Istituto Nazionale Genetica Molecolare

The persistent HIV reservoir constitutes the main obstacle to curing HIV/AIDS disease. Our understanding of how non-productive HIV infections are established in primary human CD4+ T cells during the first round of infection remains, however, incomplete. In this study, we leveraged the HIV reporter virus pMorpheus-V5 to delineate cellular expression patterns that are upregulated in non-productively infected primary CD4+ T memory stem cells (TSCM). We found that CD4+ TSCM harboring non-productive proviruses displayed a distinct transcriptomic signature comprising 118 upregulated genes. This non-productive expression profile was distinct from that of productively infected cells as well as from negative-exposed and mock-infected cells. Among the cellular genes most upregulated in CD4+ T cells harboring non-productive proviruses were CCR4-binding migratory chemokines (CCL22, CCL17), tryptophan catabolic enzymes (IDO1, KYNU), and genes encoding cytoskeletal rearrangement proteins (BASP1, TNFAIP2). Intracellular flow cytometry-based analyses confirmed that non-productively infected CD4+ TSCM cells were enriched for CCL22 and IDO1 co-expression compared to the other CD4+ memory subsets, underscoring a clear CD4+ T cell subset specificity for the upregulation of these two immune gene sets associated with non-productive infections. These findings suggest that primary human CD4+ TSCM harboring non-productive proviruses display a distinct immunoregulatory phenotype which may facilitate immune evasion and contribute to the persistence of the HIV reservoir.

Autosomal Dominant-Hyper-IgE Syndrome (AD-HIES) is caused by dominant-negative (DN) STAT3 mutations and characterized by high IgE levels, a lack of Th17-cells, and recurrent infections with extracellular pathogens. We previously identified an enigmatic population of IL-10 producing CCR6+B-helper T-cells and investigated here their relationship to Th17-cells and STAT3 signaling requirements. Human blood lymphocytes were analyzed by multiparametric flow cytometry in healthy donors and AD-HIES patients. Analysis was performed by conventional gating or with bioinformatic tools. FACS-purified T-cell subsets were activated invitro and Th17 differentiation assessed. T-cell antigen specificities were assessed by activation with heat-killed pathogens or antigenic peptide pools. B helper capacities were determined according to antibody secretion in B-T co-cultures by ELISA. CCR6+Th-cells that lacked subset-defining differentiation markers ("CCR6SP") were mostly non-polarized central memory T-cells (TCM) that produced IL-10 and expressed RORγt. They were pre-committed to a Th17 fate, since TCR stimulation in the absence of polarizing cytokines induced efficient Th17 differentiation. The latter was promoted by an autocrine loop of STAT3-activating cytokines. CCR6+Th-cells were reduced in patients with DN-STAT3 mutations but contained activated CCR6SPT-cells that produced IL-10 and responded vigorously to AD-HIES-associated pathogens. These residual CCR6+Th-cells provided B-cell help for IgG and IgE production. Th17 differentiation in AD-HIES patients was not completely impaired but arrested at an intermediate stage of IL-10-producing "pre-Th17"-cells. Surprisingly, DN-STAT3 mutations did not inhibit IL-10 production by CD4+T-cells. Pre-Th17-cells were activated by AD-HIES-associated pathogens and possessed B-helper functions, suggesting that they are not protective but may promote aberrant IgE production.

Spinal muscular atrophy (SMA) is a severe neurological disease caused by mutations in the SMN1 gene, characterized by early onset and degeneration of lower motor neurons. Understanding early neurodevelopmental defects in SMA is crucial for optimizing therapeutic interventions. Using spinal cord and cerebral organoids generated from multiple SMA type 1 male donors, we revealed widespread disease mechanisms beyond motor neuron degeneration. Single-cell transcriptomics uncovered pervasive alterations across neural populations, from progenitors to neurons, demonstrating SMN-dependent dysregulation of neuronal differentiation programs. Multi-electrode array (MEA) analysis identified consistent hyperexcitability in both spinal and brain organoids, establishing altered electrical properties as a central nervous system-wide feature of pathogenesis. Early administration of an optimized antisense oligonucleotide (ASO) that increased SMN levels rescued morphological and functional deficits in spinal cord organoids across different genetic backgrounds. Importantly, this early intervention precisely corrected aberrant splicing in here identified SMN1 targets enriched at critical nodes of neuronal differentiation. Our findings demonstrate that early developmental defects are core features of SMA pathogenesis that can be prevented by timely therapeutic intervention, providing insights for optimizing treatment strategies.

Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of the transcriptional landscape of complex tissues, enabling the discovery of novel cell types and biological functions. However, the identification and classification of cells from scRNA-seq datasets remain significant challenges. To address this, we developed a new computational tool called CIA (Cluster Independent Annotation), which accurately identifies cell types across different datasets without requiring a fully annotated reference dataset or complex machine learning processes. Based on predefined cell type signatures, CIA provides a highly user-friendly and practical solution to cell-type and functional annotation of single cells. The CIA framework is implemented in both the Python and R programming languages, making it applicable to all main single-cell analysis frameworks, and it is available under the MIT license with its documentation at the following links: Python package: https://pypi.org/project/cia-python/ . Python tutorial: https://cia-python.readthedocs.io/en/latest/tutorial/Cluster_Independent_Annotation.html . R package and tutorial: https://github.com/ingmbioinfo/CIA_R . Our results demonstrate that CIA classification performances are comparable to the other state-of-the-art approaches, while requiring a significantly lower computational running time. Overall, CIA simplifies the process of obtaining reproducible signature-based cell assignments that can be easily interpreted through graphical summaries providing researchers with a powerful tool to explore the complex transcriptional landscape of single cells.

Abstract Borrelia burgdorferi sensu lato bacteria are the causative agents of Lyme borreliosis, a multisystemic illness with an expanding epidemiology in temperate areas. Genomic studies on Borrelia are hindered by the difficulty of culturing procedures: standard protocols require extended incubation, substantial technical expertise, and are prone to failure, limiting timely recovery of isolates. This contributes to a low number of complete Borrelia genomes available in public repositories, particularly for species other than B. burgdorferi sensu stricto. Here we introduce a novel approach that overcomes the necessity for extended culture by utilizing Whole Genome Amplification (WGA) directly on freshly collected ticks, and that can be performed in parallel to classical culturing. The protocol is paired with a tailored bioinformatic pipeline designed to ensure accurate assembly and reliable downstream analyses. Benchmarking on multiple control isolates demonstrated that the method yields high-quality chromosomal assemblies. To demonstrate practical applicability, we applied the protocol to freshly collected ticks, successfully generating five high-quality Borrelia chromosomes (two B. lusitaniae , two B. afzelii and one B. garinii ). By generating sequencing-ready DNA in five days rather than months, our protocol greatly streamlines the process and minimizes the effort associated with traditional culture-based methods. This workflow will facilitate broader representation of understudied Borrelia species and support future epidemiological, ecological, and evolutionary investigations on this pathogen.

Acetoacetyl-CoA thiolase deficiency, also known as Beta-ketothiolase deficiency (BKTD), is an autosomal recessive organic aciduria included in the Italian newborn screening (NBS) panel. It is caused by mutations in the ACAT1 gene, which encodes the mitochondrial acetyl-CoA acetyltransferase. Its deficiency impairs the degradation of isoleucine and acetoacetyl-CoA, leading to the accumulation of toxic metabolites. We describe three cases of BKTD. The first newborn showed increase in C5:1, C4DC/C5OH, C3DC/C4OH in the NBS. Urinary organic acids (uOAs) revealed marked excretion of 2-methyl-3-hydroxybutyrate. Tiglylglycine was absent. Genetic testing identified the compound heterozygosity for two pathogenic ACAT1 variants. The second patient showed increased levels of C5:1, C4DC/C5OH, C3DC/C4OH in the NBS. uOAs revealed 2-methyl-3-hydroxybutyrate and tiglylglycine. A homozygous VUS in ACAT1 was identified. The third case showed elevation of C4DC/C5OH, C3DC/C4OH in the NBS, with a slight increase in C5:1. uOAs showed 2-methyl-3-hydroxybutyrate and tiglylglycine. A homozygous missense VUS was identified in the ACAT1 gene. BKTD exhibited variable NBS biochemical phenotypes across the three cases. While C5OH and C5:1, the primary markers, were not consistently elevated in all our cases, C4OH strongly increased in all three. Our findings support the use of C4OH in a combined marker strategy to improve BKTD NBS.

Intervertebral disc (IVD) degeneration (IDD) is the main contributor to chronic low back pain (LBP), the leading cause of disability worldwide, with a significant impact on the quality of life and health of common people. The etiology of IDD is still unclear, but it has been largely demonstrated the crucial role of inflammation and neuroinflammation in the pathological and degenerative cascade of events characterizing IVD degeneration. In this study, we evaluated the potential therapeutic effect of pulsed electromagnetic field (PEMF) on human degenerated IVD (D-IVD) cells collected from patients who underwent discectomy. The experimental plan to test our hypothesis, involved viability assay, reactive oxide species/nitrite production, gene, and protein expression. To recapitulate the pro-inflammatory disc microenvironment occurring during IDD, interleukin-1β (IL-1β) was administered to IVD cell culture. Then, to dissect the contribution of neuroinflammatory condition to immune component, microglial cells were co-cultured with IVD-conditioned media, and viability and expression of inflammatory markers were detected. Our data prove that in the IVD degenerative microenvironment, the increase of pro-inflammatory mediators, extracellular matrix degradative enzymes, and neuroinflammatory markers could be reduced by PEMF therapy, resulting in an overall improvement of degenerative condition and LBP. These results represent an impactful novelty for the management of people suffering from LPB, in terms of symptom relief and reduction of social-health system burden.

ABSTRACT 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.

ABSTRACTNuclear Factor I (NFI) proteins were first identified in adenovirus DNA replication and later as regulators of gene transcription, stem cell proliferation, and differentiation. They play key roles in development, cancer and congenital disorders. Within the NFI family, NFI-X is critical for neural stem cell biology, hematopoiesis, muscle development, muscular dystrophies and oncogenesis. Here, we present the first structural characterization of the NFI transcription factor, NFI-X, both alone and bound to its consensus palindromic DNA site. Our analyses reveal a novel, MH1-like fold within NFI-X DNA-binding domain (DBD) and identify crucial structural determinants for activity, such as a Zn²⁺ binding site, dimeric assembly, activation mechanism and DNA-binding specificity. Given the >95% sequence identity within the NFI DBDs, our structural data are prototypic for the entire family; a NFI Rosetta Stone that allows decoding a wealth of biochemical and functional data and provides a precise target for drug design in a wider disease context.