Biology subjects

Cerletti, D.

Publications and source records attributed to Cerletti, D..

3 recordsLinked to original sources

bioRxiv2020

Cytopath: Simulation based inference of differentiation trajectories from RNA velocity fields

AO_SCPLOWBSTRACTC_SCPLOWTrajectory inference from single-cell RNA sequencing data bears the potential to systematically reconstruct complex differentiation processes, however inferring trajectories that accurately model the biological characteristics of varied processes continues to be a challenge, notwithstanding the many available solutions. In general, trajectory and pseudotime inference methods have so far suffered from the ambiguity of static single-cell transcriptome snapshots lacking a concept of directionality and rate of transcriptional activity. We report Cytopath, a method for trajectory inference that takes advantage of transcriptional activity information from RNA velocity of single-cells to perform trajectory inference. Cytopath performs this task by defining a Markov chain model, simulating an ensemble of possible differentiation trajectories and constructs a consensus trajectory. We show that Cytopath can recapitulate the topological and molecular characteristics of the differentiation process under study. In our analysis we include differentiation trajectories with varying bifurcated, circular, convergent and mixed topology studied in single-snapshot as well as time-series single-cell RNA sequencing experiments. We demonstrate superior and enabling capability to reconstruct differentiation trajectories in comparison to state-of-the art trajectory inference approaches.

bioinformatics↗

bioRxiv2020

Fate trajectories of CD8+ T cells in chronic LCMV infection

AO_SCPLOWBSTRACTC_SCPLOWIn chronic infections CD8+ T cells acquire a state termed "exhaustion" which is characterized by impaired effector functions and expression of co-inhibitory receptors as response to continuous TCR stimulation. Recently, the pool of exhausted T cells has been shown to harbor multiple functionally distinct populations with memory-like and effector-like features, though differentiation and lineage relations between these are unclear. In this work we present a comprehensive scRNAseq time-series analysis from beginning of infection to established exhaustion in CD8 T cells. We apply lineage inference using informed cell transitions derived from RNA velocity to identify differential start and end states and connections between them. We identify a branch region early during chronic infection where pre-committed cells separate into an exhausted and a memory-like lineage and discovered molecular markers demarcating this branch event. Adoptive transfer experiments confirmed fate-commitment of cells only after this branch point. We additionally linked the progression along developmental lineages to antigenic TCR stimulation.

immunology↗

bioRxiv2019

The type IV pilin PilA couples surface attachment and cell cycle initiation in Caulobacter crescentus

Understanding how bacteria colonize surfaces and regulate cell cycle progression in response to cellular adhesion is of fundamental importance. Here, we used transposon sequencing in conjunction with FRET microscopy to uncover the molecular mechanism how surface sensing drives cell cycle initiation in Caulobacter crescentus. We identified the type IV pilin protein PilA as the primary signaling input that couples surface contact to cell cycle initiation via the second messenger c-di-GMP. Upon retraction of pili filaments, the monomeric pilin reservoir in the inner membrane is sensed by the 17 amino-acid transmembrane helix of PilA to activate the PleC-PleD two component signaling system, increase cellular c-di-GMP levels and signal the onset of the cell cycle. We termed the PilA signaling sequence CIP for cell cycle initiating pilin peptide. Addition of the chemically synthesized CIP peptide initiates cell cycle progression and simultaneously inhibits surface attachment. The broad conservation of the type IV pili and their importance in pathogens for host colonization suggests that CIP peptide mimetics offer new strategies to inhibit surface-sensing, prevent biofilm formation and control persistent infections.\n\nSignificance StatementPili are hair-like appendages found on the surface of many bacteria to promote adhesion. Here, we provide systems-level findings on a molecular signal transduction pathway that interlinks surface sensing with cell cycle initiation. We propose that surface attachment induces depolymerization of pili filaments. The concomitant increase in pilin sub-units within the inner membrane function as a stimulus to activate the second messenger c-di-GMP and trigger cell cycle initiation. Further-more, we show that the provision of a 17 amino acid synthetic peptide corresponding to the membrane portion of the pilin sub-unit mimics surface sensing, activates cell cycle initiation and inhibits surface attachment. Thus, synthetic peptide mimetics of pilin may represent new chemotypes to control biofilm formation and treat bacterial infections.

microbiology↗