Biology subjects

Ravera, S.

Publications and source records attributed to Ravera, S..

8 recordsLinked to original sources

bioRxiv2026

Recipient-driven metabolic and epigenetic remodeling of donor hematopoietic cells after transplantation in Fanconi Anemia.

Background Haematopoietic cell transplantation (HCT) restores donor-derived haematopoiesis in Fanconi anaemia (FA) but leaves recipient stromal and other non-haematopoietic cells genetically uncorrected. We investigated to what extent the persistent FA recipient environment influences the metabolic, redox, inflammatory and epigenetic phenotype of donor-derived haematopoietic cells after HCT. Methods Peripheral blood and, when available, bone marrow samples were analysed from healthy donors, patients with FA before and after HCT, and severe aplastic anaemia (SAA) patients after HCT as transplant controls. Mitochondrial function, cellular energy status, oxidative damage, antioxidant responses and circulating cytokines were assessed. Healthy donor mononuclear cells were exposed to conditioned media from FANCA-deficient mesenchymal stromal cells or FA fibroblasts, with FANCA-corrected fibroblasts as controls. DNA methylation profiling, acute inflammatory stimulation and pharmacological targeting of inflammatory pathways or mitochondrial oxidative stress were also performed. Results Despite stable full donor chimerism, FA recipients retained a pro-inflammatory and pro-oxidative circulating environment after HCT that was not observed in SAA transplant controls. Donor-derived mononuclear cells exposed to this environment acquired a distinct dysfunctional phenotype characterized by impaired mitochondrial oxidative phosphorylation and energy homeostasis, compensatory antioxidant and stress-response activation, and persistent lipid and protein oxidation. These alterations remained detectable after 96 h of ex vivo culture, suggesting relatively stable cellular remodelling, and were accompanied by a DNA methylation profile that, although globally shifted toward the donor state, retained an intermediate FA-associated episignature. Mechanistically, conditioned media from FANCA-deficient stromal cells and FA fibroblasts reproduced mitochondrial and oxidative abnormalities in healthy donor cells, whereas FANCA-corrected fibroblasts did not. Pharmacological targeting of inflammatory pathways or mitochondrial oxidative stress improved energy homeostasis and reduced oxidative damage, supporting a contributory role for chronic inflammation and oxidative stress in the microenvironment-driven phenotype acquired by donor-derived cells. Conclusions HCT corrects FA haematopoiesis without fully normalising the recipient environment. Persistent exposure to the FA milieu promotes metabolic, redox, signalling and epigenetic remodelling of donor-derived haematopoietic cells after transplantation. These findings identify the recipient environment as a determinant of post-HCT cell biology and highlight chronic inflammation and oxidative stress as mechanisms contributing to donor-cell remodelling in FA.

cell biology↗

bioRxiv2026

Convergent IGHV3-53/3-66 antibodies elicited by Omicron BA.1 infection broadly neutralize emerging SARS-CoV-2 variants

Natural SARS-CoV-2 infections or vaccinations induce neutralizing antibodies (nAbs) offer protection from severe disease. The shared use of IGHV3-53/3-66 genes makes this class of monoclonal antibodies (mAbs) a public clonotype and is well established, but the evolution and structural basis of how these public antibodies maintain broad binding and acquire potent neutralizing activity is not completely understood. To understand how these features are facilitated by the IGHV3-53/3-66 germline segments and enhanced by somatic mutations, we investigated the biology of a panel of 242 human mAbs isolated from an individual infected with SARS-CoV-2 BA.1 strain and recovered. Interestingly, a mAb designated COV2-3731 encoded by IGHV3-53/IGKV1-33 retained potent neutralizing activity against SARS-CoV-2 variants BA.2.86, JN.1, KP.2, BA.3.2, and, to some extent, KP.3. Studies using deep mutational scanning with a BA.2 lentiviral library and determination of the structural complex of the BA.2 S protein and COV2-3731 Fab fragments using cryo-EM revealed key contact residues. Further, germline revertant analysis of the COV2-3731 mAb provided additional insights into how this COV2-3731 and other IGHV3-53/3-66-encoded public antibodies evolve to gain breadth against antigenically distinct SARS-CoV-2 variants such as BA.2.86, JN.1, KP.2, and BA.3.2.

immunology↗

bioRxiv2025

miR-29a-3p and TGF-beta Axis in Fanconi Anemia: Mechanisms Driving Metabolic Dysfunction and Genome Stability

Fanconi anemia (FA) is a rare genetic disorder characterized by bone marrow failure and cancer susceptibility due to defective DNA double-strand break repair. However, FA cells are also characterized by mitochondrial dysfunction and redox imbalance. To identify a common factor among these alterations, we focused on miR-29a-3p, a microRNA involved in hematopoiesis. Our data show that miR-29a-3p is downregulated in lymphoblasts and fibroblasts mutated for the FANC-A gene, causing the overexpression of its target genes, FOXO3, SGK1, and IGF1, which results in PI3K/AKT pathway hyperactivation, altered mitochondrial metabolism and insufficient antioxidant response. Furthermore, miR-29a-3p downregulation appears associated with hyperactivation of the TGF-{beta} signal. However, restoring miR-29a-3p expression improves mitochondrial metabolism, oxidative stress response, and DNA damage repair by inhibiting the PI3K/AKT pathway and modulating TGF-{beta} signaling by a feedback mechanism. Based on these findings, miR-29a-3p appears as a promising molecular target to address several mechanisms based on FA pathogenesis.

cell biology↗

bioRxiv2022

Structural insights into sodium/iodide symporter (NIS) substrate binding and specificity

The sodium/iodide symporter (NIS) is the essential plasma membrane protein that mediates active iodide (I-) transport into the thyroid gland, the first step in the biosynthesis of the thyroid hormones--the master regulators of intermediary metabolism. NIS couples the inward translocation of I- against its electrochemical gradient to the inward transport of Na+ down its electrochemical gradient. For nearly 50 years before its molecular identification, NIS was already the molecule at the center of the single most effective internal radiation cancer therapy ever devised: radioiodide (131I-) treatment for thyroid cancer. Mutations in NIS cause congenital hypothyroidism, which must be treated immediately after birth to prevent stunted growth and cognitive deficiency. To date, the structure of NIS has been unknown. Here, we report three structures of rat NIS, determined by single-particle cryo-electron microscopy (cryo-EM): one with no substrates bound, one with 2 Na+ and 1 I- bound, and one with 1 Na+ and the oxyanion perrhenate bound. Structural analyses, functional characterization, and computational studies reveal the substrate binding sites and residues key for transport activity. Our results yield insights into how NIS selects, couples, and translocates anions--thereby establishing a framework for understanding NIS function--and into how it transports different substrates with different stoichiometries and releases substrates from its substrate-binding cavity into the cytosol.

biophysics↗

bioRxiv2021

IDENTIFICATION OF BIOCHEMICAL AND MOLECULAR MARKERS OF EARLY AGING IN CHILDHOOD CANCER SURVIVORS

PurposeSurvival rates of Childhood Cancer Patients have improved tremendously over the past four decades. However, cancer treatments are associated with an increased risk of developing an anticipated onset of chronic diseases typical of aging. Thus, we aimed to identify molecular/metabolic cellular alterations responsible for early aging in Childhood Cancer Survivors (CCS). Patients and MethodsBiochemical, proteomic and molecular biology analyses were conducted on mononuclear cells (MNCs) isolated from peripheral blood of 196 CCS, comparing the results with those obtained on MNCs of 154 healthy subjects. ResultsData demonstrate that CCS-MNCs show: i) inefficient oxidative phosphorylation associated with low energy status and a metabolic switch to lactate fermentation compared with age-matched normal controls; ii) increment of lipid peroxidation due to an unbalance among the oxidative stress production and the activation of the antioxidant defenses; (iii) significantly lower expression of genes and proteins involved in mitochondrial biogenesis and metabolism regulation, such as CLUH, PGC1-, and SIRT6 in CCS, not observed in the age-matched healthy or elderly subjects. The application of a mathematical model based on biochemical parameters predicts that CCS have a biological age significantly increased by decades compared to the chronological age. Overall, the results show that the impact of chemo/chemoradiotherapy on mitochondria efficiency in 196 CCS was rather homogeneous, irrespective of cancer type, treatment protocols, and time elapsed from the end of the curative period. ConclusionsOur study identifies some biochemical and molecular alterations possibly contributing to the pathophysiology of anticipated aging and metabolic deficiency described in CCS. These results may be useful in identifying approaches to restore the mitochondrial function, slowing down the aging and the associated pathological conditions in CCS.

cancer biology↗

bioRxiv2020

Computational quantification of global effects induced by mutations and drugs in signaling networks of colorectal cancer cells.

Colorectal cancer (CRC) is one of the most deadly and commonly diagnosed tumors worldwide. Several genes are involved in its development and progression. The most frequent mutations concern APC, KRAS, SMAD4, and TP53 genes, suggesting that CRC relies on the alteration of different pathways. However, with classic molecular approaches, it is not easy to simultaneously analyze the interconnections between these pathways. For this reason, we propose a computational model based on a huge chemical reaction network to simulate the effects induced on the global signaling associated with CRC by single or multiple concurrent mutations or by drug treatment. This approach displays several advantages. The model can quantify the alteration in the concentration of the proteins connected with the examined mutation. Moreover, working on the global signaling of CRC, it is possible to disclose unexpected interactions between the involved pathways, representing new therapeutic targets. HighlightsO_LIColorectal cancer relates to defects in many different pathways within cell signaling C_LIO_LICell signaling is modeled as a chemical ration network with 10 interacting pathways C_LIO_LIGlobal effects induced by single or multiple concurrent mutations are quantified C_LIO_LIA possible extension of the model to account for a targeted drug is discussed C_LI

cancer biology↗

bioRxiv2020

Commonalities and differences in the Oxidative Phosphorylation of Mitochondria and Neuronal Membranes.

Mitochondria are considered the exclusive site of aerobic metabolism. However, in recent years, the functional expression of the oxidative phosphorylation (OxPhos) machinery has been reported in several other membranous structures, including the plasma membrane, endoplasmic reticulum, nucleus, myelin sheath and disks of rod outer segments. Thus, to underline commonalities and differences between extra-mitochondrial and mitochondrial aerobic metabolism, we characterized the aerobic ATP synthesis in isolated myelin sheath (IM) and rod outer segment (OS) disks, using mitochondria-enriched fractions, as a positive control. Oxygen consumption and ATP synthesis were evaluated in the presence of conventional (pyruvate + malate or succinate) and unconventional (NADH) substrates. ATP synthesis was also assayed in the presence of 10-100 {micro}M ATP in the assay medium. Data show that IM and OS disks consumed oxygen and synthesized ATP both in the presence of conventional and unconventional respiratory substrates, while the mitochondria-enriched fraction did not utilize NADH. Only in mitochondria, ATP synthesis was progressively lost in the presence of increasing ATP concentrations. Conversely, only myelin sheath and rod OS disks produced ATP at a later time or after the removal of respiratory substrates, reflecting their ability to accumulate energy and this opens up exciting perspectives in the study of sleep. Thus, these data suggest that the extramitochondrial OxPhos in IM and rod OS displays a different behavior concerning the classic mitochondrial aerobic metabolism, representing a possible basic molecular process involved in the physiology of the nervous system. Significance StatementMitochondria are considered the cell powerhouse, being the site of the oxidative phosphorylation (OxPhos), which produces the major part of cellular chemical energy by oxygen consumption. However, proteomics, microscopy, and biochemical analyses have described the ectopic functional expression of the OxPhos machinery also in other membranous structures, such as isolated myelin (IM) and rod outer segments (OS). The results reported in this work shows that, although the proteins involved in IM and rod OS OxPhos appear the same expressed in mitochondria, the comparison of mitochondrial and extramitochondrial OxPhos display some differences, opening a new scenario about the energy metabolism modulation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/953729v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@126f50eorg.highwire.dtl.DTLVardef@a297dcorg.highwire.dtl.DTLVardef@9ff2fforg.highwire.dtl.DTLVardef@10a46be_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2019

FANCD2 tunes the UPR preventing mitochondrial stress-induced common fragile site instability.

Common fragile sites (CFSs) are genomic regions frequently involved in cancer-associated rearrangements. Most CFSs lie within large genes, and their instability relies on transcription- and replication-dependent mechanisms. Here, we uncover a role for the UBL5-dependent branch of the unfolded protein response pathway (UPR) in the maintenance of CFS stability. We show that genetic or pharmacological UPR activation induces CFS gene expression and concomitant relocalization of FANCD2, a master regulator of CFS stability, to CFSs. Furthermore, a genomic analysis of FANCD2 binding sites identified an enrichment for mitochondrial UPR transcriptional response elements in FANCD2 bound regions. We demonstrated that depletion of FANCD2 increases CFS gene transcription and their instability while also inducing mitochondrial dysfunction and triggering the activation of the UPR pathway. Depletion of UBL5, a mediator of the UPR, but not ATF4, reduces CFS gene expression and breakage in FANCD2-depleted cells. We thus demonstrate that FANCD2 recruitment and function at CFSs depends on transcription and UPR signaling, and in absence of transcription or UBL5, FANCD2 is dispensable for CFS stability. We propose that FANCD2 coordinates nuclear and mitochondrial activities by tuning the UPR to prevent genome instability.

cell biology↗