Biology subjects

Quenneville, J.

Publications and source records attributed to Quenneville, J..

3 recordsLinked to original sources

bioRxiv2025

Bringing the Genetically Minimal Cell to Life on a Computer in 4D

We present a whole-cell spatial and kinetic model for the 100 minute cell cycle of the genetically minimal bacterium, JCVI-syn3A. This is the first simulation of a complete cell cycle in 4D including all genetic information processes, metabolic networks, growth, and cell division. Integrating hybrid computational methods, dynamics of the morphological transformations were achieved. Growth is driven by synthesis of lipids and membrane proteins and constrained by new fluorescence imaging data. Chromosome replication and segregation is controlled by essential SMC and topoisomerase proteins in Brownian dynamics simulations with replication rates responding to dNTP pools from metabolism. The model captures the origin to terminus ratio measured in our DNA sequencing and recovers other experimental measurements like doubling time, mRNA half-lives, protein distributions, and ribosome counts. Because of stochasticity, each replicate cell is unique. Not only do we predict average behavior for partitioning to daughter cells, we predict the heterogeneity among them.

biophysics↗

bioRxiv2024

Virus-free continuous directed evolution in human cells using somatic hypermutation

The B cells of the human immune system have evolved somatic hypermutation (SHM) mechanisms that introduce mutations at the immunoglobulin genomic loci at a significantly higher frequency than the rest of the genome thereby allowing them to evolve antibody sequences without compromising fitness due to genome-wide mutations. Inspired by these observations, here we developed a continuous directed evolution platform in human B cell lines (CODE-HB) that repurposes the SHM mechanisms to a stable, non-immunoglobulin genomic locus of the human B cell lines to continuously evolve cytosolic and surface displayed proteins with a broad mutational spectrum comprising of substitutions, deletions and insertions. We developed a human B cell surface display platform and used CODE-HB to evolve neutralizing antibodies targeting avian influenza and escape variants of influenza. Given the modularity and simplicity of CODE-HB, we anticipate that this platform can be used for rapidly evolving biotechnologically relevant biomolecules directly in human cells.

synthetic biology↗

bioRxiv2023

Long-term severe hypoxia adaptation induces non-canonical EMT and a novel Wilms Tumor 1 (WT1) isoform.

The majority of cancer deaths are caused by solid tumors, where the four most prevalent cancers (breast, lung, colorectal and prostate) account for more than 60% of all cases (1). Tumor cell heterogeneity driven by variable cancer microenvironments, such as hypoxia, is a key determinant of therapeutic outcome. We developed a novel culture protocol, termed the Long-Term Hypoxia (LTHY) time course, to recapitulate the gradual development of severe hypoxia seen in vivo, to mimic conditions observed in primary tumors. Cells subjected to LTHY underwent a non-canonical epithelial to mesenchymal transition (EMT) based on miRNA and mRNA signatures as well as displayed EMT-like morphological changes. Concomitant to this, we report production of a novel truncated isoform of WT1 transcription factor (tWt1), a non-canonical EMT driver, with expression driven by a yet undescribed intronic promoter through hypoxia-responsive elements (HREs). We further demonstrated that tWt1 initiates translation from an intron-derived start codon, retains proper subcellular localization, DNA binding, and its human ortholog negatively predicts long-term patient survival. Our study demonstrates the importance of culture conditions that better mimic those observed in cancers, especially with regards to hypoxia, and identifies a novel isoform of WT1 which correlates with poor long-term survival in ovarian cancer.

molecular biology↗