The applicant established connections with Dr. Tyler Jacks (MIT, USA, CRISPR-Cas9 technology) for cancer immunotherapies and The Mimetics (Netherlands, startup with 3D culture cancer models). The attendance at the EACR Conference was a crucial step in advancing her career and expertise in cancer immunotherapy and had a positive impact on the IMMUNO-model COST Action by increasing its visibility.

Contribution details

Title of the presentation: Treatment of colon cancer cells with Lacticaseibacillus casei: induction of apoptosis and release of DAMPs associated with immunogenic cell death
Type of the presentation: Poster

Outcome of the conference participation

My participation in the 21st Meeting of the Association for Cancer Immunotherapy was a significant contribution to the development of my scientific career. During its course, my PI Prof. Katerina Chlichlia, who was also in attendance and I had the opportunity to witness the advancement being made in various fields of immunotherapy and the innovative research conducted towards the understanding and development of immunotherapeutic regimens. In addition, our work, presented as a poster in the Meeting during the session Improving Immunity, gained the attention of various participants who showed a keen interest in the bioactive properties of the probiotic strain utilized in our lab.  Each one of them, according to their expertise, was able to offer their insight and critique on our research which is already being evaluated in the context of our work and will, without a doubt prove to be indispensable when designing our future experiments and possible additions in our studies. Furthermore, throughout the Meeting I had the chance to meet and converse with participants from industry and familiarize myself with novel protocols, techniques and cutting-edge, state of the art instruments, capable of greatly enhancing and expanding the scope of the research conducted in our lab. Finally, Prof. Chlichlia and I had the opportunity to establish contacts with other colleagues, from various research institutes, including but not restricted to Dr. Claudia Paret and Prof. Dr. Viktor Umanski and we are now considering the possibilities for future collaborations, either for me individually or our research group as a whole. Overall, my trip to Mainz and my participation in the CIMT Annual Meeting have given me a unique avenue to not only present my work and receive important feedback that will help me greatly in advancing my studies, but also appreciate the innovative ideas explored in the field of immunotherapy and find among the Meeting’s participants researchers and industry scientists for possible future collaborations.

Description of the work carried out during the VM

The Virtual Mobility project focused on creating a Systematic Search Strategy to collect publicly available omics datasets from immuno-oncology experiments. The main goal was to optimize the dataset search and collection process providing easy-to-use guidelines. All the produced material is available at the link on the last page.

The work was organized into different phases, focusing on the establishment of a taskforce and the technical development of the search strategy.

1. Data Gathering Taskforce involvement and first meeting: At the beginning of the VM period, the interested researchers were involved and a Data Gathering Taskforce was established. During the first meeting the taskforce brainstormed on how to proceed in this pilot phase, and the tasks were assigned. All the documents and useful files were organized in a Google Drive shared folder.

2. Pilot Query generation and Data Collection: The query generation process was primarily centralized around the project lead. Two pilot search queries were developed to find transcriptomic datasets related to immunotherapy in breast cancer and adenocarcinoma from the Gene Expression Omnibus (GEO) database. The query results contained a summary of the datasets retrieved such as dataset ID, platform type, and number of samples. They were downloaded in txt files.

3. Conversion to Excel Format: To enhance the usability of the query results, a custom script was developed to convert the txt files into Excel spreadsheets. In these files, each row corresponded to a dataset, and each column represented its features. Additional columns were added for manual curation, such as whether the dataset was derived from bulk RNA-seq or single-cell RNA-seq, and whether the study was clinical or preclinical.

4. Pilot query results curation: The taskforce played a crucial role in the pilot manual curation of the query results. Some taskforce members downloaded a copy of the Excel file and independently reviewed the datasets found. Based on researcher’s expertise, datasets were selected or excluded using a checkbox.

5. Concordance and Similarity Analysis: After the query results curation process was completed, an analysis was carried out to evaluate the concordance between the selected datasets to define the selection criteria. Furthermore, the similarity of the dataset annotation collected by the researchers was evaluated. The goal was to assess how consistently datasets were evaluated and to identify any discrepancies or challenges in the manual curation process. This analysis was critical in highlighting potential issues with manual data selection and will inform on the development of guidelines to enhance curation accuracy.

6. Keywords and research boundaries: The taskforce members compiled a further Excel file which defines the research boundaries, underlining new fields and terms of interest and helping in the definition of selection criteria.

7. Second meeting and report writing: During the second meeting the taskforce brainstormed on the query results curation experience, discussing on the reported concordance and similarity and research boundaries. The feedback was collected in a report that will be key to establish future guidelines on the query results curation process.

Description of the VM main achievements and planned follow-up activities

The Virtual Mobility Grant led to several important achievements:

1. Systematic search strategy development: a pilot version of the systematic search strategy was developed, focusing on the optimization of search queries in GEO for RNA-sequencing datasets. The custom script to convert txt files into Excel files significantly streamlined the data processing and annotation workflow.

2. Query results curation principles: the taskforce played a central role in manually curating the query results and deciding on dataset inclusion or exclusion based on researcher’s expertise. The manual curation process proved essential in highlighting challenges and inconsistencies that can occur in dataset selection, providing a foundation for improving future selection criteria and guidelines.

3. Documentation and future refinements: comprehensive documentation of the query structure, dataset curation and analysis results were produced. This documentation will be useful to define guideline for future expansion of the project to include other data types.

Contribution to Action objective and deliverables:

1. Knowledge sharing channels: the establishment of the Data Gathering Taskforce is fostering the collaboration between researchers and facilitate the transferability of knowledge between basic, translational and clinical investigators. In particular, it will generate a data resource available for everyone in the Action and for the broader cancer community upon publication.

2. Dataset collection, processing and biobanking protocols: the documentation produced will be fundamental for the establishment of dataset collection and curation guidelines. It will lay the basis of robust protocols that can be followed to collect molecular data from clinical and preclinical samples that represent an important resource to accelerate the study of immunotherapy efficacy and toxicity and validate biomarkers to monitor these effects.

Several activities are planned to further develop and expand the project:

1. Expansion to other tumour types and treatments: the next phase will involve expanding the search strategy to include additional tumour types and other treatments by the generation of new queries.

2. Refinement of selection criteria: the insights gained from the concordance analysis of the manual curation process will inform the development of refined selection criteria for datasets and guidelines for the curation process. These criteria will help to reduce inconsistencies.

3. Ongoing taskforce collaboration: the data gathering taskforce will continue to provide feedback on the project’s progress and collaborate on refining the search strategy and curation methods. Regular online meetings will be maintained to ensure continuous knowledge sharing and collaboration.

Start and end date: 09/09/2024 to 29/09/2024
Candidate: Paula Martín Rubio, IIS Aragón

During the three-week stay at IRCM Montpellier, the main objective was to acquire proficiency in the orthotopic implantation of tumor pieces into the lungs of mice. This objective was achieved through a series of carefully structured activities, which involved both observation and hands-on practice. The work began by attending several orthotopic lung surgeries performed by the team of Dr. Maraver.

These surgeries aimed to establish murine models of lung cancer. Through direct observation, I gained detailed knowledge of the entire process—from sample preparation to the postoperative monitoring of the mice.

Under the guidance of trained personnel, I was then given the opportunity to perform the surgery myself on pre-sacrificed mice. Additionally, I could practice the suture technique required for this surgery using synthetic skin. This hands-on experience allowed me to practice and refine the technique, which is highly complex and requires precision. Alongside the practical training, I also contributed to the project by preparing a detailed protocol that outlines every step of the surgical procedure. The protocol was accompanied by audiovisual material I gathered during the surgeries to ensure clarity and accuracy. The final document was reviewed and validated by the Dr. Maraver team to guarantee its applicability in other research settings.

The main achievement of my stay at IRCM Montpellier was successfully acquiring technical expertise required for orthotopic tumor implantation into the lungs of mice. This technique is critical for developing patient-derived orthotopic models of pulmonary metastasis, which could be implemented in future research at our institution. These models would be valuable tools for testing NK cell-based immunotherapies, aligning with the Immuno Model COST Action’s objective of fostering innovation in preclinical immuno-oncology models aimed at improving cancer treatment.

As part of the stay, I developed a detailed surgical protocol that outlines the entire orthotopic implantation procedure. This protocol, which includes audiovisual material gathered during surgeries, was reviewed by the team of Dr. Maraver and ensures accurate implementation of the technique. This deliverable directly supports the Immuno Model COST Action’s goal of enhancing reproducibility and standardizing preclinical models across research groups. Sharing this protocol within the network could contribute to collaborative efforts in the field of immuno-oncology, promoting best practices in preclinical research.

The knowledge gained significantly expands our potential to develop sophisticated in vivo models for studying cancer metastasis and immunotherapy. My enhanced technical expertise could support future projects aimed at advancing preclinical cancer models, thereby contributing to the overall mission of the ImmunoModel COST Action.

In conclusion, the knowledge and skills acquired during this stay at IRCM will contribute significantly to our future research capabilities. Furthermore, this expertise aligns with and supports the broader objectives of the ImmunoModel COST Action by enhancing the quality and reproducibility of preclinical models in immuno-oncology.

Dissemination: During my 2-months long stay at the University Medical Center in Amsterdam, in the group of Febe van Maldegem, PhD, I learnt all about the Imaging mass cytometry (IMC). This novel technique enables us to determine spatial characteristics of a tissue and observe interactions between cells. I was using IMC to determine changes in the interactions within the glioblastoma microenvironment, which arise from applying treatment (radiotherapy and/or chemotherapy) to glioblastoma organoids. Understanding how cell interactions change after therapy will hopefully help us to unveil the mechanisms underlying therapy resistance.  

Tina Kolenc Milavec (left) and PhD student Sofie Koomen (right) trying to prepare organoids from the lung cancer tissue we obtained from a patient after surgery.

Me (Tina) in the laboratory, doing staining of FPPA-fixed glioblastoma tissue slices with the antibody mix for IMC analysis.

Me (left) and Sofie Koomen (right) at the Spring conference of the Dutch Society for immunology (NVVI) in Tiel, Netherlands. I sure learnt a lot of new things about immunology.

Short news/reports about the STSM were also posted on Instagram and LinkedIn.

Annual report can be found here.