OncoGen COVID-19 vaccine project recognized by the World Health Organization (WHO)

The World Health Organization (WHO) recognized OncoGen, as the only research centre in Romania that has a protein subunit COVID-19 vaccine candidate in pre-clinical tests.

OncoGen joins reputable academic institutions and private companies known for their expertise in the field of vaccine development and high-performing biomedical research.

The full list of candidate vaccines in clinical and pre-clinical tests, as of April 4, 2020, can be found at: https://www.who.int/blueprint/priority-diseases/key-action/Novel-Coronavirus_Landscape_nCoV-4april2020.pdf

OncoGen researchers propose personalized vaccinomics strategy for the novel China coronavirus

OncoGen researchers propose a novel approach for producing epitope-based peptide vaccine candidates for the novel China coronavirus (nCoV).

Wuhan seafood market pneumonia virus, also known as 2019 Novel Coronavirus (2019-nCoV) is a relative of both the deadly severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS) viruses. According to Nature Briefing, by January 28, the number of confirmed cases has jumped to more than 4,500 with more than 100 people dead as a result of the infection. By comparison, SARS spread globally in 2002-03, infecting 8000 and killing more than 700 people.

Traditional vaccines for viral diseases had limited success in the case of viral epidemics with high mutation rates. The approach that we used for designing potential peptide vaccine candidates takes a more personalized strategy, referred to as vaccinomics, which enables the selection of target viral proteins with low mutation rates, and the design of peptides tuned to the immune characteristics of the target populations, variable based on geographic location and ethnicity.

Based on the human MHC (human leukocyte antigen) allele variation, the peptide vaccines can be made more relevant to a community or individual. The selection of the peptides that could act as vaccines is determined by the binding of the processed viral peptide with the major histocompatibility complex (MHC) class I and II molecules, and the relevant HLA alleles.

Our proposed candidate peptides take into consideration the most frequent HLA alleles found in the Romanian population.

Technical details of the approach used are detailed below:

We identified multiepitope peptide vaccine candidates against nCov that can potentially trigger both CD4+ and CD8+ T cell immune response. To this end, we designed 15-30 aa synthetic long peptides (SLPs), as proposed by Rabu et al. (2019), using a cathepsin-sensitive linker (LLSVGG) for linking MHC class I-restricted epitopes to MHC class II-restricted epitopes, with the MHC class II epitope located always at the N-terminal end, to stimulate both CTLs and T helper lymphocytes (together with innate immune system).

GenBank Acc. No. of coronavirus isolate Wuhan-Hu-1 used for analysis: MN908947.3 which is identical to Ref Seq NC_045512 (provisonal ref seq, under review by NCBI): https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2

It is an enveloped, positive-sense, single-stranded poly-adenylated RNA virus, with a genome of 29.9 kb (29903 bp), among the largest of all RNA virus genomes.

Complete genomic sequences known to date: S and M proteins important as target for nCoV vaccine; S = spike (for adhesion and fusion); M = membrane (for replication and virion exocytosis).

The tool from the Immune Epitope Database (IEDB) server was used to identify potent T cell epitopes from the sequences of S and M proteins. For CD8+ T cell epitopes, the prediction method integrated MHC class I binding, proteasomal cleavage and TAP transport efficiency. Several epitopes were selected for further analysis based on high overall score and if they showed high MHC binding affinity (IC50 <50 nM). For CD4+ T cell epitopes, the highest ranking peptide based on MHC class II binding was chosen.

The list of selected T cell epitopes based on the most frequent class I and class II MHC alleles in the Romanian population (taken as an example to demonstrate a proof-of-concept) are found in our Preprints manuscript.

The candidate peptides were designed by applying to viral antigens a technology used for personalized vaccination in cancer, based on long neoantigen peptides, currently in clinical trials for cancer therapy.
Based on this model, additional peptide candidates can be identified for populations from different geographic regions of the world.
The current approach is a compromise between an industrial large-scale global vaccination strategy and an individually-targeted personalized vaccination strategy.
We will continue the validation of these candidates and of the model.

Image source: Eye of Science/SPL

Progress in personalized molecular cancer diagnostics at OncoGen

Romania-Serbia Joint Initiative against Cancer in Cross-Border Region: Improved Diagnosis and Treatment of Malignant Tumors” – ROSECAN

On October 25th 2019, OncoGen Research Center hosted the third press conference for the strategic project entitled “Romania-Serbia Joint Initiative against Cancer in Cross-Border Region: Improved Diagnosis and Treatment of Malignant Tumors – ROSECAN”, financed as part of the Interreg-IPA CBC Romania – Serbia programme.

The OncoGen Center acquired all equipment indicated in the project for personalized cancer diagnosis using genome sequencing. As of right now, the center’s acquisition procedure for the development of a software dedicated to diagnosis and treatment of cancer patients is ongoing. This software will be implemented in the Romania-Serbia cross-border region.
Next-generation sequencing (NGS) is a modern method for precise diagnosis and orienting treatment of cancer, used in the case of solid tumors, as well as haematological malignancies. Genome sequencing provides us with information regarding mutations that might appear in cancer cells during tumor development and proliferation. Based on a patient’s gene mutation panel, he/she becomes a unique entity, with a personalized molecular diagnosis, and benefits from a personalized treatment. All data acquired is interpreted using dedicated computer software such as Oncomine, IonReporter or VariantStudio. Following this methodology, new molecular targets present in tumors can be identified, allowing for the development of therapeutic strategies such as personalized vaccines or cell immunotherapy.

Genome sequencing involves no risk for the patients. This method uses DNA extracted from parafilm-enclosed tissue, after the histopathological diagnosis of the tumor is established.
Through the genome sequencing programme, OncoGen aligns to the diagnosis and anti-tumor therapy standards at the international level. As part of the ROSECAN project, 3 NGS machines have been purchased: the system for whole genome sequencing with an automatic sample preparation station (Ion Torrent Studio S5 + Ion Chef – ThermoFisher), the system for targeted DNA sequencing (Personal Genome Machine (PGM) – ThermoScientific) and the MiSeq sequencing system for validation (Illumina). These systems were used to analyze over 80 samples this year, as follows:

– 32 samples were analyzed using the PGM system; results identified gene mutations in 207 hotspots of 50 genes involved in tumorigenesis;
– 30 samples were analyzed using the Illumina MiSeq system, which provided us with data regarding the patient’s immune response to cancer, i.e. the amount and type of cytotoxic T lymphocyte clones, these being the cells that have the ability of destroying cancerous cells;
– 20 samples were analyzed using the Ion Torrent Studio S5 system and the automatic sample preparation station, identifying over 89 gene mutations in over 30 genes investigated from patients with solid tumors; the sample preparation station proved to be extremely useful for shortening processing and preparation time for sequencing samples, which meant that it only took 7 days from receiving the samples to releasing the results;
– circulating free DNA (cfDNA) from peripheral blood samples from 8 cancer patients was analyzed, identifying mutations in 25 oncogenes.

Currently, at the OncoGen Centre it is possible to perform approximately 100 additional genome sequencing analyses.

This successfully concluded phase brings us closer to achieving our goal of offering cancer patients a personalized diagnosis and therapeutic orientation for the purpose of treating malignant tumors.