Biology subjects

Pichon, J.

Publications and source records attributed to Pichon, J..

8 recordsLinked to original sources

bioRxiv2026

Karyotypic evolution in a diverse primate clade and the role of chromosomal fissions as barriers to gene flow

The classical model of chromosomal speciation is based on the observation that divergent species often differ in chromosome numbers and that heterokaryotypic hybrids show reduced fitness. Furthermore, positive correlations between the rates of karyotype evolution and speciation have been established in several groups of organisms. Yet, the mechanisms that make some lineages more prone to chromosomal fissions and fusions than others, and the causal role of such karyotype changes in speciation, are poorly understood. Here, we focus on the taxonomically and karyotypically diverse group of African monkeys, the guenons (tribe Cercopithecini), consisting of ~35 species with diploid chromosome numbers ranging from 48 to 72. We generated de novo genome assemblies for eight species with different karyotypes, and incorporated publicly available genomes from additionally three guenon species. Using the rhesus macaque as an outgroup, we identified 28 independent chromosomal fissions and 4 fusions in guenons. In line with previous cytogenetic studies, repeat composition around chromosomal breakpoints suggested that most fissions were non-centromeric, requiring the evolution of a new centromere in at least one of the fission products. In contrast to the expectation under strong underdominance, we found a paraphyletic distribution of several chromosomal fissions. Some of these phylogenetically discordant events could have resulted from interspecific hybridization, whereas others are more likely caused by incomplete lineage sorting, suggesting that fissioned and non-fissioned homologs segregated in ancestral guenon lineages for millions of years. Nevertheless, we find evidence for reduced introgression on rearranged chromosomes in an ancient cross-karyotypic gene flow event between Cercopithecus cephus and C. pogonias. Although this suggests that chromosomal fissions may have constituted barriers to gene flow in the guenon evolution, the signal was inconclusive or absent in two other investigated gene flow events. This study provides important first insights into the remarkable karyotypic diversification of guenons, and its role in generating reproductive barriers.

evolutionary biology↗

bioRxiv2026

Functional divergence of regulatory and conventional bovine neutrophils following Mycobacterium bovis infection

Bovine tuberculosis (bTB), due to Mycobacterium bovis (Mb) infection, is a chronic cattle disease and neglected cause of zoonotic tuberculosis. The role of neutrophils in bTB is overlooked. We recently identified a new neutrophil subset in cattle and mice with a similar morphology to conventional inflammatory neutrophils (Nconv). However, unlike Nconv, these regulatory neutrophils (Nreg) express MHC-II at their surface and can suppress lymphocyte proliferation. In this study, we compared the responses of bovine Nconv and Nreg to infection with a virulent Mb strain circulating in France and the attenuated Mb BCG vaccine. Nreg and Nconv had different transcriptional profiles and were differentially activated by Mb infection. Both Nreg and Nconv efficiently killed Mb, but Nreg had higher levels of phagocytosis activity and ROS production. Nreg had higher levels of mitochondrial activity and an ultrastructural organization different from that of Nconv. Our results provide the first insight into the functional characterization of bovine neutrophil subsets during Mb infection and highlight a new layer of complexity in their functional diversity that must be taken into account to improve our understanding of bTB pathophysiology, which is urgently required to improve the management of this costly disease.

immunology↗

bioRxiv2025

Characterization of the African Swine Fever Virus transcriptome and the associated innate immune response reveals key features of virulence

African Swine Fever Virus (ASFV) represents a looming threat to animal health, food safety and to the livestock industry. Virulent strains of ASFV cause a severe and often fatal illness, while attenuated strains are usually associated with mild symptoms. Naturally-occurring attenuated strains are typically deleted of more than 20 genes located at the viral genomes extremities. Whether other key differences between virulent and attenuated ASFV strains may contribute to the virulence phenotype remains however largely unexplored. In this work, we sought to determine how the dynamics of viral gene expression may shape the hosts innate immune response to ASFV infection and contribute to ASFV virulence. We conducted a medium-throughput transcriptomic study to characterize the viral transcriptome of a panel of virulent and attenuated strains (171 viral genes), as well as the host response of ASFV-infected macrophages (92 host genes). Confocal imaging allowed further characterization of cellular response to infection, by assessing the dynamics of IFN and NF-{kappa}B pathway activation in ASFV-infected cells. Our results indicate that the two types of viral pathotypes exhibit global differences in the dynamics of genome replication and viral transcription. Virulent ASFV strains displayed a burst of viral transcription early on, while attenuated strains tended to replicate to higher levels at late time points. The host response was much more pronounced in cells infected with attenuated strains compared to virulent ones, with higher expression levels of interferon-stimulated genes, some innate immunity sensors, and the inducible chaperone HSP70.2. Unexpectedly, genotype I and genotype II virulent strains exhibited some notable differences in their kinetics of viral genome replication and in the host response they provoked, with higher levels of pro-inflammatory cytokines being induced by genotype II strains. Confocal imaging analysis of ASFV-infected primary macrophages revealed that attenuated strains, but not virulent ones, caused the translocation of both p65 and STAT2 to the nucleus. Strikingly, we identified a group of 26 viral genes that were either expressed at higher levels or at an earlier stage of infection by virulent strains. Several of these genes, such as R298L, H233R, DP71L and MGF505-7R encode for proteins that inhibited the type I Interferon response in a reporter cell line system. This work sheds new light on the mechanistical drivers of ASFV virulence and will in the long run help to better understand the protection offered by ASFV Live-Attenuated Vaccine candidates. Author summaryAfrican Swine Fever (ASF), a severe infectious disease affecting domestic pigs and wild boars, presents a global threat to the livestock industry. It is caused by African Swine Fever Virus (ASFV), a large DNA virus encoding between 150 and 200 genes. While virulent ASFV strains cause a fatal illness in infected animals, attenuated strains induce only minor symptoms and some can confer subsequent protection against a pathogenic infection. While Live-Attenuated Vaccines for ASFV are under development and represent a promising tool in the fight against ASF, the mechanisms of ASFV virulence (and conversely, attenuation) are not fully understood. In particular, it is unclear whether key differences may exist between attenuated and virulent ASFV strains, beyond the extensive genomic deletions harbored by the former. In this work, we explored for the first time how the dynamics of viral gene expression may influence the innate immune response to different ASFV strains. We found that attenuated ASFV strains trigger a stronger host response compared to virulent ASFV strains, with higher expression levels of innate immune genes and a stronger activation of key signaling hubs. Finally, we identified a group of 26 ASFV genes that may drive this phenomenon and represent novel virulence factors.

microbiology↗

bioRxiv2025

Mechanistic insights into the activity of Benzoxaboroles against Cryptosporidium parvum: CPSF3 targeting and resistance implications

Benzoxaboroles are emerging as promising treatments against a broad range of protozoan parasites, including Trypanosoma, Leishmania, Plasmodium, Toxoplasma, and Cryptosporidium. We previously demonstrated that the benzoxaborole compound AN3661 inhibits the endonuclease activity of CPSF3 in Cryptosporidium hominis, likely by disrupting pre-mRNA processing, which in turn limits parasite growth. In this study, we further explored its mode of action and found that a specific mutation (Y385N) in CPSF3 of C. parvum confers strong resistance to AN3661. Interestingly, this mutation does not affect the parasites sensitivity to two other benzoxaboroles, AN13762 and AN7973, which are also thought to target CpCPSF3. All three compounds interfered with mRNA processing in C. parvum, consistent with inhibition of CPSF3 complex activity, and showed parasiticidal activity, especially during the late stages of merogony, blocking parasite egress. Two of them also impaired gamogony. In T. gondii, AN7973 remained effective against several strains carrying mutations within TgCPSF3 that confer resistance to AN3661 and AN13762, suggesting that it might represent an alternative chemotype targeting CPSF3 with the potential to overcome resistance. Notably, AN7973 successfully controlled severe infection in susceptible mice challenged with the AN3661-resistant C. parvum strain carrying the CpCPSF3Y385N mutation. Finally, we extended the known antiparasitic spectrum of AN3661 and AN7973 to include Eimeria tenella and Giardia duodenalis, two important pathogens in veterinary and human health. Altogether, our findings refine the understanding of CPSF3-targeting benzoxaboroles, identify alternative chemotypes with the potential to bypass resistance, and support their potential use in combination therapies to delay or prevent the emergence of drug resistance. Author summaryProtozoa are single-celled parasites that cause significant morbidity and mortality worldwide, affecting both humans and animals. The development of new targeted therapies with highly selective compounds requires a detailed understanding of their mode of action and precise interactions with parasite targets. Benzoxaboroles are a potent class of molecules active against Cryptosporidium, with compound AN3661 known to inhibit the endonuclease activity of the Cleavage and Polyadenylation Specificity Factor 3 (CPSF3) in Cryptosporidium hominis. Here, we show that this inhibitory effect is critical during both asexual and sexual developmental stages and that tyrosine at position 385 of C. parvum CPSF3 plays a key role in its inhibition. A mutation at this site confers resistance to AN3661 both in vitro and in vivo, but not to two other benzoxaboroles, AN13762 and AN7973. Notably, all three compounds disrupted pre-mRNA processing in Cryptosporidium, consistent with inhibition of the CPSF3 complex. Using Toxoplasma, a related protozoan that allows more efficient genetic manipulation, we found that none of the six mutations conferring resistance to compounds AN3661 and AN13762 conferred resistance to compound AN7973. AN7973, which strongly inhibits both C. parvum and T. gondii, may therefore represent an alternative chemotype targeting CPSF3. Furthermore, we demonstrated that the antiparasitic spectrum of AN3661and AN7973 extends to include E. tenella and G. duodenalis, two important pathogens in veterinary and human health. Altogether, our results refine the understanding of three CPSF3-targeting benzoxaboroles in Cryptosporidium and identify compound AN7973 as capable of overcoming resistance to AN3661, thereby supporting the rationale for combination therapies to prevent the emergence of drug resistance.

microbiology↗

bioRxiv2024

From tissue to subcellular level : imaging human precision-cut lung slices (PCLS) to gain insight into pandemic bacterial or viral infections

We describe a method for the generation and deep imaging of human precision-cut lung slices (PCLS). PCLS bridge the gap between in vivo and in vitro studies, providing a robust system for visualizing events from tissue to subcellular levels in the three-dimensional lung environment, with the preservation of all resident cell types and cell-cell interactions. They also constitute a validated model for studying host cell-pathogen interactions. Here, we detail the generation of human PCLS, followed by their infection and imaging by laser scanning confocal microscopy and transmission electron microscopy (TEM). We establish the conditions for ex vivo infection and replication of two pathogens of relevance to human respiratory health: a virus (SARS-CoV-2) and a bacterium (Mycobacterium tuberculosis, Mtb). PCLS can be obtained in a single day, infected the next day, and were successfully cultivated for up to a week in this study. Imaging was performed on fixed samples. The preparation of PCLS took one day for confocal imaging and five days for TEM imaging. All procedures are readily adaptable to explore other pathogens and other species and are easy to implement by users with experience in tissue culture. Some specialist equipment (an Alabama tissue slicer) is required for PCLS generation.

cell biology↗

bioRxiv2023

Neutrophil subsets play dual roles in tuberculosis by producing inflammasome dependent-IL-1β or suppressing T-cells via PD-L1

Neutrophils can be beneficial or deleterious during tuberculosis (TB). Based on the expression of MHC-II and programmed death ligand 1 (PD-L1), we distinguished two functionally and transcriptionally distinct neutrophil subsets in the lungs of mice infected with mycobacteria. Inflammatory [MHC-II-, PD-L1lo] neutrophils produced inflammasome-dependent IL-1{beta} in the lungs in response to virulent mycobacteria and "accelerated" deleterious inflammation, which was highly exacerbated in IFN-{gamma}R-/- mice. Regulatory [MHC-II+, PD-L1hi] neutrophils "brake" inflammation by suppressing T-cell proliferation and IFN-{gamma} production. Such beneficial regulation, which depends on PD-L1, is controlled by IFN-{gamma}R signaling in neutrophils. The hypervirulent HN878 strain from the Beijing genotype curbed PD-L1 expression by regulatory neutrophils, abolishing the braking function and driving deleterious hyper-inflammation in the lungs. These findings add a layer of complexity to the roles played by neutrophils in TB and may explain the reactivation of this disease observed in cancer patients treated with anti-PD-L1. One Sentence SummaryRegulatory and inflammatory neutrophil subsets play inverse roles in tuberculosis.

immunology↗

bioRxiv2020

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing

BackgroundThe larvacean Oikopleura dioica is an abundant tunicate plankton with the smallest (65-70 Mbp) non-parasitic, non-extremophile animal genome identified to date. Currently, there are two genomes available for the Bergen (OdB3) and Osaka (OSKA2016) O. dioica laboratory strains. Both assemblies have full genome coverage and high sequence accuracy. However, a chromosome-scale assembly has not yet been achieved. ResultsHere, we present a chromosome-scale genome assembly (OKI2018_I69) of the Okinawan O. dioica produced using long-read Nanopore and short-read Illumina sequencing data from a single male, combined with Hi-C chromosomal conformation capture data for scaffolding. The OKI2018_I69 assembly has a total length of 64.3 Mbp distributed among 19 scaffolds. 99% of the assembly is in five megabase-scale scaffolds. We found telomeres on both ends of the two largest scaffolds, which represent assemblies of two fully contiguous autosomal chromosomes. Each of the other three large scaffolds have telomeres at one end only and we propose that they correspond to sex chromosomes split into a pseudo-autosomal region and X-specific or Y-specific regions. Indeed, these five scaffolds mostly correspond to equivalent linkage groups of OdB3, suggesting overall agreement in chromosomal organization between the two populations. At a more detailed level, the OKI2018_I69 assembly possesses similar genomic features in gene content and repetitive elements reported for OdB3. The Hi-C map suggests few reciprocal interactions between chromosome arms. At the sequence level, multiple genomic features such as GC content and repetitive elements are distributed differently along the short and long arms of the same chromosome. ConclusionsWe show that a hybrid approach of integrating multiple sequencing technologies with chromosome conformation information results in an accurate de novo chromosome-scale assembly of O. dioicas highly polymorphic genome. This assembly will be a useful resource for genome-wide comparative studies between O. dioica and other species, as well as studies of chromosomal evolution in this lineage.

genomics↗

bioRxiv2019

Widespread use of the "ascidian" mitochondrial genetic code in tunicates

BackgroundAscidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBIs GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. MethodsWe collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. ResultsAll tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile [->] Met) and TGA (Trp [->] Arg) codons. ConclusionsWe recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.

genomics↗