APERIM data demonstrate that immune repertoire profiling of tumor-infiltrating lymphocytes can be efficient from RNA-Seq

The knowledge about the vast heterogeneity of immune receptors and their role in the anti -tumor response has gained high importance for precision cancer medicine. Scientists therefore have an immense interest to collect information and profiling data of immune receptor repertoires – T-cell receptors (TCR) and immunoglobulins.

However, research groups often face the problem that available tumor material is insufficient to perform immune repertoire profiling along with other analyses such as Exome-Seq and RNA-Seq. Additional analyses also need additional resources, which burdens the large scale clinical trials.

The idea then was to bypass these limiting factors and to extract TCR and immunoglobulin repertoires from the bulk transcriptome sequencing data of tumor RNA. RNA-Seq is routinely performed and could be a useful alternative way to obtain the intratumoral repertoires of immune receptors.

MiLaboratory LLC recently upgraded its flagship software product, MiXCR, enabling it to efficiently extract TCR and immunoglobulin repertoires from RNA-Seq data.

Using MiXCR RNA-Seq mode to analyse bulk transcriptomic data of human melanoma, the APERIM researchers demonstrated that the extracted TCR repertoires of medium and large tumor-infiltrating T cell clones are very similar to those obtained using targeted TCR profiling performed from the same RNA samples.

In this work that involved a bundle of research groups it was also shown that high intratumoral expression of clonal IgG1 antibodies is associated with the best prognosis in human melanoma.

Finally, the work demonstrates that RNA-Seq performed for the pure sorted T cells allows to extract nearly complete TCR repertoires for these cells, which converts bulk transcriptomic profiling into a powerful universal approach for the functional analysis of T and B cell subpopulations.

All these findings, which were recently published in Nature biotechnology, should help to use RNA-Seq data as a source for antigen receptor repertoire profiling, amplifying the possibilities for adaptive immunity studies and rising the chances to find further clinically relevant biomarkers for cancer immunotherapy.

Original paper:

Online Database of T Cell Receptor Sequences was recently published

The database called VDJdb, developed by research group around Dmitriy Chudakov from Masarykova University, helps to reach the next step towards a new level of understanding the adaptive immune system.

Modern sequencing technologies are generating huge numbers of TCR sequences. However, up to now the sequencing data could hardly be linked to functionality of the phenotype TCRs i.e. the ability to recognize certain epitopes presented on a cell surface. Within APERIM finally the comprehensive repository VDJdb was developed, which collects information on TCR sequences with known antigen specificities. The primary goal of this work was to create an open source database and to facilitate access to existing information on T-cell receptor antigen specificities.

Within the cooperation in the APERIM network the establishment of this database is also essential for the development of a further software, called TCR2Epitope. Can Keşmir and her colleagues from the University of Utrecht are working on that visionary tool, which would in the future allow to predict the interaction between TCRs and certain epitopes. The therapeutic application of that tool presents an innovative method to support T cell-mediated cancer immunotherapy.

The infrastructure behind VDJdb allows community-driven data acquisition, proofreading and aggregation in order to establish a comprehensive repository of T-cell receptor sequences with known antigen specifities. The VDJdb database accumulates data from both – previously published papers and obtained via personal communications. Several research groups around the world could be attracted to fulfil the database. Currently the VDJdb includes more than 12000 TCR variants with known specificities and it is rapidly growing.

The database was recently published in Nucleic Acids Research (full paper).

The online database VDJdb is available under https://vdjdb.cdr3.net/

BioNTech and collaboration partner TRON published promising results in “Nature”

First-ever clinical study demonstrates personalized RNA-based vaccine using mutant neo-epitopes as antigens activates immune system against individual mutations and exerts anti-cancer activity.

BioNTech AG, a fully-integrated biotechnology company pioneering individualized cancer immunotherapy, announced Phase I trial results demonstrating its IVAC® MUTANOME, an individualized RNA vaccine based on patient-specific mutations, induces strong immunogenicity as well as promising anti-tumor activity in high-risk patients with late-stage melanoma. Additionally, in this early trial, a majority of patients showed prolonged progression-free survival in comparison to historical controls. The first-in-human study applied a process covering the comprehensive identification of individual mutations from routine tumor biopsies to next generation sequencing, the computational prediction of potential neo-epitopes as vaccine targets, and the design and manufacturing of an RNA vaccine encoding multiple neo-epitopes unique for each patient. The data, published in Nature, were obtained from research conducted in collaboration with clinical partners and the translational research institute, TRON. These data are now available to APERIM consortium partners to further test developed software modules.

Press release
Nature Article – full text


“Austrian Platform for Precision Oncology” receives national funding

The Medical University of Innsbruck further expands its facilities for precision cancer.

The establishment of an accurate infrastructure for precision oncology is a major challenge for research organizations and clinics, as expertise and high-end equipment are required in various fields such as laboratory diagnostics, oncology, cellular and molecular biology as well as bioinformatics. Three Austrian medical universities in Innsbruck, Graz and Vienna have therefore bundled complementary expertise aiming to develop an Austrian platform for precision oncology.

The platform contains three components: (1) molecular characterization with next generation sequencing and T cell receptor sequencing, (2) cellular phenotyping for the determination of immune infiltrates, and (3) functional diagnostics with 3D cell culture and CRISP / Cas9 technology. “This nationwide initiative will accelerate the implementation of precision-oncology and enable the standardization of clinical procedures,” explains Zlatko Trajanoski, who is also responsible for this project, which is funded with 1.5 million € over a five-year period.

Scientists of the University of Tübingen publish a framework to improve the design of novel cancer vaccines

Epitope-based vaccines has emerged as a promising approach to treat not only infectious diseases but also to promote the battle against cancer by a patient’s own immune system. Actually, the prediction and assembly of viable epitopes and spacers in a string-of-beads like polypeptide remain one of the challenges. The design of the spacers between the epitopes and order of the epitopes thereby seem to affect crucially the probability that the selected peptides will be fully recovered and subsequently presented by patient´s HLA molecules and that risk is reduced, that adverse neoepitopes are generated within this process.

Benjamin Schubert and Oliver Kohlbacher from the University of Tübingen proposed in their work, which recently was published in Genome Medicine, a mathematical model to design spacer sequences of optimal design. First results are promising, as they showed indeed higher recovery rates and lower neoepitope generation using the proposed framework.

Together with partners, the researchers of Tübingen are going to validate the model in experimental tests within the project APERIM. Results will show if this approach helps to improve and accelerate epitope vaccine development.


Schubert B, Kohlbacher O: Designing string-of-beads vaccines with optimal spacers, Genome Medicine 2016, 8:9  full text

Benjamin Schubert; Mathias Walzer; Hans-Philipp Brachvogel; Andras Szolek; Christopher Mohr; Oliver Kohlbacher: FRED 2 – An Immunoinformatics Framework for Python. Bioinformatics 2016; doi: 10.1093/bioinformatics/btw113  full text


Further information:
Benjamin Schubert
Eberhard Karls University Tübingen
Applied Bioinformatics Group
Sand 14, D-72076 Tübingen
schubert (at) informatik.uni-tuebingen.de

Kick-off Meeting in Mainz

Partner institutions of the APERIM project participated in the project kick off meeting on May 11th 2015 in Mainz. The meeting has been an excellent occasion to get to know all consortium members and to exchange in detail about the work packages and the next steps.



Press Release

The Medical University of Innsbruck is coordinating the EU research project on personalised cancer immunotherapy

  • The “APERIM” project will start on 1 May: Precision medicine for cancer treatment
  • Cancer immunotherapy: Pioneering and targeted tumour treatment
  • Only EU project on personalised medicine coordinated in Austria

In future, cancer immunotherapy is to improve treatment of tumours. For this purpose, bioinformatics specialists at the Medical University of Innsbruck are developing a new treatment platform together with immunotherapy experts. The “APERIM” EU project is the only research project coordinated in Austria from the Horizon2020 Calls in the area of personalising health and care (H2020-PHC-2014).

Innsbruck 14/04/2015: On 1 May, the Medical University of Innsbruck will start an innovative research project to implement modern, personalised cancer immunotherapy: Univ.-Prof. Dipl.-Ing. Dr. Zlatko Trajanoski, Director of the Innsbruck Division of Bioinformatics, is coordinating the APERIM “Advanced bioinformatics platform for PERsonalised cancer IMmunotherapy” project. Eight academic partners and three companies are working on practical implementation of immunotherapy specifically for unique tumour mutations of individual patients. “We are creating the conditions needed to better treat cancer with state-of-the-art precision medicine in future,” explains Trajanoski, the project coordinator. “Many research papers have shown that cancer immunotherapy is suitable for successfully treating cancer.”

The researchers will receive three million euros in funding via the Horizon 2020 EU Grant Programme. Univ.-Prof Trajanoski from Innsbruck Biocenter is the only Austrian project coordinator in the “Personalising health and care” funding pool.


Immune system against cancer: Analysis of “next generation sequencing” data

The immune system protects the human body not only against foreign pathogens, but also against tumour cells. Cancer cells can escape the control of the immune system in various ways. However this reduced defensive reaction can be stimulated therapeutically, as numerous research papers have shown. The new findings and ways of obtaining more and more information from samples, known as “next generation sequencing” methods, require the development of new platforms to utilise the data to treat patients. Treatment platforms process the individual data of cancer patients to allow it to be used for therapy recommendations, for example. Bioinformatics methods permit the evaluation and processing of the specific information on the molecular fundamentals of individual tumours, which in turn forms the basis for personalised cancer immunotherapy.


“APERIM” – Four steps to personalised cancer immunotherapy

The “APERIM” project has four goals: A new database will store all molecular information on a tumour, a new analysis tool will permit quantification of tumour-infiltrated T cells, a software application will provide the information required to produce personalised, therapeutic vaccinations and a new method will be used to develop a special T cell gene therapy.

Univ.-Prof. Trajanoski and his colleagues plan to develop a database in which all information on a tumour – i.e. findings from the histopathological image analysis as well as genetic and clinical data – can be entered. That allows all molecular properties and specific mutations of a tumour to be stored and retreived. “This comprehensive information will then provide an important foundation for diagnosis and therapy,” explains Univ.-Prof Trajanoski, the project coordinator.

The second step will be the development of a tool for quantifying tumour-infiltrated T cells. “It is essential to determine the density and the subpopulations of the tumour-infiltrated T cells precisely to be able to identify high-risk patients. The more specific immune cells are infiltrating, the higher the chances of survival of cancer patients,” explains the expert.

The third project section will develop software to identify antigens for the development of individualised cancer vaccination based on the comprehensive detailed information. Every tumour has different properties, which makes it impossible to develop a single vaccination for a type of cancer. “Therapeutic vaccinations of this kind for treating cancer must be personalised and the software must facilitate the analysis required for this,” adds Trajanoski.

The fourth and last project target is a vision for the future in particular, as there have only been a few experimental studies to date. “We want to develop a new method which makes it possible to predict the antigen specificity and tumour activity of the T cells. Based on this information, individual T cell gene