual variable response to therapies is also influenced by inherited genetic variations. However, the results obtained to date in these pediatric cancers have been contradictory and often lack validation in independent series. Additionally, these studies frequently focused only on a limited number of polymorphisms in candidate genes. Methods In order to identify germline coding variations associated with individual differences in adverse events occurrence in pediatric patients affected by localized OS, we carried out an exome‐wide association study in 24 OS patients treated with methotrexate, cisplatin, and doxorubicin, using the SNP‐Set (Sequence) Kernel Association Test (SKAT), optimized for small sample size. Results Gene sets significantly associated (FDR  〈  .05) with neutropenia and hepatotoxicity induced by methotrexate were identified. Some of the identified genes map in loci previously associated with similar phenotypes (e.g., leukocyte count, alkaline phosphatase levels). Conclusion Further studies in larger series and with functional characterization of the identified associations are needed; nonetheless, this pilot study prompts the relevance of broadly investigating variants along the whole genome, to identify new potential pharmacogenes, beyond drug metabolism, transport, and receptor candidate genes.
    Type of Medium: Online Resource
    ISSN: 1545-5009 , 1545-5017
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2130978-4
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  • 8
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2019
    In:  European Journal of Human Genetics Vol. 27, No. 1 ( 2019-1), p. 125-132
    In: European Journal of Human Genetics, Springer Science and Business Media LLC, Vol. 27, No. 1 ( 2019-1), p. 125-132
    Type of Medium: Online Resource
    ISSN: 1018-4813 , 1476-5438
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2005160-8
    SSG: 12
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