Master’s Student opportunity in the CSM

May 2022

We are seeking a Master’s student in the interdisciplinary field of Computational biology, Biophysics, Systems biology, Bioinformatics, Data Science

Research Group

Our research group aims to identify genes, proteins and metabolites implicated in human disease. We use bioinformatics, systems biology, mathematical modelling and machine learning approaches to develop new prognostic and predictive tools for the treatment of cancer, neurological and metabolic disorders.

The student will be involved in a data driven, interdisciplinary research project about colorectal cancer. This is part of a wider research project called COLOSSUS. COLOSSUS is a 14-partner H2020 Research and Innovation action (H2020-SC1-2017-Two-Stage-RTD) funded under “Understanding health, wellbeing and disease” coordinated by the Royal College of Surgeons in Ireland.

COLOSSUS aims to provide new and more effective ways to classify patients with a specific subtype of metastatic colorectal cancer (microsatellite stable RAS mutant metastatic colorectal cancer or MSS RAS mt mCRC) and to develop new treatment options for them. The ultimate goal is to deliver a personalised medicine approach for patients with MSS RAS mt mCRC, that is currently not available.

See our website:

– https://www.systemsmedicineireland.ie/research/

Your Qualifications

o Highly creative and highly motivated candidate with excellent knowledge of either biology, physics, computer science or mathematics.

o Able to communicate clearly and fluently in English.

o For Master program: Acquired or expected undergraduate degree with at least 2:1.

o Knowledge of either Python, Julia, R, C, MATLAB is a must.

Offer

o Stipend of €18.000 for one year (registration as Master by Research student at RCSI University)

o Fees covered for EU/UK students

Admission period

October 2022 (Fall)

How to Apply?

Send an email to Prof Jochen Prehn – prehn@rcsi.ie with the following documents attached.

o A cover letter (to “Jochen Prehn”) including your research interests and training

o Your detailed CV

The deadline for application procedures is around mid-June 2022.

Contact for questions Send an email to marcsturrock@rcsi.com or annamatveeva@rcsi.com

Royal College of Surgeons in Ireland, Dublin, Ireland

Founded in 1784, RCSI is one of the most innovative and student-focused health sciences universities in the world. RCSI students enjoy an immersive educational and social experience, and study in the very heart of Dublin city. RCSI is ranked in the top 50 universities worldwide for Good Health and Well-being in the THE University Impact Rankings 2022. Based in the heart of Dublin city center, with four overseas campuses, RCSI is dedicated to the development of healthcare leaders who make a difference worldwide. The college enjoys a vibrant combination of nationalities and cultures where students from around the world exchange ideas and learn from one another. More than 60 nationalities are represented on the RCSI student body and students enjoy the full ‘RCSI Experience’, which extends beyond the curriculum to a rich tapestry of student clubs and societies that equip them for a life of leadership and civic participation. RCSI graduates are part of a global healthcare network of more than 20,000 alumni, who are highly recognized and much sought after internationally.

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Prof Prehn will speak at the 2nd International Conference of Non- Lethal Roles of Cell Death Proteins in Galway

5 – 8 September 2022 — Galway, Ireland

Prof. Jochen Prehn will discuss how death receptor signalling promotes entosis at the ‘Non-Lethal Roles of Cell Death Proteins’ conference. We look forward to hearing this exciting talk. For more information and registration, visit: https://non-lethal-roles.org

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PD Mito-quant Information Videos

Interviews with Researchers by Parkinson’s UK Volunteer

Paula Scurfield, one of the project’s PPI volunteers from Parkinson’s UK interviewed partners from Radboud University Nijmegen Medical Center and GeneXplain GmbH.

Here are the links to the videos

n November 2020, April 2021 and March/April 2022, the RCSI, Royal College of Surgeons hosted three online event series about ‘Parkinson’s Research in Ireland’.
Below are some of the talks given during the events.

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Dr Heiko Dussmann speaks at Microscopy Society and Microscopy Society Ireland joint meeting in Galway.

Wonderful talk by Dr Heiko Dussmann at the Microscopy Society and Microscopy Society Ireland joint meeting in Galway on the 7th of April about analysing mitochondrial morphology in a model of Parkinson’s Disease related to the work that the group do for PD-MitoQUANT. Acknowledged is the involvement of Franziska Walter, Anagha Jagannathan, Orla Watters, Niamh M Connolly and Jochen Prehn.

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Immuno-Oncology and the Microbiome Research Workshop- March 24th

This event will discuss the current landscape of clinical and preclinical research in cancer immunotherapy and the microbiome in Ireland.

register

https://www.eventbrite.ie/e/immuno-oncology-and-the-microbiome-research-workshop-registration-272607435177

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Parkinson’s Research In Ireland, Virtual Series March 31st and April 7th-6 pm -7 pm

To mark Parkinson’s Awareness Month, please join us for this years virtual series to provide perspectives from people with Parkinson’s, researchers, Industry, and tips from a Physiotherapist, in the form of short talks and an audience Q&A.

register: bit.ly/3C8R9Up

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Irish researchers lead new European research programme on precision medicine for motor neuron disease

Tánaiste and Minister for Enterprise, Trade and Employment, Leo Varadkar TD hastoday launchedan ambitious academic, clinical and industry research programme that will provide new insights into our understanding of Motor Neuron Disease (MND).

FutureNeuro, hosted by RCSI University of Medicine and Health Sciences, is co-lead on the Precision ALS programme which will develop advanced data-driven prediction models for progression of the disease in patients and provide next-generation data analysis that facilitates clinical insights and treatment for Motor Neuron Disease, also known as Amyotrophic Lateral Sclerosis (ALS).

Two SFI Research Centres, ADAPT and FutureNeuro, lead the programme which involves world class Irish-based researchers in clinical science, data science and artificial intelligence (AI). The researchers will work in partnership with TRICALS, an independent consortium of leading ALS experts, patients and patient advocacy groups across Europe. National and international industry partners and charities including patient organisations are also actively participating. 

The research is supported by the Irish Government through a Science Foundation Ireland investment of €5 million which will be leveraged with an additional €5 million from industry partners.

Speaking at the launch, Tánaiste and Minister for Enterprise, Trade and Employment, Leo Varadkar TD said: “This project straddles clinical research and industry, and will combine the best of our technologies, the best of our ideas, and the best of our medical expertise with the potential to change lives for the better. It will develop tools that facilitate clinical trials based on precision-medicine, and has the potential to produce benefits for other rare conditions and diseases, supporting job creation and reducing drug costs.”

Precision ALS will provide an innovative and interactive platform for all clinical research in ALS across Europe, that will then harness AI to analyse large amounts of data. As the largest international multimodal dataset aimed at precision medicine for this condition, Precision ALS will address the issues with gathering new data at scale in a timely and cost effective-manner across multiple international sites in order to present that data in real time to clinical scientists.

ALS/MND causes progressive decline in movement, cognition and behaviour. Although uniformly terminal, life expectancy can vary from three months to many years from first symptom, and there are no effective treatments. Irish researchers, along with their European collaborations in ALS/MND, have shown that the disease is caused by variable combinations of faulty genes that likely interact with lifestyle and environment. Precision ALS will provide the technology to improve our understanding of how these factors impact the development of the disease. This in turn will inform which treatments will work for each individual, instead of a one-size-fits-all approach. 

Professor David Henshall, Director of the SFI FutureNeuro Centre for chronic and rare neurological disease and Professor of Molecular Physiology and Neuroscience at RCSI University of Medicine and Health Sciences said: “The launch of Precision ALS marks an important step towards achieving FutureNeuro’s mission to change the patient journey for high-burden neurological disease. MND or ALS is one of the main brain diseases of focus at FutureNeuro where research by Professor Orla Hardiman (Precision ALS Lead), Professor Jochen Prehn and others in the Centre have led to advances in understanding disease mechanisms, predicting disease course and new ways to improve care and extend lives. A key focus has been on better data-driven approaches that will provide the right drug for the right patient at the right time.

“By working with ADAPT, this unique collaboration between clinicians, computer and data scientists is ideally positioned to bring about change and draws on our Centre’s reputation and capabilities in genomics, deep phenotyping, cognitive profiling, neuroelectrical signalling and imaging analysis and expertise in design-thinking and ethnography.”

Commenting on today’s launch, Professor Fergal O’Brien, Deputy Vice Chancellor for Research & Innovation, RCSI, University of Medicine and Health Sciences said: “Precision ALS is aligned with RCSI’s mission to deliver impactful research to address global healthcare specifically in the area of neurological and psychiatric disorders, one of RCSI’s priority research areas. In RCSI, the Precision ALS research led by Professor Jochen Prehn, will focus on the evaluation of novel biomarkers including microRNA, for ALS, and the development of data-driven prediction models that provide individual patient forecasts of ALS progression. By leveraging our world-class expertise in neurological research, FutureNeuro and RCSI can further drive improvements in care for people with Motor Neuron Disease through this exciting new programme. ” 

Speaking at the launch, Professor Philip Nolan, Director General of SFI said: “The SFI Research Centres were developed to create critical mass of excellent research in areas of national importance, and to ensure this research has tangible benefits for our health, our society and our economy through collaboration between academia, Government and industry across the island of Ireland and internationally. I am delighted to welcome the launch of Precision ALS, which will deliver outstanding science in the area of personalised and precision medicine, focused on neurodegenerative disease. This collaboration will directly benefit healthcare and patient communities, and yield new knowledge, approaches and treatments with the potential to improve the lives of many.”

Supporting the Precision ALS programme, Simon Harris T.D. Minister for Further and Higher Education, Research, Innovation and Science said: “The Covid-19 pandemic has taught us the value of research and the difference it can make to people’s lives. This is a perfect example of the impact research and innovation can have. By supporting and harnessing these types of advanced research projects we will ultimately see the benefits across society.”

On completion, Precision ALS will be a first-in-kind modular transferable pan-European ICT framework for ALS that can be easily adapted to other diseases that face similar precision medicine-related challenges.

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New relationship found between bacteria and bowel cancer

New research from Professor Prehns laboratory, has found a possible relationship between the presence of a specific type of bacteria found in tumours and the spread of bowel cancer. 

Published in the leading gastroenterology journal Gut, findings of the research can help clinicians to identify patients at risk of poorer outcomes and make decisions on treatment options for patients with bowel cancer whose tumours are infected with the bacterium Fusobacterium nucleatum.

Using genomic sequencing, researchers are now able to detect traces of an infection with bacteria or other microbes in patients’ tumours that previously would have been undetectable. The RCSI-led research set out to understand which tumours are infected with bacteria, and what the role of a bacterial infection means in terms of how the disease progresses.

The research found that a collection of bacteria that normally lives in the oral cavity infects bowel tumours, changes how tumour cells behave, and may trigger the spread of the tumour to other organs. The study suggests that there is a direct relationship between the presence of a bacteria called Fusobacterium nucleatum and the spread of bowel cancer resulting in poorer outcomes for a subset of patients.

Lead researcher, Jochen Prehn, Professor of Physiology and Director of the Centre for Systems Medicine at RCSI said: “An effective tool to help oncologists to personalise colorectal cancer treatment is urgently needed.”

“This study demonstrates the role that bacteria play in the spread of bowel cancer in patients. We hope these finding will enhance diagnostics to improve the efficacy of current treatment and help further advance the use of new therapeutics for patients infected with this bacterium”, added Professor Prehn.

According to the Irish Cancer Society, almost 3,000 people are diagnosed with bowel cancer in Ireland each year and worldwide, bowel cancer presently accounts for approximately 10% of new cancer cases diagnosed (1.9m cases, WHO 2020).

In this collaborative study with Queens University Belfast, samples from patients from Northern Ireland and from over 600 patients from the Cancer Genome Atlas were analysed. The Cancer Genome Atlas is an international programme that analyses the genetic mutations responsible for cancer types to help researchers and clinicians to better understand the disease and how to treat it.

The study was supported by the RCSI and the Irish Centre for High-End Computing (ICHEC) and funded by the Health Research Board, Science Foundation Ireland and the Northern Ireland Department for the Economy (NI DfE).

see link below for the publication in Gut

https://pubmed.ncbi.nlm.nih.gov/34497144/

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Researchers discover potential new therapy for chemotherapy-resistant breast cancer

Scientists have discovered a molecule that can selectively kill cells of a hard-to-treat subtype of breast cancer, which could lead to a new therapy.

The study, led by researchers at RCSI University of Medicine and Health Sciences, is published in the current edition of Science Advances.

Triple negative breast cancer is a subtype of breast cancer which is mainly treated with chemotherapy. Unfortunately, up to 70% of patients with this form of breast cancer develop resistance to treatment.

The researchers tested different molecules to see if they could selectively kill the cells of this type of breast cancer while sparing normal cells. They found that a specific molecule, BAS-2, was able to do this.

“Our aim now is to develop the small molecule into a more drug-like compound and to assess if we can harness the new function for potentially improved treatment of patients,” said Dr Tríona Ní Chonghaile, the study’s corresponding author and an RCSI lecturer in Physiology and Medical Physics.

To better understand how the molecule killed the cells, the researchers confirmed that it inhibited an enzyme called HDAC6. Using state-of-the art mass spectrometry, the researchers identified, for the first time, that HDAC6 plays a key role in altering energy in these cancer cells.

The work was funded by the Wellcome Trust Seed Award, L’Oreal-UNESCO For Women in Science Programme and Science Foundation Ireland’s Frontiers for the Future Programme. In addition to those from RCSI, the work was carried out by researchers from the UCD Conway Institute of Biomedical and Biomolecular Sciences, NYU Langone Medical Center, Penn State University, the Koch Institute for Integrative Cancer Research at MIT and the Dana-Farber Cancer Institute at Harvard Medical School.

With the help of RCSI’s Office of Research and Innovation, the researchers have submitted a patent around this work and are seeking industry partners to further develop this treatment.

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PD MitoQuant Webinar will host a three part Webinar Series-

PD MitoQuant are holding a three part Webinar series of talks with the Theme being: Parkinson’s research in Ireland, in November with Short lively talks, followed by Q&A session: – see flyer for details

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