Research Projects

Welcome to The Plotkin Group Research Group!

Plotkin Lab

Plotkin Group Members (pre-pandemic): Left to right: Pranav Garg, Kathryn Lande, Aina Adekunle, Kyra Boulding, Dr. Steven Plotkin, Dr. Luke McAlary, Shawn Hsueh, Lana Kashino, Tiam Heydari

Come meet the members of our team, review our current research, and find out how you can join. 

We are currently looking for experimental and computational researchers for the developmental biology, viral evolution, and protein misfolding projects below.

Molecular-Genetic Origins of Multicellularity

Multicellularity emerges when cells cooperatively differentiate and organize spatially into an integrated organism in a process that is genetically encoded for successive generations to reliably reproduce from a single progenitor cell. Depending on the degree to which cellular aggregation, sustained cell-to-cell inter-connection, communication, and cooperation are integrated, the transition to multicellularity has occurred anywhere from about a dozen to about 40 independent times across the tree of life during evolutionary history. The repeated instances of this transition across distinct environments and various epochs, and on different phylogenetic backgrounds, suggests that multicellularity is a phenomenon that arose, and can arise, as a generic physicochemical response to various environmental pressures. In this sense then it is a natural consequence of evolution, and a universal aspect of life.

This is a new project that has become one of the primary focuses of our lab. We are investigating the function and evolution of genetic regulatory networks (GRNs) involved in the process of cell differentiation; we are currently developing CRISPR/Cas9 genetic manipulation methods in emerging model organisms to address this question.

One extant animal lineage that has emerged as a candidate for the sister group to the other metazoa are the Ctenophora, which diverged from other animal clades over 550 million years ago: Ctenophores or comb jellies are a phylum of gelatinous zooplankton found in all of the world’s oceans. We are using ctenophores to obtain information on the conservation of relevant gene regulatory networks (GRNs) across the metazoans, to address questions of the GRN’s evolutionary origins. The ctenophore Mnemiopsis leidyi is in many ways an ideal embryologic system to investigate questions on the origins of animal multicellularity.

Evolution of the SARS-CoV-2 Virus

As the ongoing COVID-19 pandemic continues to affect people throughout the world, the inherent possibility of SARS- CoV-2 to mutate and evolve into further novel variants and strains of which considerable dangers and public health risks apply remains prevalent. As the world has already witnessed, these new variants carry the potential to be both more infectious and better biologically equipped to evade our current antibody and vaccine therapies. To combat this threat, this project seeks to develop, implement, and evaluate therapeutics that are effective against possible future emerging SARS-CoV-2 variants. Within the scope of this research, we use a safe and modified virus (containing CoV-2 Spike proteins) to both predict future variants and develop therapeutics that are robust and difficult for the virus to evade. We propose two strategies, one that involves using a decoy to prevent SARS-CoV-2 from entering human cells, and another that involves characterizing a region of the Spike protein that could be developed in the future as a vaccine that is effective against a wide variety of variants. Several industrial partners will play an integral role in the development of these therapeutics, in order to pursue possible “universal” vaccine candidates in the future.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has caused devastating health and economic impacts worldwide. Furthermore, the emergence of novel variants that spread more efficiently and render vaccines less efficacious is a cause for concern. In this project, we aim to develop therapeutics that are resistant to viral antigenic escape by targeting conserved regions of the SARS-CoV-2 Spike protein and conserved mechanisms of viral cell entry.

Because binding of the Spike protein to cellular receptor, ACE2, is required for entry, we propose a method to exploit this entry requirement in antibody therapeutics. We will then use replication-competent vesicular stomatitis virus pseudotypes harbouring the SARS-CoV-2 Spike protein (rVSV-SARS-CoV-2) to study the evolution of SARS-CoV-2 under selective pressures of these and other antibody therapeutics, by sequencing over several passages. By identifying conserved regions on SARS-CoV-2 Spike, we are able to propose is candidate immunogens for vaccine development. We use rational protein design to generate immunogens, and employ surface plasmon resonance to assess if convalescent sera can bind to predicted epitopes. Next steps involve testing neutralization and virus evolution in the presence of immunized sera. In sum, we aim to develop SARS-CoV-2 therapeutics that are resistant to viral escape and efficacious against current and future SARS-CoV-2 variants.

Novel computational approaches to predict misfolding-specific epitopes and design precision immunotherapeutics for neurodegenerative disease

We have developed a new way to rationally-predict disease-specific epitopes in misfolding prone proteins. I am co-inventor on >50 patents in the last 6 years on applications of this technology to personalized medicine in Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS) immunotherapy, along with my experimental colleague Neil Cashman. The
inventions focus on computationally­predicted disease­specific epitopes in Amyloid beta and tau protein, two of the primary proteins whose misfolding and aggregation is implicated in AD. We have designed and developed conformationally­selective antibodies (Abs) that selectively bind these conformational epitopes. These precision Abs are designed to spare healthy protein, but target misfolded protein when it is behaving pathogenically. They are selective to toxic oligomers. We also pursue optimal epitopes and precision Abs for other proteins and diseases, including
alpha­synuclein in PD, and TDP­43 in ALS.

The methodology involves stressing structured fibrils computationally using a “Collective Coordinates” method (see this publication: PDF and also “Systems and Methods for Predicting Misfolded Protein Epitopes by Collective Coordinate Biasing” S.S. Plotkin, PCT/CA2016/051306).

Variations on irrational design are often used as a best guess for antibody development. I emphasize that rational design of antibodies from first principles using concepts from physical chemistry and structural molecular biology is a transformative concept in neurodegenerative disease immunotherapy, whose consequences are only beginning to be explored, and are being pioneered by our lab.

Given epitope predictions, we develop precision antibodies that best target diseased protein. Epitopes are optimally presented in cyclic peptides again using a computational design protocol which we have pioneered. Our Abs will ignore an epitope if the conformation is the same as in healthy protein, and our Abs are also designed to spare off-pathway targets in the human proteome. We use a multiplecriteria decision making (MDCM) scheme to screen and discover optimal precision Abs.

This work has been done in close collaboration with my colleague Neil Cashman, in experimental neurology. The IP has been supported and licensed by ProMIS Neurosciences Inc., a development-stage biotech company developing precision therapeutics for the treatment of AD and ALS. I was the first Chief Physics Officer for ProMIS Neurosciences (and maybe the only Chief Physics Officer anywhere!)

A novel feature of our AD antibodies directed against A-beta, which has resulted from our unique computational design approach, is that they do not bind Abeta plaques. This has been verified by immunohistochemistry of normal and AD patient brain sections. This is important, because most healthy but aged individuals have brains that are abundant with plaque, but they are free from AD symptoms because they do not carry toxic oligomeric strains of Abeta. The oligomer-selectivity of our antibodies is a unique strength: Many current commercial antibody hopefuls do in fact bind plaque, and as a result, treatment with these Abs may suffer from doselimitations related to the inflammation and edema they induce.

Designing Abs that are conformationally-selective to toxic oligomers is an extremely powerful technological approach, which has the potential to transform the way therapies are developed in the pharmaceutical industry, with profound implications for human health benefits of both Canadians and people abroad.