Senior computational fellow - Altius institute for biomedical sciences

Allison
Cote

About

Updated SEPTEMBER 2022

Allison is currently a Senior Computational Fellow at Altius Institute for Biomedical Sciences, a nonprofit research organization focused on elucidating fundamental aspects of gene regulation. She completed her PhD in May of 2020 from the lab of Arjun Raj at the University of Pennsylvania. Click here for full CV.

Research Experience

Altius institute for biomedical sciences, Senior computational fellow

May 2022 - current

Allison’s current role involves investigating the relationship between genetic variation and phenotypic variation in primary and immortalized cell contexts via high throughput sequencing.

-

Barer institute, scientist

October 2020 - April 2022

Allison’s role involved investigating drugs that manipulate cancer metabolism and otherwise probing cancer metabolic pathways.

-

University of Pennsylvania, PhD/post doc, lab of arjun raj

April 2013 - October 2020

Zooming in on heterogeneity - from the tissue scale to individual molecules.

Part 1: Single-cell matrix gene expression heterogeneity does not predict matrix deposition Mesenchymal stem cells (MSCs) display substantial cell-to-cell heterogeneity, complicating their use in regenerative medicine. However, conventional bulk assays mask this variability. Here we show that both chondrocytes and chondrogenically induced MSCs exhibit substantial mRNA expression heterogeneity. Single-molecule RNA FISH to measure mRNA expression of differentiation markers in single cells reveals that sister cell pairs have high levels of mRNA variability, suggesting that marker expression is not heritable. Surprisingly, this variability does not correlate with cell-to-cell differences in cartilage-like matrix production. Transcriptome-wide analysis suggests that no combination of markers can predict functional potential. De-differentiating chondrocytes also show a disconnect between mRNA expression of the cartilage marker aggrecan and cartilage-like matrix accumulation. Altogether, these quantitative analyses suggest that sorting subpopulations based on these markers would only marginally enrich the progenitor population for ‘superior’ MSCs. Our results suggest that instantaneous mRNA abundance of canonical markers is tenuously linked to the chondrogenic phenotype at the single-cell level.

Part 2: Defining the boundaries of co-transcriptional splicing. Studies are beginning to show that splicing is on a spectrum of co- to post-transcriptionality, however, little is known about the spatial distribution of splicing within the nucleus. Most studies use biochemical means to separate the nascent RNA located at the site of transcription from the RNA in the surrounding nucleoplasm. We use RNA FISH to investigate the dispersion of introns and exons away from site of transcription and use this to infer the percentage of splicing that takes place in a post-transcriptional compartment. Even genomically proximal and distal introns within the same gene are observed with different dispersal patterns, suggesting differential regulation of splicing for those introns. This intron dispersal pattern also varies from gene to gene, and suggests that these introns are not spliced in a 5’ to 3’ order. The dispersal increases with increased transcription level, characteristic of an overwhelming of local splicing machinery. In order to further investigate what happens at the site of transcription we combined RNA FISH with expansion microscopy and discovered that, at the site of transcription, transcripts are stretched further than they are for equivalent transcripts in the nucleus. Using a splicing inhibitor increases dispersal of introns in two distinct ways, one by simply increasing the number of pre-mRNA away from the site of transcription but the other by filling a small compartment around the site of transcription with pre-mRNA, suggesting some sort of compartmental boundary for the diffusal of the pre-mRNA. Taken together, this suggests that, while most splicing occurs locally at the site of transcription, some splicing of most endogenous genes occurs post-transcriptionally, physically removed from the site of transcription.

–

University of pennsylvania, rotation student, lab of janis burkhardt

January 2013 - April 2013

Investigated the relationship between expression of the actin bundling protein fascin and ability of dendritic cells to migrate by using lentivirus to overexpress fascin and assess effects via cell migration assays. Collaborated with visiting scholar in the lab of Paul Janmey, PhD, to perform atomic force microscopy to investigate the effect of fascin overexpression on dendritic cell stiffness.

–

university of pennsylvania, rotation student, lab of rebecca wells

September 2012 - December 2012

Assessed the effects of cellular fibronectin containing extra domain A on the gene expression of transformed sinusoidal endothelial cells using qPCR.

–

Franklin w. olin college of engineering, Senior Engineering project (scope)

September 2011 - May 2012

Industry Collaborators: Boston Scientific, Position: Technical Lead

Performed mechanical testing on various tissue substitutes to aid in testing of and participated in design of endoscopic ultrasound guided fine needles.