Biology subjects

Merelli, I.

Publications and source records attributed to Merelli, I..

13 recordsLinked to original sources

bioRxiv2026

A genetic anemia disentangles the dual effect of chronically reduced thrombopoietin on hematopoietic stem cells and bone marrow niche

Many studies unraveled the reciprocal regulation between hematopoietic stem cells (HSC) and the bone marrow (BM) niche by using transgenic knock-out or reporter mice, often overlooking the pathophysiological relevance and the existence of compensatory mechanisms. Here, we exploit the th3 murine model of a genetic anemia, beta-thalassemia (BThal), to investigate the dual impact of chronically reduced thrombopoietin (TPO) production on HSC and megakaryocytic BM niche. Decreased systemic TPO downregulates stemness programs in HSC and impairs their commitment towards megakaryocytes (Mk). We uncover dysmegakaryopoiesis in the BM from BThal patients and mice with defective Mk maturation and reduced production of niche factors, altering the HSC-niche crosstalk. Notably, in vivo stimulation of the TPO signaling restores HSC quiescence, Mk maturation and niche support. These findings demonstrate that TPO regulates HSC through both direct and niche-mediated routes, underscoring the value of using a genetic disease model to disentangle general molecular mechanisms.

cell biology↗

bioRxiv2026

Glia-enriched human brain organoids for studying developmental alterations in leukodystrophies

Leukodystrophies (LKD) comprise mostly inherited white matter disorders whose developmental origins and underlying pathomechanisms remain poorly understood. Progress has been limited by restricted access to human primary tissue and by the inability of animal models to fully recapitulate human neurodevelopment. Human induced pluripotent stem cell-derived neural organoids provide an alternative approach, but most culture systems do not capture later, glia-rich developmental stages relevant to these diseases. Recent studies have shown that appropriate patterning cues and long in vitro differentiation can generate neuroglial spheroids comprising multiple neuronal and macroglial populations, including mature oligodendrocytes. Here, we adapt the human oligodendrocyte (hOLS) spheroid platform to establish 3D models of globoid cell leukodystrophy (GLD), 4H leukodystrophy (4H), and Canavan disease (CD). Here we adapt this organoid platform to establish 3D models of globoid cell leukodystrophy (GLD), 4H leukodystrophy (4H), and Canavan disease (CD). Across 150 days of differentiation, hOLS from different genetic backgrounds displayed largely comparable growth kinetics and developmental trajectories, comprising multiple neuroglial cell types with predominantly ventral forebrain and midbrain identities. Comparison of LKD and control hOLS revealed both shared and disease-specific alterations, with prominent transcriptional changes in lysosomal, metabolic, and stress-response pathways. Lineage-resolved pathway analysis further identified signatures across individual LKDs, including mitochondrial and translational stress in GLD glial lineages, disruption of RNA metabolic and cell-cycle pathways in 4H, and prominent astrocyte-centered metabolic dysregulation in CD. Our results establish hOLS as a human 3D in vitro platform for studying the impact of LKD-associated genetic variants on early neural development and for dissecting lineage-specific disease vulnerability.

neuroscience↗

bioRxiv2026

Locus-specific transposable element expression drives human hematopoietic stem cell disease pathophysiology

VEXAS syndrome (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) is a severe, inflammatory syndrome resulting from mutated UBA1 leading to hematopoietic stem cells (HSC) expansion. Although UBA1-mutant HSC show complex phenotypes including proteostasis defects, sustained inflammation and clonal expansion of myeloid biased progeny, the pathogenic mechanisms at the HSC level are unknown from these gene-centric studies alone. By focussing on the non-coding genome and using advanced functional genetic methods, we found that VEXAS HSC, compared to controls, had altered expression of individual transposable elements (TE) and are key regulators of VEXAS pathogenesis. Locus-specific TE quantification identified two L1 elements, L1-10 and L1-15, active in both normal and VEXAS HSC that drive myeloid commitment by co-opting SPI1 and IRF1 transcription factors (TF) via networks common to other myeloid-biased conditions. Lipid nanoparticle (LNP)-mediated CRISPRi of L1-10 and L1-15 in UBA1-mutant HSC also caused reversion of VEXAS-associated functional phenotypes in vitro and in vivo. Functionally, pharmacologic inhibition of UBA1 with TAK-243 led to L1-10 and L1-15 RNA accumulation, while enhancement of UBA1 activity with Auranofin reversed this effect. Our study provides direct evidence that VEXAS-specific TE govern HSC clonal dominance, thereby uncovering a regulatory axis underlying HSC biology and disease mechanisms, opening a therapeutic strategy directed towards the repetitive genome.

genetics↗

bioRxiv2026

Ex Vivo Expansion of Hematopoietic Stem and Progenitor Cells from Human Mobilized Peripheral Blood for Gene Therapy Applications

Ex vivo expansion of mobilized peripheral blood (mPB) hematopoietic stem cells (HSCs) represents a promising approach to advance cell and gene therapy strategies yet is hampered by loss of stem cell function when applying commonly used culture protocols. We performed in-depth characterization of mPB expansion cultures by single cell RNA sequencing, which highlighted differentiation trajectories with preservation of lineage fidelity in committed progenitors. Defining a putative HSC cluster allowed an estimation of transduction efficiency in ex vivo cultures, which correlated with long-term gene marking in xenografts and patients enrolled in a gene therapy study. We then developed a clinically translatable, GMP-compliant process to expand lentivirus (LV)-transduced HSCs from mPB of pediatric patients and adult donors, by biologically informed protocol improvements of cytokine supplementation, media choice, timing of LV transduction and combinations of small molecules preventing the activation of differentiation programs. Our optimized process outperforms validated state-of-the-art cord blood expansion protocols when applied to mPB. LV integration site analysis and genomic barcode-based clonal tracking provided definitive proof for symmetric HSC self-renewal divisions occurring during ex vivo culture. These results warrant clinical testing of this HSC transduction/expansion process in an upcoming clinical gene therapy trial for autosomal recessive osteopetrosis (EU CT 2024-518972-30). One Sentence SummaryA mobilized peripheral blood HSC expansion protocol optimized for gene therapy allows robust polyclonal long-term engraftment of LV-transduced cells.

cell biology↗

bioRxiv2026

Landscape of 8q24.3-Encoded microRNAs and Their Prognostic Impact in Ovarian Cancer

Ovarian cancer is the most lethal gynecological malignancy, largely because of late diagnosis and marked genomic instability, with high-grade serous ovarian cancer (HGSOC) representing its most common and aggressive subtype. Amplification of chromosome 8q24.3 is a recurrent event in HGSOC, yet the regulation and clinical relevance of the non-coding RNA output from this locus remain poorly defined. Here, we performed an integrative analysis of 8q24.3-encoded miRNAs in ovarian cancer using copy-number, transcriptomic, isoform-resolved, and clinical data from TCGA and NCBI datasets. We identified pronounced heterogeneity in miRNA abundance and strand usage across this locus. Copy-number gain broadly associated with increased miRNA expression, although this effect was not uniform across all candidates. Intronic miRNAs showed variable coupling with their host genes, indicating that mature miRNA output is shaped by both genomic dosage and post-transcriptional regulation. Isoform-level analysis revealed marked strand asymmetry and regulatory complexity, but did not strengthen copy-number or histotype associations compared with total miRNA measurements. Clinically, higher expression of miR-937, miR-4664, and miR-6849 was associated with improved overall survival in HGSOC. Functional enrichment of validated targets highlighted pathways related to cellular stress responses, senescence, p53 signaling, endocytosis, and metabolic adaptation. Together, these findings define 8q24.3 as a heterogeneous non-coding regulatory hub in ovarian cancer and provide a basis for future mechanistic and biomarker studies.

bioinformatics↗

bioRxiv2023

Human iPSC-derived neural stem cells display a radial glia-like signature in vitro and favorable long-term safety in transplanted mice

Human induced pluripotent stem cell-derived neural stem/progenitor cells (hiPSC-NSCs) are a promising source for cell therapy approaches to treat neurodegenerative and demyelinating disorders. Despite ongoing efforts to characterize hiPSC-derived cells in vitro and in vivo, we lack comprehensive genome- and transcriptome-wide studies addressing hiPSC-NSC identity and safety, which are critical for establishing accepted criteria for prospective clinical applications. Here, we evaluated the transcriptional and epigenetic signatures of hiPSCs and differentiated hiPSC-NSC progeny, finding that the hiPSC-to-NSC transition results in a complete loss of pluripotency and the acquisition of a radial glia-associated transcriptional signature. Importantly, hiPSC-NSCs share with somatic human fetal NSCs (hfNSCs) the main transcriptional and epigenetic patterns associated with NSC-specific biology. In vivo, long-term observation (up to 10 months) of mice intracerebrally transplanted as neonates with hiPSC-NSCs showed robust engraftment and widespread distribution of human cells in the host brain parenchyma. Engrafted hiPSC-NSCs displayed multilineage potential and preferentially generated glial cells. No hyperproliferation, tumor formation, or expression of pluripotency markers was observed. Finally, we identified a novel role of the Sterol Regulatory Element Binding Transcription Factor 1 (SREBF1) in the regulation of astroglial commitment of hiPSC-NSCs. Overall, these comprehensive in vitro and in vivo analyses provide transcriptional and epigenetic reference datasets to define the maturation stage of NSCs derived from different hiPSC sources, and to clarify the safety profile of hiPSC-NSCs, supporting their continuing development as an alternative to somatic hfNSCs in treating neurodegenerative and demyelinating disorders.

neuroscience↗

bioRxiv2023

CD32 allows capturing blood cells emergence in slow motion during human embryonic development

During development, in the embryo proper blood cells emerge from a subset of specialized endothelial cells, named hemogenic endothelial cells (HECs), via a process known as endothelial-to-hematopoietic transition (EHT) driven by time-specific Notch signaling activation1. HECs represent an elusive cell population as they are rare and transient, rapidly generating blood cells, and specific markers are lacking. Therefore, it remains unclear how and when the hematopoietic fate is specified and how blood cell emergence is molecularly regulated. Notably, thorough characterization of this process is essential to guide the generation of therapeutic blood products in vitro from human pluripotent stem cells (hPSCs). To identify specific human HEC markers, we performed transcriptomic analysis of 28-32-day human embryos, a developmental stage characterized by active hematopoiesis. We observed that the expression of FCGR2B, encoding for the Fc receptor CD32, is highly enriched in the ACE+CD34+ endothelial cell population that contains HECs. Functional ex vivo analyses confirmed that multilineage hematopoietic potential is highly enriched in CD32+ endothelial cells isolated from human embryos. In addition, clonal analysis revealed that 90% of CD32+ hPSC-derived endothelial cells are bona fide HECs. We leveraged this specificity to study how HECs commit to the blood fate. Remarkably, our analyses indicated that HECs progress through different states culminating with the one identified by CD32 expression. Indeed CD32+ HECs no longer require Notch to generate hematopoietic progeny and display full commitment to hematopoiesis even before the expression of hematopoietic markers. These findings provide a precise method for isolating HECs primed to the blood fate from human embryos and hPSC cultures, thus allowing the efficient generation of hematopoietic cells in vitro.

developmental biology↗

bioRxiv2022

Therapy-induced senescence upregulates antigen presentation machinery and triggers anti-tumor immunity in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is an aggressive hematological malignancy often curable only by using intensive chemotherapy. Nonetheless, resistance/early relapses are frequent, underscoring the need to investigate the molecular events occurring shortly after chemotherapy. Therapy-induced senescence (TIS) is a fail-safe tumor suppressive mechanism that may elicit immune-mediated responses contributing to senescent cell clearance. Yet, TIS functional role in AML eradication and immune surveillance early post-chemotherapy remains ill-defined. By combining transcriptional and cellular-based evaluation of senescence markers in AML patient samples, we found upregulation of senescence-associated genes and interferon gene categories with concomitant induction of HLA class I and class II molecules, pointing to a causal link between TIS and leukemia immunogenicity. Consistently, senescence-competent AML samples activated autologous CD4+ and CD8+ T cells and improved leukemia recognition by both T-cell subsets. Lastly, the anti-leukemic activity of Immune Checkpoint Blockades (ICBs) was enhanced upon senescence engagement in AML. Altogether, our results identify senescence as a potent immune-related anti-leukemic mechanism that may rapidly translate into innovative senescence-based strategies to prevent AML relapse. STATEMENT OF SIGNIFICANCEOur findings uncover a novel link between senescence induction and leukemia immune recognition by T cells via upregulation of antigen presentation machinery components, providing the basis for conceptually novel senescence-based targeted immunotherapeutic regimens for AML patients.

cancer biology↗

bioRxiv2022

Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition

Within the chromatin, distal elements interact with promoters to regulate specific transcriptional programs. Histone acetylation, interfering with the net charges of the nucleosomes, is a key player in this regulation. Here, we report that the onco-protein SET is a critical determinant for the levels of histone acetylation within enhancers. We disclose that conditions in which SET is accumulated, including the severe Schinzel-Giedion Syndrome (SGS), are characterized by a failure in the usage of the distal regulatory regions typically employed during fate commitment. This is accompanied by the usage of alternative enhancers leading to a massive rewiring of the distal control of the gene transcription. This represents a (mal)adaptive mechanism that, on one side, allows to achieve a certain degree of differentiation, while on the other affects the fine and corrected maturation of the cells. Thus, we propose the differential in cis-regulation as a contributing factor to the pathological basis of the SET-related disorders in humans, including SGS, neurodevelopmental disorders, myeloproliferative diseases, and cancer.

developmental biology↗

bioRxiv2022

In vitro selection of Engineered Transcriptional Repressors for targeted epigenetic silencing and initial evaluation of their specificity profile

Gene inactivation is instrumental to study gene function and represents a promising strategy for the treatment of a broad range of diseases. Among traditional technologies, RNA interference suffers from partial target abrogation and requirement for life-long treatments. On the other hand, artificial nucleases can impose stable gene inactivation through induction of DNA Double Strand Breaks, but recent studies are questioning the safety of this approach. Targeted epigenetic editing via Engineered Transcriptional Repressors (ETRs) may represent a solution, as a single administration of specific ETRs combinations can lead to durable silencing without DNA breaks induction. ETRs are proteins containing a programmable DNA Binding Domain (DBD) and effectors from naturally occurring transcriptional repressors. Specifically, a combination of three ETRs equipped with the KRAB domain of human ZNF10, the catalytic domain of human DNMT3A and human DNMT3Lwas shown to induce heritable repressive epigenetic states on the ETR-target gene. The hit-and-run nature of this platform, the lack of impact on the DNA sequence of the target, and the possibility to revert on-demand the repressive state by DNA demethylation, make epigenetic silencing a game-changing tool. A critical step is the identification of the proper position on the target gene where to tether the ETRs in order to maximize on target and minimizing off-target silencing. Performing this step in the final ex vivo or in vivo preclinical setting can be cumbersome. Taking CRISPR-Cas9 system as a paradigmatic DBD for ETRs, here we describe a protocol consisting in the in vitro screen of gRNAs coupled to the triple ETRs combination for efficient on-target silencing, followed by evaluation of the genome-wide specificity profile of top hits. This allows to reduce the initial repertoire of candidate gRNAs to a short list of promising ones, whose complexity is suitable for their final evaluation in the therapeutically relevant setting of interest.

synthetic biology↗

bioRxiv2021

Follicular helper T cell signature of replicative exhaustion, apoptosis and senescence in common variable immunodeficiency

BackgroundCommon variable immunodeficiency (CVID) is the most frequent primary antibody deficiency. A significant number of CVID patients are affected by various manifestations of immune dysregulation such as autoimmunity. Follicular T cells cells are thought to support the development of CVID by providing inappropriate signals to B cells during the germinal center (GC) response. ObjectivesWe determined the possible role of follicular helper (Tfh) and follicular regulatory T (Tfr) cells in patients with CVID by phenotypic, molecular, and functional studies. MethodsWe analyzed the frequency, phenotype, transcriptome, and function of circulating Tfh cells in the peripheral blood of 27 CVID patients (11 pediatric and 16 adult) displaying autoimmunity as additional phenotype and compared them to 106 (39 pediatric and 67 adult) age-matched healthy controls. We applied Whole Exome Sequencing (WES) and Sanger sequencing to identify mutations that could account for the development of CVID and associate with Tfh alterations. ResultsA group of CVID patients (n=9) showed super-physiological frequency of Tfh1 cells and a prominent expression of PD-1 and ICOS, as well as a Tfh RNA signature consistent with highly active, but exhausted and apoptotic cells. Plasmatic CXCL13 levels were elevated in these patients and positively correlated with Tfh1 cell frequency, PD-1 levels, and an elevated frequency of CD21loCD38lo autoreactive B cells. Monoallelic variants in RTEL1, a telomere length- and DNA repair-related gene, were ideintified in four patients belonging to this group. Lymphocytes with highly shortened telomeres, and a Tfh signature enriched in genes involved in telomere elongation and response to DNA damage were seen. Histopathological analysis of the spleen in one patient showed reduced amount and size of the GC that, unexpectedly, contained an increased number of Tfh cells. ConclusionThese data point toward a novel pathogenetic mechanism in a group of patients with CVID, whereby alterations in DNA repair and telomere elongation might be involved in GC B cells, and acquisition of a Th1, highly activated but exhausted and apoptotic phenotype by Tfh cells.

immunology↗

bioRxiv2021

The lysine-rich intracellular loop and cell type-specific co-factors are required for IFITM3 antiviral immunity in hematopoietic stem cells

The interferon-induced transmembrane protein 3 (IFITM3) inhibits lentiviral gene therapy vector entry into hematopoietic stem cells and can be overcome by Cyclosporine H (CsH), but underlying mechanisms remain unclear. Here, we show that mutating the evolutionarily conserved lysines of the IFITM3 intracellular loop abolishes its antiviral activity without affecting either its localization or its degradation by CsH through non-canonical lysosomal pathways. When confined to the plasma membrane, the lysine-competent IFITM3 lost restriction against VSV-G pseudotyped viral vectors but gained antiviral activity against vectors that fuse directly at the plasma membrane. Interestingly, altering the lysines did not alter IFITM3 homodimerization but impacted higher-order protein complex formation, suggesting loss of interaction with cellular co-factors. In agreement, IFITM3 expression was not sufficient to restrict viral vectors in myeloid K562 cells as opposed to promonocytic THP1 or primary HSC. We exclude the involvement of previously identified factors affecting IFITM3 biology and propose a novel model for IFITM3 restriction that depends on the presence of cellular co-factor(s) that may interact with IFITM3 through the intracellular loop lysine residues. Overall, our work provides significant insight into the mechanisms of action of IFITM3 and CsH that can be exploited for improved gene therapies and broadly acting antiviral strategies.

microbiology↗

bioRxiv2017

Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks

Gene and protein networks are very important to model complex large-scale systems in molecular biology. Inferring or reverseengineering such networks can be defined as the process of identifying gene/protein interactions from experimental data through computational analysis. However, this task is typically complicated by the enormously large scale of the unknowns in a rather small sample size. Furthermore, when the goal is to study causal relationships within the network, tools capable of overcoming the limitations of correlation networks are required. In this work, we make use of Bayesian Graphical Models to attach this problem and, specifically, we perform a comparative study of different state-of-the-art heuristics, analyzing their performance in inferring the structure of the Bayesian Network from breast cancer data.

bioinformatics↗