IMMUcan biological sample and data workflows are up and running for more than 6 years now. 1464 patients were confirmed eligible for IMMUcan as of Feb 2025. To accelerate the access to sample and data, the Consortium secured access to sample from six external trials (EORTC 1559 UPSTREAM, EORTC SPECTAlung, UZL Dutrelasco, IJB-Synergy, NVALT-30 Dedication, UNICANCER Nirvana) and four retrospective sample collections for the CRC indication (UZL, CLB and UCL) and the RCC indication with UroCCR. Current collaborations should lead to more than 1100 patients before the end of the IMMUcan project in addition to the SPECTA patients.
In the broad profiling, RNAseq analysis and WES of germline and tumor DNA are running smoothly, with more than 1,440 molecular reports generated by SIB in collaboration with EORTC and sent to treating physicians. 59 molecular tumour board meetings took place between EORTC and treating physicians to discuss treatment options taking based on IMMUcan results. With regards to molecular data fully uploaded on the KMS, WES is available on 2,315 samples derived from close to 2,000 patients and RNA-seq approx. 2,000 samples from 1,675 patients. In a similar vein, multiplexed IF data is available for >2,000 samples derived from approx. 1,800 patients. IMC analyses for panel 1 have been performed on approx. 1,300 samples from 1,200 patients. The progress for the IMC is closely being monitored by the IMMUcan PCT. Relatively complete datasets (e.g. data from only one of the four profiling modalities missing) have been generated in more than 2,000 samples derived from 1,774 patients.
On the deep profiling side, KUL completed the recruitment phase of the Dutrelasco trial. All the planned scRNA-seq and spatial transcriptomics activities have been performed. CyTOF analyses and exosome data generation were completed for all Dutrelasco samples. All 20 patients were included for scRNAseq in January 2023 and shallow and deep sequencing was finalized in June 2023. Data were uploaded on KMS in March 2024. After shifting techniques from 10X VISIUM to 10X XENIUM for quality reasons, KUL team performed spatial transcriptomics using a 418 marker panel. Data generation was finalized in October 2024 and data upload to KMS was finalized in November 2024. Integration of single cell and spatial transcriptomics data is ongoing. For CyTOF profiling on blood samples, KCL teams have finalized the alterations on the CyTOF panel, including re-titrations on the antibodies.
IMMUcan Knowledge Management System (KMS) is live and active. The KMS is providing a centralized storage of clinical, molecular and cellular data collected or generated with IMMUcan. The KMS is providing samples and data tracking from the IBBL to the different labs, H&E slides viewer, platform for generating patient molecular report. A patient view summarizes major clinical, molecular, mIF and IMC data for a given patient. An instance of cBioPortal enables cohort clinical and molecular data mining. Several tools are integrated in the KMS, including a tool to explore results of scRNAseq experiments, IFQuant to analyse images from multiplex fluorenscence images, a tool to align images of consecutive tissue sections and a curation tool for drug names and lines of therapies. EORTC, CHUV and SIB are working on cleaning and formatting the clinical data, especially the detailed treatment history of each patient. The cohort datasets are accessible to the IMMUcan partners via the KMS after clearing the GDPR risk assessment.
In WP6, biomarker validation examples that were formulated in 2022 can now be tested on newly generated data from new patients. Concrete examples of how automatic biomarker calling can be performed with real-time interim evaluation on currently available patients will be shared through the IMMUcan file server.
WP7 was discussing with WP4.1 and 4.2 labs the integration of IF/IMC results with molecular data, Integration of deep and broad profiling data, Immune cell type-based deconvolution of whole tumor RNAseq. The single-cell directory was completed and single cell database is on the KMS covering 32 public datasets. The related publication will be submitted shortly to the consortium for review.
The project website targeting clinicians, study sponsors, researchers and the specific section targeting patients is live since last period and maintained with IMMUcan latest news and regular communications released in professional social media linked to the project.
