Biology subjects

Lore, N. I.

Publications and source records attributed to Lore, N. I..

5 recordsLinked to original sources

bioRxiv2026

PatHoST: weakly supervised reconstruction of pathogen spatial distributions from host transcriptomes

Dual host-pathogen spatial transcriptomics enables spatially resolved investigation of infection, yet the completeness of pathogen detection remains poorly characterized. Here, we generated pathogen-only spatial transcriptomic sections from a chronic Mycobacterium abscessus lung infection model to experimentally benchmark pathogen detection, revealing substantially increased pathogen transcript recovery compared with conventional dual profiling. Building on these data, we developed PatHoST, a weakly supervised computational framework that uses pathogen-derived information to generate silver-standard labels and learns host transcriptional programs predictive of pathogen presence. PatHoST reconstructed pathogen spatial distributions across independent tissue sections and enabled the identification of localized host regulatory programs beyond conventional cluster-based analyses. Application to human SARS-CoV-2 lung spatial transcriptomics supported generalization across host species and pathogen classes. Together, PatHoST combines purpose-built experimental benchmarking with weakly supervised inference to recover latent pathogen information and extend the analytical capabilities of dual host-pathogen spatial transcriptomics.

bioinformatics↗

bioRxiv2024

Chronic mycobacteria infection triggers macrophage senescence

Chronic infections with intracellular pathogens such as Mycobacterium abscessus (Mab) pose significant health challenges due to their capacity to persist within host cells and evade immune responses. This study investigates the cellular responses to chronic Mab infection in macrophages, particularly focusing on cellular senescence. Using an in vitro model of chronic infection in murine alveolar-like macrophages, we found that Mab induces a senescent phenotype characterised by decreased proliferation, altered morphology, DNA damage signalling activation, and upregulation of senescence markers such as p21 and SA-{beta}-galactosidase. Intriguingly, senescent macrophages secreted pro-inflammatory cytokines, consistent with a senescence-associated secretory phenotype (SASP), which promoted secondary senescence in neighbouring uninfected cells. This paracrine transmission of senescence underscores a potentially deleterious effect of Mab-induced SASP on tissue microenvironments, fostering a pro-inflammatory niche that may contribute to pathogen persistence. These findings highlight Mab-induced senescence as a key factor in chronic infection pathology, suggesting that targeting senescent cells and SASP-related pathways could enhance treatment outcomes in chronic bacterial infections.

microbiology↗

bioRxiv2024

Dual host-bacterial gene expression to study pathogenesis and the regulation of virulence factors in tissue during respiratory infections

Co-localization of spatial transcriptome information of host and pathogen can revolutionize our understanding of microbial pathogenesis. Here, we aimed to demonstrate that customized bacterial probes can be successfully used to identify host-pathogen interactions in formalin-fixed-paraffin-embedded (FFPE) tissues by probe-based spatial transcriptomics technology. We analyzed the spatial gene expression of bacterial transcripts with the host transcriptomic profile in murine lung tissue chronically infected with Mycobacterium abscessus embedded in agar beads. Customized mycobacterial probes were designed for the constitutively expressed rpoB gene (an RNA polymerase {beta} subunit) and the virulence factor precursor lsr2, modulated by oxidative stress. We found a correlation between the rpoB expression, bacterial abundance in the airways, and an increased expression of lsr2 virulence factor in lung tissue with high oxidative stress. Overall, we demonstrate the potential of dual bacterial and host gene expression assay in FFPE tissues, paving the way for the simultaneous detection of host and bacterial transcriptomes in pathological tissues.

microbiology↗

bioRxiv2023

DeltaF508-Cftr mutation in genetically diverse Collaborative Cross mice yields novel disease-relevant phenotypes for cystic fibrosis

Mutations of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) lead to Cystic Fibrosis (CF), but the substantial phenotypic variations are determined by non-CFTR allelic diversity. To map novel disease phenotypes in a CF mouse model, we used Collaborative Cross (CC) mice, a highly genetically diverse mouse resource population.{Delta} F508-Cftr homozygosity produced a fully penetrant lethal phenotype by eight weeks in two CC lines. The lethality of CC006{Delta}F508/{Delta}F508 was fully prenatal while CC037{Delta}F508/{Delta}F508 showed either prenatal or postnatal lethality. Novel phenotypes of CC037{Delta}F508/{Delta}F508 were revealed early in life including respiratory and systemic inflammatory profiles, and blood, bone marrow, pancreas, heart, and reproductive tract pathologies. Severe intestinal blockage was observed as common in other CF mouse models. These results suggest that the exploration of CF disease phenotypes in a mouse population with diverse genetic profiles is needed to map the genetic origin of currently unidentified disease traits and their potential translation to humans.

pathology↗

bioRxiv2022

The small non-coding RNA B11 regulates multiple facets of Mycobacterium abscessus virulence

Mycobacterium abscessus causes severe, virtually incurable disease in young patients with cystic fibrosis. Little is known in M. abscessus about the roles of small regulatory RNAs (sRNA) in gene expression regulation. Here, we show that the sRNA B11 controls gene expression and virulence-associated phenotypes in this pathogen. B11 deletion from the smooth strain ATCC_19977 produced a rough colony morphology, increased pro-inflammatory signaling and virulence in in-vivo infection models, and increased resistance to clinically relevant antibiotics. Examination of clinical isolate cohorts revealed some isolates with B11 mutations or reduced expression. We used RNAseq and proteomics to investigate the effects of B11 on gene expression and test the impact of two mutations found in clinical isolates. Approximate 230 genes were differentially expressed in the B11 deletion mutant. Strains with the clinical B11 mutations showed similar expression trends to the deletion mutant but of a lesser magnitude, suggesting partial loss of function. Among genes upregulated in the B11 mutant, there was a strong enrichment for genes with B11-complementary sequences in their predicted ribosome binding sites (RBS), consistent with a model of translational repression via base-pairing of B11 to RBSs. Comparing the proteomes similarly revealed that upregulated proteins were strongly enriched for B11-complementary sequences in their RBS, consistent with B11 functioning as a negative regulator through direct binding of target mRNAs. Intriguingly, the genes upregulated in the absence of B11 included components of the ESX-4 secretion system, known to be critical for M. abscessus virulence. One of these genes had a B11-complementary sequence at its RBS, and fusing the UTR of this gene to a reporter was sufficient to make the reporter suppressible by B11. Taken together, our data show that B11 may act as either a negative or positive regulator with pleiotropic effects on gene expression and clinically important phenotypes in M. abscessus. The presence of hypomorphic B11 mutations in clinical strains supports the idea that lower B11 activity may be advantageous for M. abscessus in some clinical contexts. To our knowledge, this is the first report of the role of an sRNA in M. abscessus.

microbiology↗