Biology subjects

Lagarde, J.

Publications and source records attributed to Lagarde, J..

11 recordsLinked to original sources

bioRxiv2026

Experimental and natural peripheral HSV-1 infection: Neurotropism and impact on Alzheimer's disease-related molecular markers

Herpes Simplex virus type 1 (HSV-1) is a highly prevalent neurotropic virus from the alphaherpesviruses family. In recent years, a growing body of research has focused on the potential role of HSV-1 infections and recurrent reactivations in the pathophysiology of Alzheimers disease (AD). In particular, it has been hypothesized that HSV-1 could initiate or amplify the formation of neuropathological lesions characteristic of AD. To explore further this hypothesis, we adopted an integrated approach aiming at deciphering the impact of HSV-1 infection on AD molecular markers (A{beta} and Tau pathologies) and combining experimental animal models of in vivo infection, postmortem neuropathological analysis of AD brains, as well as in-vivo clinical analysis in AD patients. In animal models of peripheral (labial) infection with HSV-1 virus, we analyzed viral dissemination from peripheral tissues to the CNS, and the associated neuropathological consequences. Histological and molecular analyses revealed the occurrence of viral material (RNA, proteins) in the brainstem, the primary site of viral neuroinvasion, and in more anterior regions of the brain. Viral signatures were accompanied by early abnormal deposits of A{beta} peptides and accumulation of phosphoTau (pTau) proteins in various brain areas. Neuropathological examination of AD/control participants also underlined the presence of HSV-1 DNA in the human brainstem (pons) that was always associated with local A{beta}/Tau aggregates. Finally, in AD patients, associations were found between HSV-1 seropositivity and neuropathological lesion burden (region-specific Tau and A{beta} deposition detected by neuroimaging). Taken together, these data provide new evidence in favor of the involvement of HSV-1 in the pathophysiology of AD, stressing a possible causal link between HSV-1 infection, neuroinvasion and AD neuropathological hallmarks (A{beta} lesions and tauopathy).

neuroscience↗

bioRxiv2025

Systematic cross-study assessment of RNA-Seq experimental workflows for plasma cell-free transcriptome profiling

Plasma cell-free RNA (cfRNA) is a promising source of non-invasive biomarkers, but its clinical translation is hindered by technical challenges and a lack of protocol standardization, which compromises reproducibility and comparability across studies. There is a need for a systematic evaluation of existing cfRNA-Seq workflows to understand the drivers of technical variability. Here, we address this gap by performing a comprehensive cross-study analysis of 2,166 cfRNA-Seq samples from 15 published studies and an in-house generated dataset, applying a uniform bioinformatics pipeline to enable a controlled comparison of experimental workflows. Our analysis reveals that the donor phenotype typically explains a negligible fraction of the transcriptomic variation, whose main determinants are technical - principally protocol choice, genomic DNA contamination levels and library diversity. Remarkably, this technical noise is so profound that variation within plasma cfRNA samples exceeds that found across a wide range of human tissues. Finally, we demonstrate that critical pre-analytical factors are often confounded with patient phenotypes, jeopardizing the validity of biomarker discovery efforts. Our work serves as a comprehensive benchmark of current cfRNA-Seq methodologies and provides evidence-based guidelines to improve experimental design. By highlighting the dominance of controllable technical factors, we offer a path towards more robust and reproducible cfRNA research.

bioinformatics↗

bioRxiv2025

Large extracellular vesicles containing mitochondria (EVMs) derived from Alzheimer disease cells harbor pathologic functional and molecular profiles and spread mitochondrial dysfunctions

In addition to small extracellular vesicles known as exosomes, cells release large extracellular vesicles containing mitochondria (EVMs). However, the molecular and functional characteristics of EVMs, as well as the impact of EVM secretion on the spreading of mitochondrial dysfunction between cells, remain unknown in the context of Alzheimers Disease (AD). Here, we provide an ultrastructural, biochemical, and functional characterization of EVMs isolated from cells expressing the amyloid precursor protein (APP) with the familial Swedish mutation (APPswe). We identified differential proteomic and lipidomic signatures in APPswe-derived EVMs compared to control EVMs and revealed a specific proteomic profile in EVMs isolated from conditioned media of fibroblasts from AD patients at the prodromal stage of the disease. Our findings show that APP-C terminal fragments (APP-CTFs) pathogenic accumulation in cells potentiates EVM secretion through the budding of the plasma membrane. We lastly demonstrated that APP-CTFs loaded EVMs are active carriers of dysfunctional mitochondria that transfer mitochondrial pathology to naive control recipient cells.

neuroscience↗

bioRxiv2024

GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing

Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For more than twenty years, the GENCODE consortium has developed reference annotations for the human and mouse genomes, becoming a foundation for biomedical and genomics communities worldwide. Nevertheless, collections of important yet poorly-understood gene classes like long non-coding RNAs (lncRNAs) remain incomplete and scattered across multiple, uncoordinated catalogs. To address this, GENCODE has undertaken the most comprehensive lncRNA annotation effort to date. This is founded on the manually supervised computational annotation of full-length targeted long-read sequencing, on matched embryonic and adult tissues, of orthologous regions in human and mouse. Altogether 17,931 human genes (140,268 transcripts) and 22,784 mouse genes (136,169 transcripts) have been added to the GENCODE catalog representing a 2-fold and 6-fold growth in transcripts, respectively - the greatest increase in the number of annotated human genes since the sequencing of the human genome. Our targeted design assigned human-mouse orthologs at a rate beyond previous studies, tripling the number of human disease-associated lncRNAs that have mouse orthologs. Novel lncRNA genes consistently exhibit biological signals of functionality, and they greatly enhance the functional interpretability of the human genome. While poorly expressed in bulk RNA-Seq samples, many of them are highly expressed in specific cell populations, maybe even contributing to cell-type determination. The expanded GENCODE lncRNA annotations mark a critical step toward deciphering the human and mouse genomes.

genomics↗

bioRxiv2023

Mitochondria alterations in fibroblasts from sporadic Alzheimer's disease (AD) patients correlate with AD-related clinical hallmarks

INTRODUCTIONMitochondria dysfunctions are key features in Alzheimers disease (AD). The occurrence of these disturbances in AD patients peripheral cells and their potential correlation with disease progression are under investigated. METHODSWe studied mitochondrial structure, function and mitophagy in fibroblasts including healthy volunteers and AD patients at the prodromal (AD-MCI) or demented (AD-D) stages. We carried out correlation studies with clinical cognitive scores, A{beta} plaques burden and the accumulation of peripheral amyloid precursor protein C-terminal fragments (APP-CTFs). RESULTSWe unveiled progressive alteration of mitochondria structure as well as specific mitochondrial dysfunctions signatures in AD-MCI and AD-D fibroblasts and show defective mitophagy and autophagy linked to impaired lysosomal activity in AD-D fibroblasts. We reported on significant correlations of a subset of these dysfunctions with cognitive decline, AD-related clinical hallmarks and peripheral APP-CTFs accumulation. DISCUSSIONThis study emphasizes the potential use of peripheral cells for investigating AD pathophysiology and likely diagnosis.

cell biology↗

bioRxiv2023

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

AbstractThe Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

genomics↗

bioRxiv2023

CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing

Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a challenge for long-read sequencing methods. To address this limitation, we developed CapTrap-seq, a cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming to detect 5capped, full-length transcripts, together with the data processing pipeline LyRic. We benchmarked CapTrap-seq and other popular RNA-seq library preparation protocols in a number of human tissues using both ONT and PacBio sequencing. To assess the accuracy of the transcript models produced, we introduced a capping strategy for synthetic RNA spike-in sequences that mimics the natural 5cap formation in RNA spike-in molecules. We found that the vast majority (up to 90%) of transcript models that LyRic derives from CapTrap-seq reads are full-length. This makes it possible to produce highly accurate annotations with minimal human intervention.

genomics↗

bioRxiv2021

A lineage tree-based hidden Markov model to quantify cellular heterogeneity and plasticity

Cell plasticity operates alongside other sources of cell-to-cell heterogeneity, such as genetic mutations and variation in signaling, together preventing most cancer therapies from being curative. The predominant methods of quantifying tumor-drug response operate on snapshot, population-level measurements and therefore lack evolutionary dynamics, which are particularly critical for dynamic processes such as plasticity. Here we apply a lineage tree-based adaptation of a hidden Markov model that employs single cell lineages as input to learn the characteristic patterns of single cell phenotypic heterogeneity and state transitions in an unsupervised fashion. To benchmark our model, we paired cell fate with either cell lifetimes or individual cell cycle phase lengths on synthetic data and demonstrated that the model successfully classifies cells within experimentally tractable dataset sizes. As an application, we analyzed experimental measurements of same measurements in cancer and non-cancer cell populations under various treatments. We find that in each case multiple phenotypically distinct states exist, with significant heterogeneity and unique drug responses. In total, this framework allows for the flexible classification of single cell heterogeneity across lineages.

systems biology↗

bioRxiv2020

Reference-free reconstruction and quantification of transcriptomes from long-read sequencing

Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes from any sample. However, current methods for transcript identification and quantification rely of mapping reads to a reference genome, which precludes the study of species with a partial or missing reference or the identification of disease-specific transcripts not readily identifiable from a reference. Here we present RATTLE, a tool to perform reference-free reconstruction and quantification of transcripts using only Nanopore reads. Using simulated data and experimental data from isoform spike-ins, human tissues, and cell lines, we show that RATTLE accurately determines transcript sequences and their abundances, and shows good scalability with the number of transcripts. RATTLE provides unprecedented access to transcriptomes from any sample and species without relying on a reference or additional technologies.

bioinformatics↗

bioRxiv2018

Nearly all new protein-coding predictions in the CHESS database are not protein-coding

In a 2018 paper posted to bioRxiv, Pertea et al. presented the CHESS database, a new catalog of human gene annotations that includes 1,178 new protein-coding predictions. These are based on evidence of transcription in human tissues and homology to earlier annotations in human and other mammals. Here, we reanalyze the evidence used by CHESS, and find that nearly all protein-coding predictions are false positives. We find that 86% overlap transposons marked by RepeatMasker that are known to frequently result in false positive protein-coding predictions. More than half are homologous to only nine Alu-derived primate sequences corresponding to an erroneous and previously withdrawn Pfam protein domain. The entire set shows poor evolutionary conservation and PhyloCSF protein-coding evolutionary signatures indistinguishable from noncoding RNAs, indicating lack of protein-coding constraint. Only four predictions are supported by mass spectrometry evidence, and even those matches are inconclusive. Overall, the new protein-coding predictions are unsupported by any credible experimental or evolutionary evidence of function, result primarily from homology to genes incorrectly classified as protein-coding, and are unlikely to encode functional proteins.

genomics↗

bioRxiv2017

High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS)

Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. As a result, reference gene collections remain incomplete: many gene models are fragmentary, while thousands more remain uncatalogued-particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), combining targeted RNA capture with third-generation long-read sequencing. We present an experimental re-annotation of the GENCODE intergenic lncRNA population in matched human and mouse tissues, resulting in novel transcript models for 3574 / 561 gene loci, respectively. CLS approximately doubles the annotated complexity of targeted loci, outperforming existing short-read techniques. Full-length transcript models produced by CLS enable us to definitively characterize the genomic features of lncRNAs, including promoter- and gene-structure, and protein-coding potential. Thus CLS removes a longstanding bottleneck of transcriptome annotation, generating manual-quality full-length transcript models at high-throughput scales.\n\nAbbreviations

genomics↗