Collaborating Authors

Experimental cancer vaccine is being tested on dogs

Daily Mail - Science & tech

A vaccine to try and prevent or delay cancer in dogs could one day be trialled on people, according to researchers. Scientists are preparing to test a drug that is hoped to train the immune system to recognise and attack a specific part of cancer cells. They have chosen a part of cancer cells which the immune cells – white blood cells – normally attach to, and which they believe are common to various cancers. Teaching the body to attack this whenever it finds it could mean dogs' bodies have a very early line of defence against tumours. And because cancer in dogs develops in a similar way to humans, and may be triggered by similar environmental factors, the jab could one day be given to people.

Using ``epitomes'' to model genetic diversity: Rational design of HIV vaccine cocktails

Neural Information Processing Systems

We introduce a new model of genetic diversity which summarizes a large input dataset into an epitome, a short sequence or a small set of short sequences of probability distributions capturing many overlapping subsequences fromthe dataset. The epitome as a representation has already been used in modeling real-valued signals, such as images and audio. The discrete sequence model we introduce in this paper targets applications in genetics, from multiple alignment to recombination and mutation inference. Inour experiments, we concentrate on modeling the diversity of HIV where the epitome emerges as a natural model for producing relatively smallvaccines covering a large number of immune system targets known as epitopes. Our experiments show that the epitome includes more epitopes than other vaccine designs of similar length, including cocktails of consensus strains, phylogenetic tree centers, and observed strains. We also discuss epitome designs that take into account uncertainty about T-cell cross reactivity and epitope presentation. In our experiments, we find that vaccine optimization is fairly robust to these uncertainties.

Pair of antibodies that BLOCK coronavirus from infecting human cells are discovered

Daily Mail - Science & tech

Chinese scientists have discovered two antibodies which prevent the coronavirus from invading human cells. The distinct antibodies are called H4 and B38 and prevent SARS-CoV-2, the virus which causes COVID-19, from latching on to uninfected cells. In preliminary trials on mice, the amount of virus inside infected lungs was reduced by up to a third after just three days and the rodents suffered less damage to their respiratory system. The antibodies were discovered in the blood of a recovered patient and block the pathogen from binding to the ACE2 receptor on the surface of many human cells. Previous studies have found ACE2 -- an enzyme which sticks out from the surface of our cells and creates small proteins which help regulate blood pressure, wound healing and inflammation -- acts as an inadvertent gateway for the virus.

Potential Neutralizing Antibodies Discovered for Novel Corona Virus Using Machine Learning: Model and Code


The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. Recent outbreak of novel coronavirus infected and killed thousands of people in the world. Rapid methods in finding peptides or antibody sequences that can inhibit the viral epitopes of COVID-19 will save the life of thousands. In this paper, we devised a machine learning (ML) model to predict the possible inhibitory synthetic antibodies for Corona virus. We collected 1933 virus-antibody sequences and their clinical patient neutralization response and trained an ML model to predict the antibody response.

Targeting of cancer neoantigens with donor-derived T cell receptor repertoires Science


Accumulating evidence suggests that clinically efficacious cancer immunotherapies are driven by T cell reactivity against DNA mutation–derived neoantigens. However, among the large number of predicted neoantigens, only a minority is recognized by autologous patient T cells, and strategies to broaden neoantigen-specific T cell responses are therefore attractive. We found that naïve T cell repertoires of healthy blood donors provide a source of neoantigen-specific T cells, responding to 11 of 57 predicted human leukocyte antigen (HLA)– A*02:01–binding epitopes from three patients. Many of the T cell reactivities involved epitopes that in vivo were neglected by patient autologous tumor-infiltrating lymphocytes. Finally, T cells redirected with T cell receptors identified from donor-derived T cells efficiently recognized patient-derived melanoma cells harboring the relevant mutations, providing a rationale for the use of such "outsourced" immune responses in cancer immunotherapy.