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Integrated IMMUnoprofiling of large adaptive CANcer patients cohorts

Periodic Reporting for period 3 - IMMUcan (Integrated IMMUnoprofiling of large adaptive CANcer patients cohorts)

Reporting period: 2021-03-01 to 2022-02-28

Immune checkpoint inhibitors have shown promising results in some cancer types, but biomarkers to select patients that might respond to the treatment still need to be established. Similarly, rationale for combining immune checkpoint inhibitors with conventional therapy, targeted agents, or other immune checkpoint inhibitors are lacking. Finally, a better understanding of resistance mechanisms (primary and secondary) to immune checkpoint inhibitors is still lacking. One of the main challenges is the limited amount of comprehensive empirical data that integrate molecular, cellular, and clinical information to guide future translational and clinical research development.

IMMUcan is proposing an inclusive and integrated European immuno-oncology profiling platform. IMMUcan will generate broad molecular and cellular profiling data of the tumour and its microenvironment from high-risk cancer patients. The molecular and cellular information will be integrated with clinical data, to better understand how the immune system and tumours interact, and the impact of current therapeutic interventions.

IMMUcan will access human biological material including tumour tissue, blood, stool, and saliva as well as longitudinal clinical information from up to 3000 patients treated with standard of care treatment, including immune checkpoints inhibitors, or enrolled in clinical trials. IMMUcan is focusing on colorectal, lung, head & neck, breast, and renal cancers. About half of the patients will be recruited via SPECTA, the integrated research infrastructure under EORTC legal sponsorship. The other half will come from independently planned and funded academic clinical trials or cohort studies.

A centralized workflow of samples, via a state-of-the-art biobank, will increase reproducibility, as all tissues will be processed and stored in a uniform way, following proofed SOPs. IMMUcan will perform in depth immune profiling with cutting edge technologies including the following:
- Spatial distribution of immune cell subtypes: imaging Cytof and multiplex immunofluorescence (IF);
- RNAseq analysis: Total RNA;
- DNA analysis: WES;
- Single cell on immune populations based on 10x Genomics technology, including dendritic cell deep characterization;
- Liquid CyTOF on PBMCs;
- ctDNA and exosome analysis;

IMMUcan will develop a sustainable data platform and legal contractual framework where participants from both academia and industry can pursue their own independent investigations utilizing the IMMUcan data and effectively test and improve the functioning and relevance of the database throughout the duration of the project. IMMUcan will also support the future use of the data generated by the project by the research community.

Lay version of of this summary is available from https://immucan.eu/patients
IMMUcan biological sample and data workflows are up and running. This encompasses passing of the samples from the clinical sites to the central biobank and then to the many laboratories and generation and collection of profiling data in the specified data platforms.

Prospective patient recruitment was initiated via the EORTC SPECTA platform in June 2020. Around 134 principal investigators from 98 SPECTA clinical sites from 17 countries are today (at the end of the period) authorized to recruit patients. 862 patients were registered in SPECTA in the five targeted indications as of the 28th February 2022, and 557 patients were confirmed eligible for IMMUcan. In order to accelerate the access to sample and data for IMMUcan broad and deep profiling, the Consortium secured access to sample from three external trials (EORTC 1559 UPSTREAM, EORTC SPECTAlung and UZL Dutrelasco) which contributed with a total of around 320 eligible patients at the end of February 2022 in addition to the SPECTA patients.

In the broad profiling, RNAseq analysis and WES of germline and tumor DNA are running smoothly, with 626 molecular reports generated by SIB in collaboration with EORTC and sent to treating physicians. 15 molecular tumour board meetings took place between EORTC and treating physicians to discuss treatment options taking based on IMMUcan results.

The consortium agreed to replace the Agilent SureSelect v7 with the Twist Comprehensive Exome for WES activities. Tools for selecting regions of interest for the Imaging Mass Cytometry based on immunofluorescence data have been newly developed by SIB, UZH and CHUV and are up and running. CHUV has started to implement a new software, in house deigned, for IF analysis, called IFQuant. We started the upload of imaging mass cytometry (IMC) data on the KMS. Complete broad profiling datasets (RNA-seq, WES, multiplex IF and IMC) are now available for patients from the first batches.

On the deep profiling side, KUL completed the recruitment phase of the Dutrelasco trial. The secondary use of the Dutrelasco samples in IMMUCAN has been approved by the UZL Ethical Committee, and all the planned scRNA-seq and spatial transcriptomics activities have been performed. Also all Dutrelasco samples were transferred for broad and blood profiling. CyTOF analyses and exosome data generation was completed for all Dutrelasco samples. Concerning the CRC cohort, ethical approval/MTA/lab agreement were completed at KUL/UZL. 15 patients were included for scRNAseq by August 2022. The consortium had agreed to perform MILAN multiplex immunofluorescence on CRC samples to study intra tumor heterogeneity. KUL has a milan panel up and running. Activities will start when sample collection is completed (foreseen October 2022). Last but not least, a manuscript describing the pilot study on liquid biopsies is in preparation.

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, an interface to request access to data and the GDPR where partners access to project data can be enabled. 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. First datasets are accessible to the IMMUcan partners via the KMS after clearing the GDPR risk assessment.

There are several pilot projects (TMB and RNA) in discussion between WP6 and partners. WP6 is looking to discuss new biomarker validation studies in collaboration with interested clinical investigators for IMMUcan core indications (e.g. lung and breast cancer).

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.
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