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Rinaldi, F.

Publications and source records attributed to Rinaldi, F..

10 recordsLinked to original sources

Awakening intracellular immunity for functional HIV cure

HIV persists in long-lived CD4 T cell reservoirs despite antiretroviral therapy (ART)1. Elite controllers suppress viraemia without ART2, yet reservoir reactivation emerges with immune ageing3. Here we show that transient reprogramming of patient-derived CD4 T cells restores their ability to eliminate HIV-infected reservoirs, excising integrated proviral DNA. A defined compound, or physiological induction, drove rapid reprogramming ex vivo, enabling clearance of HIV DNA within hours to days of treatment, independently of ART. Single-cell RNA sequencing revealed activation of an antiviral telomere transfer programme4 that exceeds elite-like control. In humanised mice, adoptive transfer of reprogrammed patient CD4 T cells, or in vivo reprogramming of murine T cells, eliminated HIV DNA across reservoirs, with undetectable viral genomes persisting for months. Modelling predicted that residual proviral reactivation would be governed by rare stochastic events, rendering viral rebound unlikely within a human lifespan. These findings identify a previously unrecognised form of intracellular immunity and establish a defined route to a functional HIV cure arising from the CD4 T cell itself.

immunology↗

CD4⁺ T cells confer transplantable rejuvenation via Rivers of telomeres

The role of the immune system in regulating organismal lifespan remains poorly understood. Here, we show that CD4 T cells release "telomere Rivers" into circulation after acquiring telomeres from antigen-presenting cells (APCs). River formation requires fatty acid oxidation at the T cell-APC synapse, which selectively excludes glyceraldehyde 3-phosphate dehydrogenase (GAPDH) from the telomere vesicles. The resulting Rivers are depleted of glycolytic enzymes but enriched in T cell-derived stemness factors, enabling targeted rejuvenation of senescent tissues across multiple organs. In aged mice, adoptive transfer of young or metabolically reprogrammed CD4 T cells triggered River production in vivo, and Rivers isolated from these animals could be transplanted into other aged mice to propagate the rejuvenation phenotype independently of T cells. River therapy extended median lifespan by [~]17 months, with several mice surviving to nearly five years. This immune-driven telomere transfer pathway is conserved across kingdoms, including plants, defining the first systemic, transplantable programme of youth.

cell biology↗

Breaking new ground into RAD51-BRC repeats interplay in Homologous Recombination

Homologous recombination (HR) is a critical repair pathway involving numerous proteins that ensure error-free DNA double-strand breaks (DSBs) repair. Dysfunction in HR components can compromise genome integrity. Despite advances, many aspects of HR remain poorly understood. Notably, even one of the earliest identified and most critical interactions, between RAD51 and BRCA2, remains incompletely characterized, mainly due to the lack of structural data. This study presents a comprehensive biophysical analysis of the RAD51-BRC repeats interaction, integrating computational and experimental approaches. Starting with assessing the correlation between the binding affinities of individual BRC repeats and their impact on RAD51 disassembly, our investigation extends to larger BRCA2 truncations, offering unprecedented insights into the molecular determinants of RAD51 recognition. As mutations in the BRC repeats impair RAD51 recruitment and are associated with cancer, these results provide a valuable framework for interpreting pathogenic variants and guiding precision medicine therapies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/688182v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@8c5cc9org.highwire.dtl.DTLVardef@11f9066org.highwire.dtl.DTLVardef@14159bdorg.highwire.dtl.DTLVardef@16ac161_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Integrating computational and experimental biophysics reveals novel insights into the RAD51-BRC4 interaction

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=63 SRC="FIGDIR/small/642044v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@32e13org.highwire.dtl.DTLVardef@c60a6forg.highwire.dtl.DTLVardef@1d6fdceorg.highwire.dtl.DTLVardef@1b10541_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGRAPHICAL ABSTRACTC_FLOATNO C_FIG The interaction between the RAD51 and BRCA2 proteins is central for homologous recombination, a crucial pathway ensuring high-fidelity DNA repair. Recruitment of RAD51 involves eight highly conserved regions on BRCA2, named BRC repeats. To date, only the interaction between the fourth BRC repeat (BRC4) and the RAD51 C-terminal domain has been structurally characterized, while the complex of full-length RAD51 with the peptide still remains elusive. Here, we report an integrative experimental and in silico approach to reconstruct the conformational ensemble in solution for full length RAD51 in complex with BRC4. We combined AlphaFold2, crosslinking mass spectrometry (XL-MS) and small angle x-ray scattering (SAXS) data with molecular dynamics simulations (MD). These data show that the full-length RAD51-BRC4 complex is a mixture of compact and elongated conformations. Detailed analysis of the reweighted ensemble, achieved through the maximum entropy principle, identifies key residues at the N-terminal-BRC4 interface mediating complex conformational dynamics. Our evidence provides robust atomic-level insights into the interaction of RAD51 and BRC4. These findings are crucial for understanding the molecular features underlying the recognition between RAD51 and BRCA2, which are essential for developing therapeutic intervention strategies in cancer treatment.

biophysics↗

From literature to biodiversity data: mining arthropod organismal and ecological traits with machine learning

The fields of taxonomy and biodiversity research have witnessed an exponential growth in published literature. This vast corpus of articles holds information on the diverse biological traits of organisms and their ecologies. However, access to and extraction of relevant data from this extensive resource remain challenging. Advances in text and data mining (TDM) and Natural Language Processing (NLP) techniques offer new opportunities for liberating such information from the literature. Testing and using such approaches to annotate articles in machine actionable formats is therefore necessary to enable the exploitation of existing knowledge in new biology, ecology, and evolution research. Here we explore the potential of these methods to annotate and extract organismal and ecological trait data for the most diverse animal group on Earth, the arthropods. The article processing workflow uses manually curated trait dictionaries with trained NLP models to perform labelling of entities and relationships of thousands of articles. A subset of manually annotated documents facilitated the formal evaluation of the performance of the workflow in terms of entity recognition and normalisation, and relationship extraction, highlighting several important technical challenges. The results are made available to the scientific community through an interactive web tool and queryable resource, the ArTraDB Arthropod Trait Database. These methodological explorations provide a framework that could be extended beyond the arthropods, where TDM and NLP approaches applied to the taxonomy and biodiversity literature will greatly facilitate data synthesis studies and literature reviews, the identification of knowledge gaps and biases, as well as the data-informed investigation of ecological and evolutionary trends and patterns.

bioinformatics↗

Disruptors of sestrin-MAPK interactions rejuvenate T cells and expand TCR specificity

Whereas treatments that reactivate exhausted T cells are available, strategies to rejuvenate terminally differentiated senescent lymphocytes are yet to be developed. Senescent T cells, with short telomeres and inactive telomerase, are different from exhausted cells, and may form due to defective telomere transfer reactions upon contact with antigen presenting cells (APCs). Senescent T cells are characterized by presence of sestrin-MAPK kinase activation complexes (sMACs), large immune-inhibitory protein assemblies of sestrins bound to a stress/energy sensing kinase (AMPK) and three functional effector kinases (ERK, JNK and p38 MAPKs). Here we described first in class Disruptors of the Sestrin-MAPK immune-inhibitory Complex (DOS), which target sMAC to ubiquitin-dependent proteasomal degradation, resulting in long-term sestrin transcriptional inhibition, increased T cell fitness, and generation of long-lived stem like memory features. Strikingly, the DOS generated stem T cells present de novo antigen-specific T-cell receptor DNA rearrangements that precede their future expansion. Although largely senescent at the point of treatment, the DOS regenerated T cells, with stem features and new TCRs, initiated immune-protective rejuvenation-dependent responses to new challenges, with or without vaccination. Therefore, it is possible to generate new T cell clones from formerly senescent cells and expand immune specificity. HighlightsO_LIDOS are the first sestrin-MAPK binding disruptors C_LIO_LIDOS rejuvenate T cells (DOS-juvenation) C_LIO_LIDOS-juvenated T cells protect old mice from lethal infections, with or without vaccination C_LIO_LIDOS-juvenated T cells exist as stem-like cells that undergo antigen-specific TCR revisions C_LI

immunology↗

Novel structural insights on full-length human RAD52: Cryo-EM and beyond

Human RAD52 is a DNA-binding protein involved in many DNA repair mechanisms and genomic stability maintenance. In the last few years, this protein was discovered to be a promising novel pharmacological target for anticancer synthetic lethality strategies since its inhibition or modulation, under specific genetic conditions, was proved to enhance therapies efficacy in various cancer cell types. Although the interest in RAD52 has exponentially grown in the last decade, most information about its structure and mechanism of action is still missing. This work provides novel insights into full-length RAD52 (RAD52 FL) protein, focusing on its structural and functional characterization. The Cryo-Electron Microscopy (Cryo-EM) structure of RAD52 FL, here presented at a resolution (2.16 [A]) higher than the one currently available for RAD52 N-terminal X-ray structure, allows hypothesizing the role of individual amino acid residues. While the N-terminal region of RAD52 FL is structured in an undecameric ring, the C-terminal part is intrinsically disordered as fully characterized through SAXS and biophysical analyses. These detailed (atomic level) structural analyses will substantially impact future characterizations of RAD52 mechanisms of action and inhibitors development, particularly in the context of novel approaches to synthetic lethality.

biophysics↗

RAD51 nuclear recruitment and inhibition towards innovative strategies against pancreatic cancer

RAD51, a key player in the homologous recombination (HR) mechanism, is a critical protein to preserve genomic stability. BRCA2, upon DNA damage, promotes RAD51 fibrils disassembly and its nuclear recruitment. Here, we use BRC4, a peptide derived from the fourth BRC repeat of BRCA2; BRC4 induces RAD51 defibrillation through a domino effect, eroding fibrils from their termini, and yielding monomeric RAD51. The congruence among several techniques (static and dynamic light scattering, negative staining transmission electron microscopy (TEM), and microscale thermophoresis) allows an accurate estimation of the kinetic and thermodynamic parameters of this process. BRC4 lacks, however, a nuclear localization sequence; therefore, it cannot transport RAD51 into the nucleus, thus behaving as a RAD51 inhibitor. Cellular assays (BxPC-3, pancreatic cancer cells) indeed show that BRC4 efficiently inhibits HR and enhances the cytotoxic effect of cisplatin, a DNA-damaging drug. The present study sheds further light on the complexity of the HR pathway, paving the way for designing peptide and small organic molecule inhibitors of RAD51 as innovative anticancer and chemo/radiosensitizer compounds.

biophysics↗

Lisen&Curate: A platform to facilitate knowledge tools for curation of regulation of transcription initiation in bacteria

The amount of published papers in biomedical research makes it rather impossible for a researcher to keep up to date. This is where machine processing of scientific publications could contribute to facilitate the access to knowledge. How to make use of text mining capabilities and still preserve the high quality of manual curation, is the challenge we focused on. Here we present the Lisen&Curate system designed to enable current and future NLP capabilities within a curation environment interface used in curation of literature on the regulation of transcription initiation in bacteria. The current version extracts regulatory interactions with the corresponding sentences for curators to confirm or reject accelerating their curation. It also uses an embedded metrics of sentence similarity offering the curator an alternative mechanism of navigating through semantically similar sentences within a given paper as well as across papers of a pre-defined corpus of publications pertinent to the task. We show results of the use of the system to curate literature in E. coli as well as literature in Salmonella. A major advantage of the system is to save as part of the curation work, the precise link for every curated piece of knowledge with the corresponding specific sentence(s) in the curated publication supporting it. We discuss future directions of this type of curation infrastructure.

bioinformatics↗

Revisiting the decay of scientific email addresses

Email is the primary means of communication for scientists. However, scientific authors change email address over time. Using a new method, we have calculated that approximately 18% of all authors contact email addresses in MEDLINE are invalid. While an unfortunate number, it is, however, lower than previously estimated. To mitigate this problem, institutions should provide email forwarding and scientific authors should use more stable email addresses. In fact, a steadily growing share already use free private email addresses: 32% of all new addresses in MEDLINE in 2018 were of this kind.

scientific communication and education↗