Biology subjects

Fumagalli, M. J.

Publications and source records attributed to Fumagalli, M. J..

5 recordsLinked to original sources

bioRxiv2025

PRISM-Seq: An Ultra-sensitive Sequencing Approach For Mapping Lentiviral Integration Sites

Retroviral integration into host genomes is central to both HIV-1 persistence and the safety and function of lentiviral vectors used in gene and cell therapies. However, existing integration site assays remain limited by sensitivity, input requirements, and analytical complexity, and none have been validated at the single-molecule detection limit. Here, we introduce PRISM-seq, an ultra-sensitive workflow for genome-wide recovery of lentiviral-host junctions, paired with BulkIntSiteR, an open-source, fully automated pipeline for integration site annotation. We show that PRISM-seq accurately identifies proviral insertions across diverse genomic contexts, including euchromatin, heterochromatin, and repeat-rich centromeric regions, and detects high-confidence integration events down to a single input template molecule. By systematically characterizing assay- and amplification-associated noise, we developed a five-step quality control framework that removes PCR- and sequencing-derived artifacts. PRISM-seq also enables quantitative clonal tracking through replicate-based sampling and achieves performance comparable to or exceeding high-input assays at substantially reduced cost.

bioinformatics↗

bioRxiv2025

HIV-1 expression is heterogeneous among clones of CD4+ T cells carrying authentic intact latent proviruses

Antiretroviral therapy suppresses HIV-1 infection but is not curative because it fails to eliminate a reservoir of intact latent proviruses that reside primarily in CD4+ T cells. This compartment is composed of rare T cells that predominantly express memory and effector memory markers. The lack of precise understanding of the latent compartment has made it challenging to develop curative strategies for HIV-1 infection. Here we report on the properties of CD4+ T cells clones carrying intact latent proviruses, expanded in vitro from single cells obtained from the reservoir of people living with HIV-1. The latent proviruses in the clones were integrated into ZNF genes, non-genic satellite and centromeric regions, frequently associated with latency. Notably, the transcriptome of the cultured clones resembled their cells of origin. Despite their descent from single cells, only a fraction of the cells ranging from 0.4-14% expressed relatively low levels of HIV-1 that did not measurably alter host gene transcriptome. Latency reversing agents (LRAs) variably increased the number and amount of expression per cell, but the effects were modest and clone and LRA specific. The results suggest that pharmacologic and immunologic approaches to clear the reservoir should be optimized to accommodate intra- and inter-clonal diversity.

immunology↗

bioRxiv2022

Airway epithelial cells and macrophages trigger IL-6-CD95/CD95L axis and mediate initial immunopathology of COVID-19

Airway epithelial cells (AEC) are the first in contact with SARS-CoV-2 and drive the interface with macrophage to generate inflammation. To elucidate how those initial events contribute to the immunopathology or to dysregulate the immune response observed in severe and critical COVID-19, we determined the direct and indirect interactions of these cells. AEC lineage (Calu-3) infected with SARS-CoV-2 and epithelial cells (CD45-EpCAM+) from intubated COVID-19 patients showed high expression of CD95L. Infected-Calu-3 cells secreted IL-6, and expressed annexin V and caspase-3, apoptosis markers. The direct interaction of macrophages with sorted apoptotic Calu-3 cells, driven by SARS-CoV-2 infection, resulted in macrophage death and increased expression of CD95, CD95L and CD163. Macrophages exposed to tracheal aspirate supernatants from intubated COVID-19 patients or to recombinant human IL-6 exhibited decreased HLA-DR and increased CD95 and CD163 expression. IL-6 effects on macrophages were prevented by tocilizumab (anti-IL-6 receptor mAb) and Kp7-6 (CD95/CD95L antagonist). Similarly, lung inflammation and death of AEC were decreased in CD95 and IL-6 knockout mice infected with SARS-CoV-2. Our results show that the AEC-macrophage interaction via CD95/CD95L signaling is an initial key step of immunopathology of severe COVID-19 and should be considered as a therapeutic target. O_FIG O_LINKSMALLFIG WIDTH=181 HEIGHT=200 SRC="FIGDIR/small/504760v1_ufig1.gif" ALT="Figure 1"> View larger version (88K): org.highwire.dtl.DTLVardef@aadef5org.highwire.dtl.DTLVardef@13d033org.highwire.dtl.DTLVardef@c9c555org.highwire.dtl.DTLVardef@ba821e_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- SARS-CoV-2-infected airway epithelial cells (AEC) secrete IL-6, express Fas/FasL and undergo apoptosis; - SARS-CoV-2-infected apoptotic AEC induces Fas/FasL expression and death in macrophages; - IL-6 induces IL-1{beta} secretion, reduction of HLA-DR and increase of Fas and CD163 expression in macrophages; - Blockade of IL-6 signaling and Fas/FasL restores the expression of HLA-DR and reduces the expression of Fas and CD163, and secretion of IL-1{beta} on isolated macrophages; in vivo, the deficiency of Fas and IL-6 decreases acute pulmonary inflammation in SARS-CoV-2-infected mice.

immunology↗

bioRxiv2019

MKPV (aka MuCPV) and related chapparvoviruses are nephro-tropic and encode novel accessory proteins p15 and NS2

Mouse kidney parvovirus (MKPV) is a member of the provisional Chapparvovirus genus that causes renal disease in immune-compromised mice, with a disease course reminiscent of polyomavirus-associated nephropathy in immune-suppressed kidney transplant patients. Here we map four MKPV transcripts, created by alternative splicing, to a common transcription initiation region, and use mass spectrometry to identify \"p10\" and \"p15\" as novel chapparvovirus accessory proteins produced in MKPV-infected kidneys. p15 and a splicing-dependent putative accessory protein NS2 are conserved in all near-complete tetrapod chapparvovirus genomes currently available (from mammals, birds and a reptile). In contrast, p10 may be encoded only by viruses with >60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that chapparvoviruses with >60% VP1 amino acid identity to MKPV be classified into a genus dubbed Nephroparvovirus, which is consistent with nomenclature for the genus Erythroparvovirus.

microbiology↗

bioRxiv2018

Whole-genome sequencing of parvoviruses from wild and domestic animals in Brazil provides new insights into parvovirus distribution and diversity

AbstractParvoviruses (family Parvoviridae) are small, single-stranded DNA viruses. Many parvoviral pathogens of medical, veterinary and ecological importance have been identified. In this study, we used high-throughput sequencing (HTS) to investigate the diversity of parvoviruses infecting wild and domestic animals in Brazil. We identified 21 parvovirus sequences (including twelve nearly complete genomes and nine partial genomes) in samples derived from rodents, bats, opossums, birds and cattle in Pernambuco, Sao Paulo, Parana and Rio Grande do Sul states. These sequences were investigated using phylogenetic and distance-based approaches, and were thereby classified into eight parvovirus species (six of which have not been described previously), representing six distinct genera in the subfamily Parvovirinae. Our findings extend the known biogeographic range of previously characterized parvovirus species, and the known host range of three parvovirus genera (Dependovirus, Aveparvovirus, and Tetraparvovirus). Moreover, our investigation provides a window into the ecological dynamics of parvovirus infections in vertebrates, revealing that many parvovirus genera contain well-defined sub-lineages that circulate widely throughout the world within particular taxonomic groups of hosts.

microbiology↗