National Institute of Molecular Genetics (INGM)

Introduction: Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic condition characterized by abnormal immune responses and intestinal inflammation. Emerging evidence highlights the vital role of gut microbiota in IBD's onset and progression. Recent advances have shaped diagnostic and therapeutic strategies, increasingly focusing on microbiome-based personalized care. Methodology: this review covers studies from 2004 to 2024, reflecting the surge in research on luminal microbial ecology in IBD. Human studies were prioritized, with select animal studies included for mechanistic insights. Only English-language, peer-reviewed articles - clinical trials, systematic reviews, and meta-analyses - were considered. Studies without clinical validation were excluded unless offering essential insights. Searches were conducted using PubMed, Scopus, and Web of Science. Areas covered: we explore mechanisms for managing IBD-related microbiota, including microbial markers for diagnosis and novel therapies such as fecal microbiota transplantation, metabolite-based treatments, and precision microbiome modulation. Additionally, we review technologies and diagnostic tools used to analyze gut microbiota composition and function in clinical settings. Emerging data supporting personalized therapeutic strategies based on individual microbial profiles are discussed. Expert opinion: Standardized microbiome research integration into clinical practice will enhance precision in IBD care, signaling a shift toward microbiota-based personalized medicine.

Carbohydrate-based therapeutic vaccines are actively pursued as targeted immunotherapy to treat cancer. Aberrant glycosylation is indeed of paramount importance in tumors, leading to the formation of "neo-epitopes", known as tumor-associated carbohydrate antigens (TACAs), crucial in cancer onset, development and spread. Accordingly, the over-simplified mucin-type O-glycans Tn and STn have been confirmed among the most promising candidates for the development of cancer vaccines. In this work, we first propose genetically manipulated bacteria outer membrane vesicles (OMVs), namely GMMA, as a vaccine formulation platform to display glycan antigens. GMMA were glycosylated with multiple copies of structurally locked Tn mimetic or STn mimetic as cancer vaccine prototypes. These constructs, in non-adjuvanted formulations, showed sounding immunogenic properties in vivo and impressive efficacy in a mouse model of aggressive triple-negative breast cancer. This example of tailor-made therapeutic vaccine might revolutionize the approach to cancer therapy.

MicroRNAs (miRNAs) are a prominent class of small non‐coding RNAs that control gene expression. This comprehensive review explores the intricate roles of miRNAs in metabolism and immunity, as well as the emerging field of immunometabolism. The core of this work delves into the functional and regulatory capabilities of miRNAs, examining their complex influence on glucose and lipid metabolism, as well as their pivotal roles in shaping T‐cell development and function. Specifically, this review addresses how miRNAs orchestrate the complex interaction between cellular metabolic processes and immune responses, underscoring the essential nature of these small regulatory molecules in maintaining homeostasis. Finally, we examine the emerging role of Artificial Intelligence (AI) in miRNA research, focusing on how machine learning techniques are revolutionizing the identification and validation of potential miRNA biomarkers. By integrating these diverse aspects, this review underscores the multifaceted roles of miRNAs in biological processes and their significant potential in advancing biomedical research and clinical applications.

Lamin A/C is a nuclear type V intermediate filament protein part of the meshwork structure underlying the inner nuclear membrane (nuclear lamina), which plays numerous roles, including maintenance of nuclear shape, heterochromatin organization, and transcriptional regulation. Our group has demonstrated the role of Lamin A/C in different pathophysiological conditions. Here, we investigated for the first time how Lamin A/C affects neuronal maturation in rat cerebellar granule cells (GCs). Primary rat cerebellar GCs where we silenced the Lmna gene constituted our key model; this provided a rather homogeneous cellular system showing a neuronal population in vitro. We then validated our findings in another in vivo murine model with knock-out of the Lmna gene and in an in vitro human neuronal model with silencing of the LMNA gene. We observed across three different models that Lamin A/C down-regulation affects neurons maturation by protecting the cells from glutamate-evoked excitotoxicity and correlates with an inhibition of calcium influxes and a down-regulation of pro-inflammatory cytokine pathways. Consistent with previous findings from our group, this study corroborates that Lamin A/C plays a key role in neural development and opens new significant implications for a better comprehension of the mechanisms involved in neurodegenerative diseases, where changes in the nuclear envelope are linked to neuroinflammatory processes and damage.

Background Cachexia is a severe form of muscle wasting disorder particularly observed in patients with advanced cancer. The absence of effective strategies to ameliorate cachexia indicates our poor understanding of the mechanisms of cachexia. By employing system‐wide approaches, we investigated molecular mechanisms underlying cancer secreted pro‐inflammatory cytokine‐induced cachexia (CIC). Methods As cellular model systems, we employed mouse satellite stem cell‐derived primary muscle cells, mouse C2C12 myoblast progenitor cell‐derived myotubes, and neonatal rat cardiomyocytes. We induced CIC by incubating striated muscle cells with pro‐inflammatory cytokines TNF‐α and IFN‐γ. To understand the physiological effects of CIC, we probed the contractile properties of muscle cells following electrical stimulation and measured intracellular calcium transients. Effects of CIC on sarcomere organization were monitored by confocal microscopy. Large‐scale quantitative proteomics and RNA sequencing assays enabled us to examine molecular mechanisms underlying CIC. Using chromatin immunoprecipitation experiments, chromatin signalling and modulation of epigenetic marks on muscle‐specific genes were investigated. Results Here, we observed a drastic loss of striated muscle cell contraction in CIC, primarily, due to acutely disorganized sarcomere structures and impeded calcium handling process. In calcium transients, the extent of calcium (Ca ²⁺ ) release, as indicated by the calcium amplitude during the excitation–contraction coupling (ECC) process, was reduced (19.6 ± 2.35% in control to 8.6 ± 1.52% in CIC, p = 4.8 * 10 ⁻¹¹ ). Kinetics of calcium transients, i.e., the Ca ²⁺ release rate (26 ± 0.5 ms in control to 29 ± 5.1 ms in CIC, median p = 0.014), and calcium re‐uptake rate (137 ± 13 ms in control to 185 ± 24 ms in CIC, p = 0.032) were both prolonged. Proteomic analysis showed altered proteostasis in CIC, particularly related to sarcomere and sarcoplasmic reticulum (SR). Transcriptomic analysis unravelled upstream deregulation of global transcriptional events for sarcomeric and SR genes. Mechanistically, chromatin loading of transcriptionally active RNA Polymerase II on muscle‐specific genes, including Myh1 and Atp2a1 , was impeded. This was due to diminished transcriptionally active epigenetic marks H3K4 trimethylation on Myh1 and Atp2a1 , resulted in lower transcriptional activity of these muscle‐specific genes in CIC and ultimately reduced MyHC‐IId molecular motor protein and SERCA1 protein levels. Conclusions Our top‐down approach elucidated that the altered transcriptional mechanism and proteomic state perturbed functionally related machinery responsible for calcium handling and sarcomere organization in CIC. Knowledge of the underlying cause of muscle mass loss and compromised muscle function is key for developing therapeutic solutions to ameliorate cachectic conditions.

Gene expression involves a series of consequential processes, beginning with mRNA synthesis and culminating in translation. Traditionally studied as a linear sequence of events, recent findings challenge this perspective, revealing coupling mechanisms that coordinate key steps of gene expression, even when spatially and temporally distant. In this review, we focus on translation, the final stage of gene expression, and examine its coupling with key stages of mRNA metabolism: synthesis, processing, export, and decay. For each of these processes, we provide an overview of known instances of coupling with translation. Furthermore, we discuss the role of high-throughput technologies in uncovering these intricate interactions on a genome-wide scale. Finally, we highlight key challenges and propose future directions to advance our understanding of how coupling mechanisms orchestrate robust and adaptable gene expression programs.

Recognition of glycans by simple synthetic receptors is a key issue in supramolecular chemistry, endowed with relevant implications in glycobiology and medicine. In this context, glycoproteins featuring N‐glycans represent an important biological target, because they are often exploited by enveloped viruses in adhesion and infection processes. However, a direct evidence for their recognition by a synthetic receptor targeting N‐glycans is still missing in the literature. Using a combination of glycoengineering and mass spectrometry techniques, we present here the direct evidence of biomimetic recognition of complex‐type N‐glycans exposed on the receptor‐binding domain (RBD) of the wild‐type spike protein of SARS‐CoV‐2 by a biologically active, synthetic receptor.

The urgent need for safer and innovative antitubercular agents remains a priority for the scientific community. In pursuit of this goal, we designed and evaluated novel 5-phenylfuran-2-carboxylic acid derivatives targeting Mycobacterium tuberculosis (Mtb) salicylate synthase (MbtI), a key enzyme, absent in humans, that plays a crucial role in Mtb virulence. Several potent MbtI inhibitors demonstrating significant antitubercular activity and a favorable safety profile were identified. Structure-guided optimization yielded 5-(3-cyano-5-isobutoxyphenyl)furan-2-carboxylic acid (1e), which exhibited strong MbtI inhibition (IC50 = 11.2 μM) and a promising in vitro antitubercular activity (MIC99 = 32 μM against M. bovis BCG). Esters of 1e were effectively loaded into poly(2-methacryloyloxyethyl phosphorylcholine)-poly(2-(diisopropylamino)ethyl methacrylate) (PMPC–PDPA) polymersomes (POs) and delivered to intracellular mycobacteria, resulting in reduced Mtb viability. This study provides a foundation for the use of POs in the development of future MbtI-targeted therapies for tuberculosis.

Epidemiological studies have revealed significant sex differences in the incidence of tumors unrelated to reproductive functions, with females demonstrating a lesser risk and a better response to therapy than males. However, the reasons for these disparities are still unknown and cancer therapies are generally sex-unbiased. The tumor-suppressor protein p53 is a transcription factor that can activate the expression of multiple target genes mainly involved in the maintenance of genome stability and tumor prevention. It is encoded by TP53, which is the most-frequently mutated gene in human cancers and therefore constitutes an attractive target for therapy. Recently, evidence of sex differences has emerged in both p53 regulations and functions, possibly providing novel opportunities for personalized cancer medicine. Here, we will review and discuss current knowledge about sexual disparities in p53 pathways, their role in tumorigenesis and cancer progression, and their importance in the therapy choice process, finally highlighting the importance of considering sex contribution in both basic research and clinical practice.

Advances in understanding the mechanisms behind genetic diseases like Duchenne muscular dystrophy (DMD) underscore the critical role of the extracellular matrix (ECM) composition in disease progression. Effective in vitro models must replicate the intercellular relationships and physicochemical properties of native ECM to fully capture disease‐specific characteristics. Although recent biomaterials support the in vitro biofabrication of pathophysiological environments, they often lack disease‐specific ECM features. In this study, DystroGel, a hydrogel derived from the cardiac ECM of a porcine DMD model, replicates the distinct molecular composition of dystrophic cardiac tissue for the first time. The findings indicate that the dystrophic ECM matrix exhibits a unique protein profile, impacting cellular processes critical to DMD pathology. This work demonstrates the importance of using a 3D substrate that recreates intercellular dynamics within a defined pathological environment, enhancing the ability to model genetic disorders and providing a valuable tool for advancing personalized therapeutic strategies.

Silver nanoparticles (AgNPs) hold great promise in biomedical applications due to their unique properties and potential for specific tissue targeting. However, the clinical translation of nanoparticle-based therapeutics remains challenging, primarily due to an incomplete understanding of how nanoparticle properties influence interactions at the nano-bio interface, as well as the role of surface-adsorbed proteins (i.e. protein corona) in modulating nanoparticle-cell interactions. This study demonstrates that surface charge has a greater influence than protein corona formation in determining the cytotoxicity, cellular uptake, and biodistribution of AgNPs. Using negatively and positively charged AgNPs, we show that while protein corona formation is essential for ensuring nanoparticle availability for cellular interactions, the adsorption of biomolecules is non-specific and independent of surface charge. Conversely, surface charge significantly influences the interactions of AgNPs with cells. Positively charged nanoparticles exhibit enhanced cellular uptake, preferential accumulation in lysosomes, and pronounced mitochondrial damage compared to their negatively charged counterparts, resulting in greater cytotoxic effects. This effect is particularly evident in human breast cancer cells, where negatively charged nanoparticles show minimal uptake and cytotoxicity. These findings demonstrate that surface charge is the primary factor governing nanoparticle-cell interactions, rather than protein corona formation. Nonetheless, the protein corona plays a critical role in stabilizing nanoparticles within physiological environments.

Cancer is one of the major challenges in medicine, necessitating continuous advancements in therapeutic approaches. Autophagy, an intracellular pathway essential for cellular homeostasis and stress response, has emerged as a promising target for cancer treatment. In this context, FAM46C, a novel pan-cancer tumour suppressor, has been shown to induce apoptosis in multiple myeloma cells through indirect inhibition of autophagy. Here, we discuss how FAM46C-induced autophagic dampening could offer new opportunities for global cancer therapy. Specifically, we explore two scenarios in which the expression of a functional FAM46C may either sensitize cancer cells to autophagic inhibition or antagonize their sensitivity. We further comment on how this synergism/antagonism could be used to refine strategies for cancer treatment, positioning FAM46C as a pivotal factor in future cancer therapy development.

Silver nanoparticles (AgNPs) hold great promise in biomedical applications due to their unique properties and potential for specific tissue targeting. However, the clinical translation of nanoparticle-based therapeutics remains challenging, primarily due to an incomplete understanding of how nanoparticle properties influence interactions at the nano-bio interface, as well as the role of surface-adsorbed proteins (i.e. protein corona) in modulating nanoparticle-cell interactions. This study demonstrates that surface charge has a greater influence than protein corona formation in determining the cytotoxicity, cellular uptake, and biodistribution of AgNPs. Using negatively and positively charged AgNPs, we show that while protein corona formation is essential for ensuring nanoparticle availability for cellular interactions, the adsorption of biomolecules is non-specific and independent of surface charge. Conversely, surface charge significantly influences the interactions of AgNPs with cells. Positively charged nanoparticles exhibit enhanced cellular uptake, preferential accumulation in lysosomes, and pronounced mitochondrial damage compared to their negatively charged counterparts, resulting in greater cytotoxic effects. This effect is particularly evident in human breast cancer cells, where negatively charged nanoparticles show minimal uptake and cytotoxicity. These findings demonstrate that surface charge is the primary factor governing nanoparticle-cell interactions, rather than protein corona formation. Nonetheless, the protein corona plays a critical role in stabilizing nanoparticles within physiological environments.

In the last few years, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been the cause of a worldwide pandemic, highlighting the need for novel antiviral agents. The main protease (Mpro) of SARS-CoV-2 was immediately identified as a crucial enzyme for viral replication and has been validated as a drug target. Here, we present the design and synthesis of peptidomimetic Mpro covalent inhibitors characterized by quinoline-based P3 moieties. Structure–activity relationships (SARs) were also investigated at P1 and P2, as well as for different warheads. The binding modes of the designed inhibitors were assessed using X-ray crystallographic and molecular docking studies. The identified Mpro inhibitors were tested for their antiviral activities in cell-based assays, and the results were encouraging. The SAR studies presented here can contribute to the future design of improved inhibitors by addressing some of the current or prospective issues regarding Mpro inhibitors currently used in therapy.

Historically considered downstream effects of tumorigenesis—arising from changes in DNA content or chromatin organization—nuclear alterations have long been seen as mere prognostic markers within a genome‐centric model of cancer. However, recent findings have placed the nuclear envelope (NE) at the forefront of tumor progression, highlighting its active role in mediating cellular responses to mechanical forces. Despite significant progress, the precise interplay between NE components and cancer progression remains under debate. In this review, we provide a comprehensive and up‐to‐date overview of how changes in NE composition affect nuclear mechanics and facilitate malignant transformation, grounded in the latest molecular and functional studies. We also review recent research that uses advanced technologies, including artificial intelligence, to predict malignancy risk and treatment outcomes by analyzing nuclear morphology. Finally, we discuss how progress in understanding nuclear mechanics has paved the way for mechanotherapy—a promising cancer treatment approach that exploits the mechanical differences between cancerous and healthy cells. Shifting the perspective on NE alterations from mere diagnostic markers to potential therapeutic targets, this review calls for further investigation into the evolving role of the NE in cancer, highlighting the potential for innovative strategies to transform conventional cancer therapies.

Background Glioblastoma (GBM) is a lethal brain tumor characterized by the glioma stem cell (GSC) niche. The V-ATPase proton pump has been described as a crucial factor in sustaining GSC viability and tumorigenicity. Here we studied how patients-derived GSCs rely on V-ATPase activity to sustain mitochondrial bioenergetics and cell growth. Methods V-ATPase activity in GSC cultures was modulated using Bafilomycin A1 (BafA1) and cell viability and metabolic traits were analyzed using live assays. The GBM patients-derived orthotopic xenografts were used as in vivo models of disease. Cell extracts, proximity-ligation assay and advanced microscopy was used to analyze subcellular presence of proteins. A metabolomic screening was performed using Biocrates p180 kit, whereas transcriptomic analysis was performed using Nanostring panels. Results Perturbation of V-ATPase activity reduces GSC growth in vitro and in vivo. In GSC there is a pool of V-ATPase that localize in mitochondria. At the functional level, V-ATPase inhibition in GSC induces ROS production, mitochondrial damage, while hindering mitochondrial oxidative phosphorylation and reducing protein synthesis. This metabolic rewiring is accompanied by a higher glycolytic rate and intracellular lactate accumulation, which is not exploited by GSCs for biosynthetic or survival purposes. Conclusions V-ATPase activity in GSC is critical for mitochondrial metabolism and cell growth. Targeting V-ATPase activity may be a novel potential vulnerability for glioblastoma treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-025-03280-3.

Autoimmune hepatitis (AIH) is a rare chronic inflammatory liver disease characterized by the presence of autoantibodies, including those targeting O-phosphoseryl-tRNA:selenocysteine-tRNA synthase (SepSecS), also known as soluble liver antigen (SLA). Anti-SepSecS antibodies have been associated with a more severe phenotype, suggesting a key role for the SepSecS autoantigen in AIH. To analyze the immune response to SepSecS in patients with AIH at the clonal level, we combined sensitive high-throughput screening assays with the isolation of monoclonal antibodies (mAbs) and T cell clones. The anti-SepSecS mAbs isolated were primarily IgG1, affinity-matured compared with their germline versions, and recognized at least 3 nonoverlapping epitopes. SepSecS-specific CD4⁺ T cell clones were found in patients with AIH who were anti-SLA-positive and anti-SLA-negative,and, to a lesser extent, in patients with non-AIH liver diseases and in healthy individuals. SepSecS-specific T cell clones from patients with AIH produced IFN-γ, IL-4, and IL-10, targeted multiple SepSecS epitopes, and, in one patient, were clonally expanded in both blood and liver biopsy. Finally, SepSecS-specific B cell clones, but not those of unrelated specificities, were able to present soluble SepSecS to specific T cells. Collectively, our study provides the first detailed analysis of B and T cell repertoires targeting SepSecS in patients with AIH, offering a rationale for improved targeted therapies.

Psoriasis is characterized by aberrant keratinocyte activity and immune cell infiltration, driven by immune-mediated pathways. MicroRNAs (miRNAs) play crucial roles in regulating these processes, offering insights into disease mechanisms and therapeutic targets. This study aimed to investigate changes in circulating miRNAs in psoriasis patients undergoing risankizumab therapy, an anti-IL-23 monoclonal antibody, to understand its impact on disease pathogenesis and treatment response. Plasma samples from 12 psoriasis patients were collected before (T0) and after 1 year (T1) of risankizumab treatment and analyzed using small RNA sequencing. Findings were validated in a separate cohort of 23 patients using quantitative real-time PCR (qRT-PCR). T-regulatory cell (Treg) numbers and pro-inflammatory cytokine levels were also assessed. Significant clinical improvement was observed in all patients after 1 year of treatment, accompanied by increased Treg counts and reduced levels of pro-inflammatory cytokines. Twenty-four miRNAs exhibited differential expression post-treatment; 9 were downregulated and 15 upregulated. Notably, miR-200a-3p showed a significant correlation with baseline Psoriasis Area Severity Index (PASI), indicating its potential as a severity marker. Risankizumab therapy also decreased peripheral blood levels of IL-23, IL-1β, and IL-8. This study identifies specific circulating miRNAs, including miR-200a-3p, as potential biomarkers for monitoring treatment responses in psoriasis patients. The findings underscore the therapeutic efficacy of risankizumab in modulating miRNA profiles and immune pathways associated with psoriasis pathogenesis. Overall, these results provide new insights into the mechanisms of risankizumab action and highlight miRNAs as promising candidates for personalized medicine approaches in psoriasis management.

PARP inhibitors (PARPi) have received regulatory approval for the treatment of several tumors, including prostate cancer (PCa), and demonstrate remarkable results in the treatment of castration-resistant prostate cancer (CRPC) patients characterized by defects in homologous recombination repair (HRR) genes. Preclinical studies showed that DNA repair genes (DRG) other than HRR genes may have therapeutic value in the context of PARPi. To this end, we performed multiple CRISPR/Cas9 screens in PCa cell lines using a custom sgRNA library targeting DRG combined with PARPi treatment. We identified LIG1, EME1, and FAAP24 losses as PARPi sensitizers and assessed their frequencies from 3 to 6% among CRPC patients. We showed that concomitant inactivation of LIG1 and PARP induced replication stress and DNA double-strand breaks, ultimately leading to apoptosis. This synthetic lethality (SL) is conserved across multiple tumor types (e.g., lung, breast, and colorectal), and its applicability might be extended to LIG1-functional tumors through a pharmacological combinatorial approach. Importantly, the sensitivity of LIG1-deficient cells to PARPi was confirmed in vivo. Altogether, our results argue for the relevance of determining the status of LIG1, and potentially other non-HRR DRG for CRPC patient stratification and provide evidence to expand their therapeutic options.