Biology subjects

Moscona, R.

Publications and source records attributed to Moscona, R..

4 recordsLinked to original sources

bioRxiv2025

HIV-1 infection of human microglia activates inflammatory pathways associated with HIV-associated neurocognitive disorders (HAND)

HIV-associated neurocognitive disorders (HAND) cause significant dysfunction among people living with HIV. Microglia are the primary immune cells of the central nervous system and are readily infected by HIV. Microglia are thought to contribute to neuroinflammation and cognitive dysfunction in neurodegenerative diseases such as Alzheimers Disease and are likely to play an important role in the pathogenesis of HAND. In order to identify pathways that may contribute to neuropathogenesis in HAND, we infected induced pluripotent stem cell-derived microglia (iMG) with HIV and defined gene expression changes over an 8-day period. Monocyte-derived macrophages (MDMs) were studied in parallel to identify common pathways stimulated in myeloid cells versus the unique aspects of microglia infection. Infection of iMG led to the induction of a robust early inflammatory response triggered within hours of infection, a pattern that differed significantly from that seen in MDMs. Remarkably, gene expression changes in iMG reproduced many of the characteristic genetic signatures previously identified in brain tissues obtained from individuals clinically diagnosed with HAND. Inflammatory activation representing interferon-mediated signaling, TNF/NF-{kappa}B, and IL-6/JAK/STAT pathways were particularly prominent over the time course of infection. Interferon-mediated signaling led to enhanced expression of multiple HIV restriction factors, yet viral replication in iMG remained robust. These findings suggest that HIV infection of microglia is the key cellular driver of neuroinflammation in the CNS of HIV-infected individuals. Further studies of infected microglia are likely to aid in understanding the pathogenesis of HAND and in evaluating therapeutic strategies to limit or eliminate HIV-induced neuropathogenesis. Author SummaryPersons living with HIV frequently develop debilitating problems with brain function that are collectively known as HIV-associated neurocognitive disorders (HAND). Treatment with antiretroviral drugs to control HIV has largely eliminated the most severe form of HIV-related brain dysfunction, HIV encephalitis, but a significant proportion of HIV-infected individuals receiving antiviral therapy still develop significant problems with cognitive function. Microglia are the major macrophage-like cells of the brain and are highly susceptible to HIV infection. Inflammation in the brain following infection contributes to damage to neurons and is the likely source of decline of brain function. This study used microglia that were derived from induced pluripotent stem cells, termed iMG, to study the kinetics of gene expression changes in HIV-infected microglia and compared those changes to those seen in monocyte-derived macrophages (MDMs). iMG were found to be easily infected with a macrophage-tropic HIV strain and exhibited a rapid increase in gene expression associated with inflammatory signaling through interferon- and tumor necrosis factor/NF-kappa B-mediated pathways. Remarkably, the patterns of gene expression in microglia strongly overlapped with gene expression signatures derived from brain tissue samples of HIV patients with HAND. The rapid onset and magnitude of inflammation as well as induction of specific HIV restriction factors differed from that seen in infected macrophages/MDMs. These studies reinforce the central role of microglia in the pathogenesis of HAND and provide insights into HIV-microglia interactions that can help direct interventions to reduce inflammation and preserve brain function.

microbiology↗

bioRxiv2024

Novel Amplicons based Method for Near-Full-Length Genome (NFLG) Sequencing of HIV-1 Group M Recombinant Forms

Over the years the spread of HIV-1 across the globe resulted in the creation of multiple subtypes and new recombinant forms (RFs). While the pol gene region of the HIV-1 genome is used for resistance mutations analysis and initial detection of RFs, whole genome sequencing analysis is required to determine recombination events across the viral genome. Here, we present a novel robust near-full length genome (NFLG) sequencing approach for the sequencing of HIV-1 genomes, out of clinical whole blood samples. This method has been successfully tested for various HIV-1 subtypes and RFs. The method is based on an in-house developed set of 32 pan-genotypic primer pairs, divided into two pools, each containing 16 primer pairs covering the entire HIV-1 genome. Two parallel multiplex PCR reactions were used to generate 32 overlapping DNA fragments spanning the HIV-1 genome. Nextera XT protocol was used to obtain barcoded DNA libraries, which were sequenced with the Illumina Miseq platform using a V3 kit. A consensus sequence was determined for each sample and was used to define recombination events across the genome. For this aim, a combined analysis of several computational tools including HIV BLAST, phylogenetic analysis, RIP, SimPlot++ and jpHMM were employed. Overall, plasma samples from 33 patients suspected to carry RFs and 2 different, known pure subtypes controls, were included in this study. Genome coverage varied between RFs, while the gag and pol genes were nearly fully covered, the highly variable env gene region was not. Yet, these NFLG analyses enabled the identification of recombination events genome wide. In summary, we describe a methodology for HIV-1 NFLG sequencing, which is based on partially overlapping, multiple PCR fragments, spanning the HIV-1 genome. Additionally, this newly refined method was compared to HIV-1 NFLG results of PCR-free metagenomic sequencing and proved to obtain greater coverage of the HXB2 reference genome. Yet, further testing and validation on a larger cohort is required. Still, this method enables sequencing of 20 different patient samples in a single MiSeq sequencing run and was used for the characterization of different HIV-1 RFs and pure subtypes circulating in Israel.

molecular biology↗

bioRxiv2022

ATAC-Seq and RNA-Seq combined analysis elucidates the impact of BORIS/CTCFL on melanoma progression, mediated by chromatin accessibility and gene expression alterations

Melanoma is the deadliest form of skin cancer, due to its tendency to metastasize early. Brother of Regulator of Imprinted Sites (BORIS), also known as CCCTC binding factor-Like (CTCFL), is a transcription regulator that becomes ectopically expressed in melanoma. We recently showed that BORIS contributes to melanoma phenotype switching by altering the gene expression program of proliferative melanoma cells in favor of a more invasive phenotype. However, how BORIS alters the transcriptome remains unclear. Here, ATAC-seq was used to study BORIS-mediated chromatin accessibility alterations in proliferative melanoma cells. Genes that gained promoter accessibility following ectopic BORIS expression, were enriched for melanoma-specific invasive genes as well as invasion-associated biological processes, while promoters of genes associated with proliferation show reduce accessibility. Integration of ATAC-Seq and RNA-Seq data demonstrates that increased chromatin accessibility is associated with transcriptional upregulation of genes involved in tumor progression processes, and the aberrant activation of oncogenic transcription factors, while reduced chromatin accessibility and downregulated genes, were associated with repressed activity of tumor suppressors. Together, these findings indicate that BORIS mediates transcriptional reprogramming in melanoma cells by altering chromatin accessibility and gene expression, shifting the cellular transcription landscape of proliferative melanoma cells towards a pro-invasive genetic signature. SignificanceWe recently reported that BORIS contributes to melanoma phenotype switching by altering the transcriptional landscape of melanoma cells from a proliferative to an invasive state. In this study, using ATAC-Seq, we demonstrate that ectopic BORIS expression in proliferative melanoma cells leads to increased chromatin accessibility at promoters of upregulated invasion-associated genes. Importantly, by integrating the ATAC-Seq data with RNA-Seq data, we were able to identify key cancer-associated transcription factors that become aberrantly activated or repressed following ectopic BORIS expression. Taken together, this study sheds light on the mechanisms by which BORIS mediates phenotype switching in melanoma cells.

cancer biology↗

bioRxiv2019

BORIS/CTCFL promotes a switch from a proliferative towards an invasive phenotype in melanoma cell lines

Melanoma is among the most aggressive cancers due to its tendency to metastasize early. Phenotype switching between a proliferative and an invasive state has been suggested as a critical process for metastasis. The mechanisms that regulate these transitions are poorly understood, but are associated with transcriptional changes. Brother of Regulator of Imprinted Sites (BORIS), also known as CCCTC binding factor-Like (CTCFL), is a transcriptional modulator that becomes aberrantly expressed in melanoma. Here, we provide the first evidence that BORIS is involved in phenotype switching in melanoma. Genetic modification of BORIS expression in melanoma cells combined with whole transcriptome analysis indicated that BORIS expression contributes to an invasion-associated transcriptome. In agreement with this finding, inducible BORIS overexpression in melanoma cells reduced proliferation and increased migration and invasion, demonstrating that the transcriptional switch is accompanied by a phenotypic switch. Overall, our study indicates a pro-invasive role for BORIS in melanoma via transcriptional reprogramming.

cancer biology↗