Biology subjects

Cossa, A.

Publications and source records attributed to Cossa, A..

6 recordsLinked to original sources

bioRxiv2025

MiTo: tracing the phenotypic evolution of somatic cell lineages via mitochondrial single-cell multi-omics

Mitochondrial single-cell lineage tracing (MT-scLT) has recently emerged as a scalable and non-invasive tool to trace somatic cell lineages. However, the reliability and resolution of MT-scLT remains highly debated. Here, we present MiTo, the first end-to-end framework for robust MT-scLT data analysis. Thanks to highly-optimized algorithms and user-friendly interfaces, this modular toolkit offers unprecedented control across the entire MT-scLT workflow. Benchmarked against novel real-world datasets (375-2,757 cells; 8-216 lentiviral clones), MiTo outperformed state-of-the-art methods and baselines in MT-scLT data pre-processing and clonal inference. Applied to a time-resolved dataset of breast cancer evolution (>2,500 cells), MiTo accurately inferred ground-truth cell lineages (ARI=0.94) and cell state transitions, detected clonal fitness markers, and quantified heritability of gene regulatory networks. Comparing alternative lineage markers, MiTo quantified the resolution limit of existing MT-scLT systems, which currently enable reliable inference of coarse-grained cellular ancestries, but not high-resolution phylogenetic inference. In conclusion, this work provides robust tools and practical guidelines to dissect somatic evolution with single-cell multi-omics.

bioinformatics↗

bioRxiv2024

Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets

Soil-transmitted helminths (STHs) are intestinal pathogens affecting over a billion people worldwide. STH control relies on microsopy-based diagnostics to monitor parasite prevalence and enable post-treatment surveillance, however, molecular diagnostics are rapidly being developed due to increased sensitivity, particularly in low-STH-prevalence settings. The genetic diversity of helminths and its potential impact on molecular diagnostics remains unclear. Using low-coverage genome sequencing, we assessed the presence of STHs in worm, faecal and purified egg samples from 27 countries, identifying differences in the genetic connectivity and diversity of STH-positive samples across regions and cryptic diversity between closely related human- and pig-infective species. We defined substancial copy number and sequence variants in current diagnostic targets and validated the impact of genetic variants on qPCR diagnostics using in vitro assays. Our study provides insights into the diversity and genomic epidemiology of STHs, highlighting challenges and opportunities for developing molecular diagnostics needed to support STH control efforts.

genomics↗

bioRxiv2023

INDOCYANINE GREEN IMAGING BY VITAL TISSUE SLICES SCANNING ALLOWS FOR THE ISOLATION OF INTACT LIVER MICRO-METASTASIS FOR SINGLE-CELL ANALYSIS

Metastasis represents the deadliest outcome in cancer, leading to the vast majority of cancer-related deaths. Understanding the progression from micro-to macro-metastasis might improve future therapeutic strategies aimed at blocking metastatic disease. However, the difficulty of investigating vital, clinically undetectable, micro-metastases hindered our capacity to unravel phenotypic determinants of micro-metastases. In this work, we leveraged indocyanine green (ICG) dye to detect small sized liver micro-metastases across several cancer models. We exploited a method for infrared fluorescence scanning of fresh tissue and coring of cancer micro-metastases and succeeded in processing them for single-cell RNA sequencing. Our analysis revealed that distinct liver micro-metastases upregulate both shared and specific genes that can successfully predict breast cancer patient prognosis. Moreover, the ontology classification of these genes allowed the validation of several pathways, namely interferon response, extracellular matrix remodeling, and antioxidant response in metastatic progression. Ultimately, we showed that ICG can be successfully used to quantify breast cancer micro- and macro-metastases to lungs, which we showed to be abrogated through inhibition of H2O2-producing enzyme monoamine oxidase. Therefore, the ICG approach allowed us to identify not only determinant of breast cancer metastatization, but also to assess the therapeutic efficacy of targeting these genes which can be further investigated in clinic.

cancer biology↗

bioRxiv2022

The breast cancer pro-metastatic phenotype requires concomitant hyper-activation of ECM remodeling and dsRNA-IFN1 signaling in rare clone cells

The molecular determinants of breast cancer (BC) pro-metastatic phenotype are largely unknown. Here, we leveraged lentiviral barcoding coupled to single-cell RNA sequencing to trace clonal and transcriptional evolution during BC metastatization. We showed that metastases derive from rare pro-metastatic clones that are under-represented in primary tumors. Both low clonal-fitness and high metastatic-potential are independent of clonal origin. Differential expression and classification analyses revealed that the pro-metastatic phenotype is acquired in rare cells by concomitant hyper-activation of extracellular-matrix remodeling, dsRNA-interferon signaling, and stress-response pathways. Notably, genetic silencing of single pro-metastatic genes from different pathways significantly impairs migration in vitro and metastatization in vivo, with negligible effects on cell proliferation and tumor growth. In addition, gene-expression signatures from identified pro-metastatic genes predicts metastatic progression in BC patients, independently of known prognostic factors. This study elucidates previously unknown mechanisms of BC metastatization, and provides novel prognosis predictors and therapeutic targets for metastasis prevention.

cancer biology↗

bioRxiv2021

Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodelling by Hfq master regulator

Bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, thanks to proteins called Nucleoid Associated Proteins (NAPs). The NAP composition of the nucleoid varies during the bacterial life cycle and is growth phase-dependent. Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq belongs to the bridging family of NAPs. Its bridging mechanism relies on the formation of the amyloid-like structure of Hfq C-terminal region. Here, using cryo soft X-ray tomography imaging of native unlabelled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid, especially during the stationary growth phase. Hfq influences both nucleoid volume and absorbance. Hfq cumulates direct effects and indirect effects due to sRNA-based regulation of other NAPs. Taken together, our findings reveal a new role for this protein in nucleoid remodelling that may serve in response to stress conditions and in adapting to changing environments. This implies that Hfq regulates nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNA.

microbiology↗

bioRxiv2021

Plasmodium falciparum and helminth coinfections increase IgE and parasite-specific IgG responses

Coinfection with Plasmodium falciparum and helminths may impact the immune response to these parasites since they induce different immune profiles. We studied the effects of coinfections on the antibody profile in a cohort of 715 Mozambican children and adults using the Luminex technology with a panel of 16 antigens from P. falciparum and 11 antigens from helminths (Ascaris lumbricoides, hookworm, Trichuris trichiura, Strongyloides stercoralis and Schistosoma spp.) and measured antigen-specific IgG and total IgE responses. We compared the antibody profile between groups defined by P. falciparum and helminth previous exposure (based on serology) and/or current infection (determined by microscopy and/or qPCR). In multivariable regression models adjusted by demographic, socioeconomic, water and sanitation variables, individuals exposed/infected with P. falciparum and helminths had significantly higher total IgE and antigen-specific IgG levels, magnitude (sum of all levels) and breadth of response to both types of parasites compared to individuals exposed/infected with only one type of parasite (p[≤] 0.05). There was a positive association between exposure/infection to P. falciparum and exposure/infection to helminths or the number of helminth species, and vice versa (p[≤] 0.001). In addition, children coexposed/coinfected tended (p= 0.062) to have higher P. falciparum parasitemia than those single exposed/infected. Our results suggest that an increase in the antibody responses in coexposed/coinfected individuals may reflect higher exposure and be due to a more permissive immune environment to infection in the host. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/445753v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@a1dc3corg.highwire.dtl.DTLVardef@82128corg.highwire.dtl.DTLVardef@18fcd98org.highwire.dtl.DTLVardef@2d5bb_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗