Biology subjects

Lucier, J.-F.

Publications and source records attributed to Lucier, J.-F..

9 recordsLinked to original sources

bioRxiv2025

NLRC5 expression in tumor cells is critical to activate adaptive and innate antitumor immune responses

Tumors evade cytotoxic T lymphocyte (CTL)-mediated killing by downregulating MHC class-I, mainly resulting from the loss of its transcriptional activator NLRC5. Expressing full-length NLRC5 (NLRC5-FL) or a shorter NLRC5-CIITA fusion protein termed NLRC5 super-activator (NLRC5-SA) in cancer cells upregulates MHC-I expression and promotes antitumor immunity. To distinguish the role of NLRC5 expressed within tumor cells and antigen presenting cells, we studied B16-F10 melanoma expressing NLRC5-FL (B16-N-FL) or NLRC5-SA (B16-N-SA) in Nlrc5+/+ and Nlrc5-/- mice. Both tumors were efficiently controlled in both Nlrc5+/+ and Nlrc5-/- hosts with abundant immune cell infiltration, enriched for activated and differentiated CD8+ and CD4+ T cells, NK, NKT and iNKT cells. B16-N-FL and B16-N-SA tumors showed increased collagen deposition and vascularization, with upregulation of CCL4 and CXCL9 chemokine genes in B16-N-SA tumors. Depletion of either CD8+ T cells or NK1.1+ cells increased the growth of B16-N-FL and B16-N-SA tumors in Nlrc5+/+ mice, and that of B16-N-SA tumors in Nlrc5-/- hosts. Proteomes of B16-N-FL and B16-N-SA cells showed downmodulation of dominant tumor antigens and upregulation of ubiquitination and protein processing pathway proteins. Differentially expressed proteins shared between B16-N-FL and B16-N-SA cells showed enrichment in phagosome and autophagy pathways. We conclude that tumor cell-intrinsic NLRC5 expression is critical for the activation of adaptive and innate immune cells, and establishment of an immune-supportive tumor microenvironment to permit immune cell infiltration and their effector functions and achieve tumor control. NLRC5 expression in APCs is dispensable to mediate these effects. Delivering NLRC5-SA is a promising approach to restore antitumor immune responses in MHC-I-low immune evasive tumors. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/695247v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1bc4f51org.highwire.dtl.DTLVardef@1fb5b03org.highwire.dtl.DTLVardef@11448edorg.highwire.dtl.DTLVardef@bff26c_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients

Urban vegetation varies with socio-economic gradients, as lower-income neighborhoods often host sparser and less diverse green spaces. This disparity may affect respiratory health by influencing exposure to bioaerosols. Understanding the characteristics of this aerobiome could help anticipate risks related to allergies and other respiratory conditions. Here, we hypothesized that urban vegetation cover and socio-economic status shape urban bioaerosols. We sampled bioaerosols at 65 sites across three Canadian cities of varying population size and density using an active air sampler over four months, and characterized their bacterial, fungal, and pollen composition using amplicon sequencing. Seasonal alpha diversity varied significantly for fungi and pollen. Based on beta diversity, sampling period alone explained up to 40% of pollen, 29% of fungal, and 11% of bacterial community composition variation. In contrast, vegetation cover explained only a minor portion of the variance in bioaerosol composition, and median household income, almost none. These findings provide a critical baseline for understanding the urban aerobiome and highlight the need to study how vegetation identity and diversity, rather than cover alone, may shape bioaerosol dynamics in cities. As cities grow and urban greening initiatives expand, demystifying the aerobiome dynamics becomes an urgent public health priority.

microbiology↗

bioRxiv2025

Molecular Insights into Long COVID: Plasma Proteomics Reveals Oxidative Stress, Coagulation Cascade Activation, and Glycolytic Imbalance

Persistent symptoms following SARS-CoV-2 infection are the hallmark of post-COVID condition (PCC), also referred to as long COVID. However, our knowledge is limited on the underlying molecular mechanisms. In this study, we performed data-independent acquisition mass spectrometry plasma proteomics (DIA-MS) to identify molecular alterations associated with PCC. DIA-MS proteomic analysis revealed a few proteins linked to oxidative stress that had altered expression. Notably, PCC samples exhibited downregulation of the antioxidant protein peroxiredoxin 6 (PRDX6) and upregulation of oxidative stress-associated proteins particularly vanin-1 (VNN1) and paraoxonase-3 (PON3). Additionally, the PCC group showed significantly higher levels of six proteins (PCSK9, CST3, C1Q, CPB2, KNG1 GAPDH), which were linked to pathways involving glycolysis, complement and coagulation cascades, and inflammation. Oxidative stress analysis confirmed that PCC samples had significantly higher levels of DNA damage (8-OHdG) than the convalescent group, whereas antioxidant markers, such as reduced and oxidized glutathione (GSH and GSSG), were significantly lower in PCC samples than in uninfected controls. Our observations point towards ongoing oxidative and inflammatory processes in PCC and suggest potential targets for biomarker development and therapeutic intervention.

immunology↗

bioRxiv2025

Deciphering the RNA-based regulation mechanism of the phage-encoded AbiF system in Clostridioides difficile

Clostridioides difficile is the major cause of nosocomial infections associated with antibiotic therapy. The severity of C. difficile infections increased worldwide with the emergence of hypervirulent strains, including 027 ribotype epidemic strains. Many aspects of C. difficiles adaptation strategies during pathogenesis remain poorly understood. This pathogen thrives in gut communities that are rich in microbes and phages. To regulate horizontal transfer of genetic material during its infection cycle, C. difficile relies on diverse mechanisms. More specifically, CRISPR (clustered regularly interspaced short palindromic repeats)-Cas and Toxin-Antitoxin (TA) systems contribute to prophage maintenance, prevention of phage infection, and stress response. Abortive infection (Abi) systems can provide additional lines of anti-phage defense. RNAs have emerged as key components of these systems including CRISPR RNAs and antitoxin RNAs within type I and type III TA. We report here the identification of a new AbiF-like system within a prophage of the hypervirulent C. difficile strain R20291. It is associated with an Abi_2/AbiD/F protein family largely distributed in Bacillota and Pseudomonadota with structural links to ancestral Cas13 proteins at the origin of the RNA-targeting CRISPR-Cas13 systems. We demonstrated toxic activity of the AbiFCd protein in C. difficile and in Escherichia coli and negative regulation of the abiFCd expression by an associated non-coding RNA RCd22. RCd22 contains two conserved abiF motifs and is active both in cis and in trans to neutralize the toxin by direct RNA-protein interaction, similar to RNA antitoxin in type III TA. A mass spectrometry interactomics analysis of protein fractions from MS2-Affinity Purification coupled with RNA sequencing (MAPS) revealed the AbiFCd protein among the most enriched RCd22 partners in C. difficile. Structural modeling of the RNA-protein complex and mutagenesis analysis revealed key positions on both protein and RNA partners for this interaction and toxic activity. In summary, these findings provide valuable insights into the mechanisms of interaction between bacteria and phages, which are pertinent to the advancement of phage therapy, genome editing, epidemiological surveillance, and the formulation of novel therapeutic approaches.

microbiology↗

bioRxiv2025

Essential role of NLRC5 in cancer immune surveillance and cancer immunoediting

A key mechanism of immune escape from CD8+ T cell-mediated tumor control occurs via downregulation of NLRC5, the IFN{gamma}-induced transcriptional activator of MHC class-I. As NLRC5 deficiency does not abrogate CD8+ T cell development, we investigated whether NLRC5-dependent antitumor immune mechanisms are required for immune surveillance. Development of 3-methylcholanthrene (MCA)-induced endogenous fibrosarcoma was studied in Nlrc5-/- mice with Nlrc5+/+ and Rag1-/- mice serving as controls. Nlrc5-/- and Rag1-/- mice showed increased propensity to develop MCA-induced tumors with elevated growth rate compared to Nlrc5+/+ mice, and displayed significantly reduced survival. Tumors from Nlrc5+/+ and Nlrc5-/-mice, but not from Rag1-/- mice, contained necrotic areas and displayed T cell infiltration. Tumor cell lines established from MCA- induced tumors were evaluated for their sensitivity to immune-mediated growth control following implantation into immunocompetent C57BL/6 and immunodeficient Rag1-/- hosts. Tumors formed by Nlrc5+/+ tumor cell lines progressed unhindered in C57BL/6 hosts that reflected their immunoedited status, whereas cell lines from Nlrc5-/- and Rag1-/-tumors were efficiently controlled, indicating their non-immunoedited status. Proteomic analysis by mass spectrometry followed by pathway analysis revealed enrichment of granzyme-mediated cytolytic pathway in Nlrc5+/+ tumors that were absent in Nlrc5-/- tumors, which showed enrichment of humoral and innate immune pathways. Overall, our findings show that NLRC5 is required for robust tumor immune surveillance and tumor immunoediting and that compensatory humoral and innate immune mechanisms activated by the loss of NLRC5 are insufficient for cancer immune surveillance and cancer immunoediting.

immunology↗

bioRxiv2024

A mechanism for telomere-specific telomere length regulation

Telomere length is a critical determinant of telomere function and hence chromosome stability. Critically short telomeres induce cellular senescence and division arrest, which eventually may lead to devastating age-related degenerative diseases. Conversely, maintenance of telomere length is a hallmark of cancer. How telomere set-length is established and molecular mechanisms for telomere-specific length regulation remained unknown. Here we detail a mechanism of a telomere-specific set-length regulation that causes drastic differences in telomere length between individual telomeres in the same cell. Indeed, the results show that telomerase recruitment is modulated in cis in a telomere-specific way. Increased Sir4 abundance on yeast TEL03L subtelomeric heterochromatin leads to a set-length maintenance that is two to three times higher than on any other telomere. Remarkably, the distal 15 kb of TEL03L are sufficient to transfer this telomere specific set-length regulation to another chromosome. Furthermore, a mutation in the telomere boundary element protein Tbf1 allows increased Sir4 binding on all telomeres and hence results in longer set-lengths. The results therefore will force a rethinking of telomere length regulation away from the generalized view that all telomeres are treated the same to a more telomere-specific treatment. HIGHLIGHTSO_LIRegulation of the set-length of telomeric repeats is telomere-specific. C_LIO_LITEL03L on yeast chromosome III displays a set-length regulation that confers an extremely long repeat tract. C_LIO_LITransferring the distal part of TEL03L onto chromosome XV is sufficient to impose the very long set-length regulation. C_LIO_LITelomere-specific tract set-length regulation depends on the alternate telomerase recruitment pathway involving Sir4 and yKU and the chromatin boundary protein Tbf1. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/598646v2_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1c3bb52org.highwire.dtl.DTLVardef@13f338forg.highwire.dtl.DTLVardef@51f91aorg.highwire.dtl.DTLVardef@1b95ac0_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Molecular responses of agroinfiltrated Nicotiana benthamiana leaves expressing suppressor of silencing P19 and influenza virus-like particles

The production of influenza vaccines in plants is achieved through transient Agrobacterium-mediated expression of viral hemagglutinins (HAs). These proteins are produced and matured through the secretory pathway of plant cells, before being trafficked to the plasma membrane where they induce formation of virus-like particles (VLPs). Production of VLPs unavoidably impacts plant cells, as do viral suppressors of RNA silencing (VSRs) that are often co-expressed to increase protein yields. However, little information is available on host molecular responses to these foreign proteins. The present work provides a comprehensive overview of transcriptomic, metabolic, and signaling changes occurring in Nicotiana benthamiana leaf cells transiently expressing the VSR P19, or co-expressing P19 and an influenza HA. Our data identifies generic responses to Agrobacterium-mediated expression of foreign proteins, including shutdown of chloroplast gene expression, activation of oxidative stress responses, and reinforcement of the plant cell wall through lignification. Our results also indicate that P19 expression promotes salicylic acid (SA) signaling, a process apparently antagonized by co-expression of HA. As the latter induces specific signatures, with effects on lipid metabolism, lipid distribution, and oxylipin signaling, dampening of P19 responses suggests crosstalk between SA and oxylipin pathways. Consistent with the upregulation of oxidative stress-related genes and proteins, we finally show that reduction of oxidative stress damage through exogenous application of ascorbic acid improves plant biomass quality during production of VLPs. One-sentence summaryAgrobacterium-mediated expression of influenza virus-like particles induces a unique molecular signature in Nicotiana benthamiana leaf cells.

plant biology↗

bioRxiv2023

SARS-CoV-2 spike antigen-specific B cell and antibody responses in pre-vaccination period COVID-19 convalescent males and females with or without post-covid condition

BackgroundFollowing SARS-CoV-2 infection a significant proportion of convalescent individuals develop the post-COVID condition (PCC) that is characterized by wide spectrum of symptoms encompassing various organs. Even though the underlying pathophysiology of PCC is not known, detection of viral transcripts and antigens in tissues other than lungs raise the possibility that PCC may be a consequence of aberrant immune response to the viral antigens. To test this hypothesis, we evaluated B cell and antibody responses to the SARS-CoV-2 antigens in PCC patients who experienced mild COVID-19 disease during the pre-vaccination period of COVID-19 pandemic. MethodsThe study subjects included unvaccinated male and female subjects who developed PCC or not (No-PCC) after clearing RT-PCR confirmed mild COVID-19 infection. SARS-CoV-2 D614G and omicron RBD specific B cell subsets in peripheral circulation were assessed by flow cytometry. IgG, IgG3 and IgA antibody titers toward RBD, spike and nucleocapsid antigens in the plasma were evaluated by ELISA. ResultsThe frequency of the B cells specific to D614G-RBD were comparable in convalescent groups with and without PCC in both males and females. Notably, in females with PCC, the anti-D614G RBD specific double negative (IgD-CD27-) B cells showed significant correlation with the number of symptoms at acute of infection. Anti-spike antibody responses were also higher at 3 months post-infection in females who developed PCC, but not in the male PCC group. On the other hand, the male PCC group also showed consistently high anti-RBD IgG responses compared to all other groups. ConclusionsThe antibody responses to the spike protein, but not the RBD-specific B cell responses diverge between convalescent males and females, and those who develop PCC or not. Our findings suggest that sex-related factors may also be involved in the development of PCC via modulating antibody responses to the SARS-CoV-2 antigens. Short SummaryPost-COVID Condition (PCC) is lingering illness that afflicts a significant proportion of COVID-19 patients from three months after clearing SARS-CoV-2 infection. Therapy for PCC is only palliative and the underlying disease mechanisms are unclear. The wide spectrum of PCC symptoms that can affect different organs and the detection of viral components in tissues distant from lungs raise the possibility that PCC may be associated with aberrant immune response due to presence of viral antigens. Therefore, we studied B cell and antibody responses to the spike and nucleoprotein antigens in PCC patients who cleared mild SARS-CoV-2 infection during the pre-vaccination COVID-19 pandemic period. We observed divergent patterns of immune reactivity to the spike protein in PCC males and females at different times post-infection, suggesting that the immune responses in PCC may also be influenced by sex-related factors.

immunology↗

bioRxiv2017

Deep transcriptome annotation suggests that small and large proteins encoded in the same genes often cooperate

Recent studies in eukaryotes have demonstrated the translation of alternative open reading frames (altORFs) in addition to annotated protein coding sequences (CDSs). We show that a large number of small proteins could in fact be coded by altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and evolutionary patterns indicate that altORFs are particularly constrained in CDSs that evolve slowly. Thousands of predicted alternative proteins are detected in proteomic datasets by reanalysis with a database containing predicted alternative proteins. Protein domains and co-conservation analyses suggest potential functional cooperation or shared function between small and large proteins encoded in the same genes. This is illustrated with specific examples, including altMID51, a 70 amino acid mitochondrial fission-promoting protein encoded in MiD51/Mief1/SMCR7L, a gene encoding an annotated protein promoting mitochondrial fission. Our results suggest that many coding genes code for more than one protein that are often functionally related.

biochemistry↗