The genetic basis of the immune response to SARS-CoV-2 infection and vaccination in the Italian municipality of Vo’ Ettore Zapparoli, Enrico Lavezzo, Hélène Tonnelé, Fabio Simeoni, Jing Guo, et al. Frontiers in Immunology, 2026 Introduction It is becoming increasingly evident that SARS-CoV-2 infection is here to stay. Therefore, understanding whether genetic variants may impact the response to the virus or vaccination is crucial. Studies on the genetic determinants of immune responses to SARS-CoV-2 have been limited by the scarcity of genetically homogenous populations and longitudinal designs that assess responses to both infection and vaccination in relation to individual genetic variation. Methods Here we performed genotyping and whole-genome sequencing in a well-annotated and intensively followed population from the municipality of Vo’, which has previously provided critical insights into SARS-CoV-2 transmission, infection dynamics and COVID-19 clinical manifestations. Results We identified 99 variants within the major histocompatibility complex (MHC) associated with altered T cell response dynamics following infection. These variants clustered into two semi-independent linkage disequilibrium (LD) blocks, respectively tagged by the HLA-A*01:01 allele and by SNP rs1611581. Additionally, when examining the response to vaccination, we identified 617 MHC genetic variants clustering into 27 semi-independent LD blocks that correlated with either increased or decreased TCR responses. We constructed a polygenic risk score (PRS) that comprehensively captures this genetic variation. Finally, structural modelling of selected variants affecting HLA proteins identified specific amino acid residuals most likely to influence interactions with SARS-CoV-2 epitopes, including arginine at position 114, isoleucine at position 97, and alanine at position 152 of the HLA-A molecule. Conclusion Together, these findings provide robust evidence that genetic profiles modulate the immune response to SARS-CoV-2 in a longitudinal setting, offering insights that may inform further public health interventions.
The italian national genomic strategy: current status, challenges, and future perspectives in clinical practice and public health Francesco Andrea Causio, Sara Farina, Alessandra Maio, Flavia Beccia, Luigi Russo, et al. Journal of Community Genetics, 2025 This article presents the outcomes of a national initiative aimed at developing a technical document to support the future Italian National Genomic Strategy, carried out from 2021 to 2024 through the collaboration of 14 research institutions. The project was designed to align with major European genomic initiatives, particularly the “1 + Million Genomes” (1 + MG) Declaration and its supporting programs, including Beyond 1 Million Genomes (B1 + MG), the Genomic Data Infrastructure (GDI), and Genome of Europe (GoE). The initiative was structured around 12 National Mirror Groups (NMGs), each addressing a specific domain such as clinical implementation, ethical and legal issues, data governance, health economics, and public engagement. Through expert consensus and coordinated activities, the project produced a comprehensive technical document outlining seven strategic lines and related intervention areas. These include the integration of genomic testing into clinical practice, development of specialized genomic centers, creation of a national genomic data infrastructure, professional training, and public education. The proposed strategy emphasizes equitable access to genomic medicine, the use of health technology assessment to evaluate new technologies, and the importance of citizen engagement and literacy. By fostering collaboration among institutions, healthcare professionals, and the public, the final goal is to position Italy as a leader in genomic medicine and ensure the responsible, effective, and ethical use of genomics in public health and clinical care.
Imprints of somatic hypermutation on B-cell receptor immunoglobulins post-infection versus post-vaccination against SARS-CoV-2 Elisavet Vlachonikola, Nikolaos Pechlivanis, Georgios Karakatsoulis, Massimo Degano, Fotis Psomopoulos, et al. Immunohorizons, 2025 Published evidence supports significant heterogeneity of immune responses among individuals infected with or vaccinated against SARS-CoV-2. This highlights the need for in-depth investigation of the implicated processes toward refined understanding and improved management of COVID-19. The main objective of the present study was to investigate the dynamics of B cell responses to SARS-CoV-2, focusing on how initial infection and subsequent vaccination influence the immunoglobulin gene repertoire, with special emphasis on the impact of somatic hypermutation (SHM) on antibody maturation. Samples were collected from 81 individuals infected by SARS-CoV-2 in the municipality of Vo' during the first pandemic wave in 2020. For 25 of them, sampling was repeated 7 d after completing the primary vaccination series. Deep immunogenetic analysis of the B-cell receptor immunoglobulin (BcR IG) gene repertoire was performed using targeted next-generation sequencing. Bioinformatics analysis focused on repertoire metrics, prediction of IG antigen specificity, and detailed profiling of the SHM patterns. Significant expansions of unmutated sequences early post-infection suggest extrafollicular B cell maturation. In contrast, vaccination promoted SHM acquisition, indicating a germinal center–dependent response, and pronounced repertoire renewal. Restricted SHMs in SARS-homologous clonotypes along with preferential targeting of specific codons within the VH domain post-vaccination support ongoing affinity maturation within germinal centers. Differences in the BcR IG profiles post-infection versus post-vaccination allude to distinct trajectories in B cell maturation. Distinct profiles of SHM targeting reflect ongoing affinity maturation post-vaccination, with implications for optimizing preventive and therapeutic interventions against COVID-19.
Systemic delivery of cadherin 17–specific CAR T cells allows effective and safe targeting of colorectal cancer liver metastases Beatrice Greco, Rita El Khoury, Chiara Balestrieri, Camilla Sirini, Alice Machado, et al. Science Translational Medicine, 2025 Liver metastases represent the leading cause of death in patients with colorectal cancer (CRC). Chimeric antigen receptor (CAR) T cell therapy holds promise in this context, but any effort to bring it to the bedside requires careful antigen selection and testing in clinically relevant models. Here, we identified cadherin-17 (CDH17) as a candidate antigen for CAR T cell therapy of CRC liver metastases. We hence designed human CDH17 CARs differing in antigen binding and extracellular spacer regions and compared the different constructs in preclinical models of antitumor efficacy, cytokine release syndrome, and on-target off-tumor toxicity. Whereas the binding domains differed in efficacy in vitro, the spacer region shaped the kinetics of the CAR T cells in vivo. When used in a CRC liver xenograft model, CDH17 CAR T cells efficiently suppressed tumor growth upon either systemic or locoregional administration. However, when tested in mice reconstituted with a human immune system, CAR T cells injected locally caused a particularly harsh cytokine release syndrome. Confocal microscopy revealed that CDH17 is exposed on the entire surface of tumor cells, whereas its expression in healthy colon is restricted to lateral junctions between epithelial cells. Accordingly, CDH17 CAR T cells showed dose-dependent cytokine release in response to CRC tissue slices while displaying no reaction against healthy colon tissue samples. Overall, these findings support systemic delivery of CDH17 CAR T cells as a safe and effective approach to treat CRC liver metastases and pave the way for a phase 1/2 clinical trial.
Leveraging the potential of 1.0-mm i.d. columns in UHPLC-HRMS-based untargeted metabolomics Danila La Gioia, Emanuela Salviati, Manuela Giovanna Basilicata, Claudia Felici, Oronza A. Botrugno, et al. Analytical and Bioanalytical Chemistry, 2025 Untargeted metabolomics UHPLC-HRMS workflows typically employ narrowbore 2.1-mm inner diameter (i.d.) columns. However, the wide concentration range of the metabolome and the need to often analyze small sample amounts poses challenges to these approaches. Reducing the column diameter could be a potential solution. Herein, we evaluated the performance of a microbore 1.0-mm i.d. setup compared to the 2.1-mm i.d. benchmark for untargeted metabolomics. The 1.0-mm i.d. setup was implemented on a micro-UHPLC system, while the 2.1-mm i.d. on a standard UHPLC, both coupled to quadrupole-orbitrap HRMS. On polar standard metabolites, a sensitivity gain with an average 3.8-fold increase over the 2.1-mm i.d., along with lower LOD (LODavg 1.48 ng/mL vs. 6.18 ng/mL) and LOQ (LOQavg 4.94 ng/mL vs. 20.60 ng/mL), was observed. The microbore method detected and quantified all metabolites at LLOQ with respect to 2.1, also demonstrating good repeatability with lower CV% for retention times (0.29% vs. 0.63%) and peak areas (4.65% vs. 7.27%). The analysis of various samples, in both RP and HILIC modes, including different plasma volumes, dried blood spots (DBS), and colorectal cancer (CRC) patient-derived organoids (PDOs), in full scan-data dependent mode (FS-DDA) reported a significant increase in MS1 and MS2 features, as well as MS/MS spectral matches by 38.95%, 39.26%, and 18.23%, respectively. These findings demonstrate that 1.0-mm i.d. columns in UHPLC-HRMS could be a potential strategy to enhance coverage for low-amount samples while maintaining the same analytical throughput and robustness of 2.1-mm i.d. formats, with reduced solvent consumption.
DNA methylation alterations in prostate cancer: from diagnosis to treatment Francesco Barletta, Marco Bandini, Giuseppe Ottone Cirulli, Paolo Zaurito, Roberta Lucianò, et al. Translational Andrology and Urology, 2025 Epigenetics, particularly DNA methylation, plays a crucial role in gene activation and deactivation. Indeed, modification of this pathway has been well described as promoter of cancer development in many settings. Hypermethylation of CpG islands has also been described as a significant epigenetic alteration in prostate cancer (PCa), being associated with gene silencing and tumour progression. Key studies have shown that specific genes, such as GSTP1, APC, and RARb2, exhibit significant epigenetic alterations in PCa, with their methylation profiles showing potential utility as biomarkers in the diagnostic setting. Furthermore, comprehensive methylation analyses have identified numerous differentially methylated CpGs and relative molecular pathways associated with PCa carcinogenesis and progression, thus enhancing the understanding of its molecular underpinnings. Finally, therapies targeting DNA methylation, such as DNA methyltransferases (DNMTs) inhibitors, show potential in overcoming drug resistance in advanced PCa treatment. Consequently, dissecting epigenetic mechanisms, and in particular DNA methylation, is fundamental for understanding PCa carcinogenesis, providing valuable insights for clinical decisions and development of targeted therapies. Given the above premises, this review aims to provide an overview of the role of DNA methylation aberrations in PCa, highlighting current and future directions for exploring the epigenetic landscape to better understand the origins and progression of this disease.
Microfluidics for 3D dynamic cell cultures in 384 multiwell format Convegno Nazionale Di Bioingegneria, 2025
