EPICIR

Epigenetics of Immunity in Cancer

EPICIR
  • Project duration: September 2019 - December 2022
  • Project status:
    Ongoing
  • Funding:
    Italy-Austria 2014-2020 (EUTC / EU funding / Project)
  • Total project budget: €216,404.00

"Cancer inhibitors" in immune therapy: initiation of a promising research project

Cancer is characterized by uncontrolled cell growth, which can spread to otherwise healthy tissue and organs. Only five to ten percent of cancers are caused by inherited genetics, the majority of the cases are triggered by external factors such as tobacco consumption, diet, infections, or radiation. These external factors may induce so-called epigenetic changes, which may result in cancer cells being no longer recognized by the immune system. Cancer cells thus "hide" from the immune system.

However, some of these epigenetic changes are reversible, and that's where the scientists are going to act on. Utilizing inhibitory compounds (in short, inhibitors) allows prevention of these changes and reactivate previously deactivated genes, so that the immune system can retake action and remove degenerated cells.

The "Epigenetics of Immunity in Cancer" (EPIC) project was started in September 2019, focusing on histone deacetylase (HDAC) inhibitors. The research team comprises of chemists, clinicians, biologists, and bioinformaticians from the universities of Udine, Salzburg, and Trieste, as well as the Institute for Biomedicine at Eurac Research in Bolzano. The team is testing the effect of HDAC inhibitors in cancer cells and their suppressive role in tumor progression. In particular, the University of Udine is checking HDAC inhibition based on a library of HDAC compounds, whereas the University of Trieste is optimizing promising compounds with the aid of computer programs followed by their synthesis. At the University of Salzburg, selected inhibitors are being tested in cell models with respect to their influence on the immune system. Data generated by all partners are shared with bioinformaticians at Eurac Research, who are tasked with their analysis. Invoking next generation sequencing methods, the differences between cancer cells with and without inhibitors are measured: which genes are active, where are they active and what consequences could these compounds have in the human organism. Data obtained from theses analyses are compared to international databases in order to gain additional knowledge on cancer development. In this way, the three-year lasting project is supposed to create the basis for novel advances in cancer immune therapy.

Partner
University of Salzburg
University of Trieste
University of Udine

This project is funded by the European Regional Development Fund and the Interreg V-A Italia-Österreich 2014-2020.

Scientific Output

How to organize the EPIC blog - examples

Method 1: accordion. Click on the + to expand

Method 1: accordion. Click on the + to expand

Science administration

05-28-2021 Most people think of scientists working at the lab bench, performing experiments or sitting in front of the computer working on theoretical problems. And this is mostly true. However, science also needs to be administrated. Planning, coordination and reporting to the stakeholder are the tasks that are performed at the (home) office desk. Since EPIC is financed by Interreg V-A Italy-Austria, which is a dedicated regional EU fund, there clearly is a proper interest on our activities from the funding agency's perspective. Is the project progressing as documented in the proposal? Do the different partners cooperate productively? How is the budget spent?

Every half a year all partners are thus submitting their progress reports (coordinated by the lead partner in Udine) to their regional funding offices for evaluation. And that's exactly what we are currently doing here at the end of May: we formally demonstrate the progress made in our EPIC project.

Congrats, Emanuela!

05-18-2021

Today is a special day: Dr. Kerschbamer joined the EPIC team exactly a year ago.

Online meetings with Udine partner

04-16 04-01 2021 02-23 02-04 2021

It's paper writing time. We have already had a series of meetings with the Lead Partner in Udine, who is also the driving force behind the manuscript. We are interpreting gene expression changes of leiomyosarcoma cells in different classes of HDAC inhibitors, which were the basis for the RNA-seq experiments mentioned earlier. We might have some interesting candidate genes, that's something we need to dive into a bit more, though. Overall, it looks like we have an interesting wetlab/bioinformatics paper growing here these days

Online meeting with Udine partner

12-23-2020 Last working day in this year and still fully focused on EPIC with another meeting. Today we had a look at the commonalities in gene expression change between different HDAC inhibitors. It is interesting to see a big expression landscape change already after 6 hours past inhibition. Maybe the commonalities will lead us to some sort of a first simple HDACi signature.

Method 2 : simple list

Online meeting with Udine partner

12-11 2020

In the beginning of October we have received our first RNA-seq dataset from Udine. A couple of samples were re-sequenced and now it's time to look at it in more detail than we could spend in our virtual workshop. Today we compared two orthogonal approaches to analyzing the sequencing data and agreed on the next steps. Another meeting briefly before Christmas will serve as a follow-up.

Second virtual workshop with all partners

12-03 2020 Today we had our second meeting with all network partners. Needless to say, it was online again. We have seen a total of seven presentations in the course of this four hour meeting. It's great to see how the different threads in the project converge to the overall goal of improving HDAC inhibition. Dr. Kerschbamer has summarized our ongoing collaborative work with Salzburg and then went into detail on her RNA-seq analysis, where she has investigated the cellular response to HDAC inhibition looking at a dataset originating from the Udine lab

Online meeting with Salzburg collaborators

10-21-2020

In our monthly get together with our partners from Salzburg, we have identified an interesting experimental setup that can use the transcription factor binding data we have obtained recently and discussed during the meeting

First dataset has arrived​

10-08-2020

We have received our first transcriptome dataset from the Udine partner. It contains experiments on several HDAC inhibitors and a time series of RNA production in cells after 6 and 24 hours of treatment.

Method 3:simple paragraph

09-16-2020

Online meeting with Salzburg collaborators

Off into the next round of scientific exchange with our lab partners from Salzburg. This time Dr. Kerschbamer has presented her test runs of software that can assign immune cell types from a mixture of RNA-sequenced cells, in this case we have chosen to look at colorectal cancer samples. She further demonstrated how we can use our immune system gene panel on restricting output from differential gene expression data.

Poster has arrived

08-05-2020

Even though most of us are in their smart offices at home, from time to time we are visiting our workplace. What a coincidence, today we spent a day at work and our EPIC poster has finally arrived freshly from the press.

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EPICIR

Epigenetics of Immunity in Cancer

Duration: September 2019 - September 2021Funding:
Italy-Austria 2014-2020 (EUTC / EU funding / Project)

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