Modelling patient data to improve personalised cancer therapies

Hashem Koohy was awarded a PhD in Systems Biology from Warwick University in 2010. He then moved to the Sanger Institute for a postdoc position with Prof. Tim Hubbard to work on transcriptional regulation and gene function. He subsequently took on a postdoc at the  Babraham institute where he became interested in the regulation of the mammalian adaptive immune system. In 2017, Hashem joined Oxford as a junior group leader. He is currently an MRC-funded group leader at the Human Immunology Unit based at the Weatherall Institute of Molecular Medicine (WIMM), studying mechanisms underlying heterogeneity of response in personalised cancer immunotherapies.

Over the past decade, different types of personalised immunotherapy treatments have revolutionised cancer treatment and significantly expanded survival time for cancers such as melanoma. However not all patients with these cancers benefit from or respond to immunotherapy the same way, and therefore biomarkers for improved response are highly sought. Moreover, cost reductions and advancements in sequencing technologies such as single-cell methods mean that patients may be associated with giga- (if not tera) bytes of data. A serious challenge lies in understanding and extracting biologically and immunologically significant information from these data, to develop insights into the complexity of the disease at question.

Hashem’s group applies mathematical and machine-learning models to high throughput sequencing patient data such as genomics, transcriptomics, epigenomics and proteomics. The data they are using to develop new models and algorithms comes from tens of thousands of patients. Their aim is to find out about the heterogeneity of response to treatment between cancer patients, ultimately hoping to hone our ability to offer personalised treatments to patients. Cancer vaccine targets are also part of this search, with a further aim being to predict vaccine targets that can be used as part of personalised vaccines to either prevent cancer initiation or train the immune system to find and destroy cancerous cells.

Hashem’s research is, by its nature, challenging and multi-disciplinary. He collaborates with a number of renowned immunologists within Oxford including the teams of Prof Cerudolo, Prof Simmons, and Prof Dong. Hashem is funded by the Medical Research Council (MRC) and HIU’s core budget.

Find out more about our research below

Finding extracellular vesicle biomarkers for oesophageal cancer early detection

Prof Deborah Goberdhan’s lab is investigating extracellular vesicles and the proteins they express as potential biomarkers for the progression from Barrett’s Oesophagus to oesophageal cancer
Christina Ye

Christina Ye awarded CRUK pre-doctoral fellowship

Christina Ye has been awarded CRUK pre-doctoral fellowship, she tells us about her upcoming project into T cell trafficking between the blood and skin when patients undergo checkpoint immunotherapy

Understanding how cancer arises from infected tissue

Dr Francesco Boccellato is investigating the mechanisms behind the pre-cancerous condition known as atrophic gastritis. This may help to identify those who may have cancer, as well as find new ways to prevent cancer from progressing
The NMR machine in the lab of James Larkins, with samples lined up to be analysed

Following the cancer metabolomic breadcrumb trail

By analysing the metabolic molecules that tumour cells leave behind, Dr James Larkin is investigating the applications of metabolomics in the early detection of many cancers.

SCALOP team discover new pancreatic cancer biomarker

The SCALOP clinical trial team have uncovered a new therapeutic target for locally advanced pancreatic cancer. Read more about it and the next steps for the SCALOP-2 trial.

The search for pancreatic cancer biomarkers

Nuffield Department of Population Health researchers are using the China Kadoorie Biobank to identify potential protein biomarkers in the blood that could be used to predict the presence or development of pancreatic cancer

What we can learn from cancer survivors

Understanding how an individual survives cancer, and why they respond well to therapy, can be vital in identifying new therapeutic targets. A new project seeks to see why some advanced pancreatic cancer patients overcome the odds and respond positively to treatment.

Early stage ‘red flag’ symptoms for pancreatic cancer

The ADEPTS study uses the QResearch database to better understand what ‘red flag’ symptoms may be associated with pancreatic cancer, in the hopes of promoting earlier diagnosis from primary care.

Detecting pancreatic cancer through blood tests

The Song Lab recently developed an effective and accurate way of detecting cancer biomarkers in the blood. Now, they are looking at the application of TAPS technology in pancreatic cancer