This task aim to define molecular features associated with primary and secondary resistance to therapies in advanced soft-tissue sarcomas.

The MULTISARC study will provide omic, biological and clinic data for a 900 sarcoma patients to be included between 2019 and 2022. We expect that subgroups of tumors characterized by known cancer phenotype, clinical and biological criteria can be established with minimum sample size of 20-30 samples per group. For all these patients, liquid biopsies will be performed from the diagnosis of metastatic disease to death to assess the genetic evolution of disease through therapies.

Our goal is to identify genomic and transcriptomic networks of features that are associated with primary and secondary resistance.

Methodology

To identify omic networks superseding “resistance” we are going to use Supervised Learning and Deep Learning strategies.

The task aim to define the immune landscape of immune cells in soft-tissue sarcoma and to evaluate the association between immune gene profiling and clinical outcome of soft-tissue sarcoma patients treated with immune checkpoint inhibitors

Soft-tissue sarcomas (STS) represent a heterogeneous group of rare tumours, including more than 70 different histological subtypes and representing 1% of cancer in adults and 15% in children. We have recently reported a novel classification of STS, based on the composition of the tumour microenvironment in large cohorts of STS. We have more particularly identified a subgroup of sarcomas encompassing several histological subtypes and characterized by the highest expression of genes specific of immune populations such as T cells, CD8+ T cells, NK cells, cytotoxic lymphocytes. Strikingly, the strongest determinant of this class of sarcomas was the high expression of the B lineage signature. We validated in two independent cohorts by using immunohistochemistry that this class of sarcomas was characterized by a high density of B cells and the presence of tertiary lymphoid structures (TLS). Moreover, we have shown by analysing retrospective data that TLS-positive sarcomas have better outcome and are more likely to respond to PD1 inhibition. Based on these data, we have set up two studies, the PEMBROSARC and the CONGRATS studies (sponsor: Institut Bergonié, Bordeaux, France) investigating the efficacy of immune-checkpoint inhibitors in patients with advanced sarcoma characterized by the presence of TLS. These studies are the first biomarker-driven study investigating immunotherapy in sarcoma patients. All patients included in these studies had sequential blood and tumor sampling (at baseline, at cycle 2 and at secondary progression). We will perform an integrative analysis (multiplex IF, exome/seq RNA, metabolomics, PBMC profiling) of this large collection of biological samples in order to investigate predictive biomarkers of long-term efficacy of PD1 inhibition in TLS+ sarcomas and to understand more in depth mechanisms of secondary resistance. Moreover, in order to better assess the prognosis (risk of relapse) of patients with localized sarcoma who underwent surgery, we have planned to investigate the prognostic value of the presence of TLS in a large cohort of sarcoma patients. Altogether, this project will provide significant insights for deciphering the role of immunotherapy in sarcomas and therefore propose new strategies for patient stratification that might benefit from current immunotherapies.

Gene expression profiling of a large cohort of STS by allowed the identification and validation of a 67 gene signature of chromosome instability named CINSARC (for genome Complexity INdex in SARComas) and which is the most significant predictor of metastasis free survival in these tumors (Chibon et al Nat Medicine 2010) . Many of the genes identified encode for proteins involved in DNA repair.

Moreover, a recent international study has shown that germline variants in several genes encoding proteins involved in DNA repair such as BRCA2, ATM, ATR, and ERCC2, contributed significantly to sarcoma risk (Ballinger et al Lancet Oncol 2016).

Our group was the first to investigate the clinical impact of DNA Damage Repair targeting in patients with locally advanced sarcoma by combining the PARP inhibitor olaparib with radiation therapy (study RADIOSARP, NCT02787642). The clinical results are quite encouraging and will be presented as an oral presentation at the 62^nd Annual Meeting of American Society for Radiation Oncology (ASTRO), 2020. All the patients in this study had initial biopsy and post-treatment resection allowing an analysis of the impact of PARP inh in combination with radiotherapy on DNA damage and tumor microenvironment.

We have also recently reported the first pre-clinical and clinical evidence that inhibition of the ATR/CHK1 pathway is synergistic with chemotherapy in patients with advanced sarcomas (Laroche-Clary et al Ann Oncol 2018; Laroche-Clary et al Scientific Reports 2020). Based on this date, we will start in 2021 the first randomized trial investigating an inhibitor of ATR in combination with chemotherapy versus chemotherapy alone in patients with advanced leiomyosarcomas. All the patients will have sequential biopsies (pre-treatment and on –treatment). An integrated analysis of the tumor samples obtained during this clinical trial will allow to investigate for the first time the impact of ATR inhibition on DNA damage (H2AX staining) and expression profile (RNA seq).

We will also investigate a new target, the activity of a new DNA-PK inhibitor (AZD7648) as a single agent and in combination with chemotherapy in a panel of 20 STS cell lines and in Patient-derived xenograft models. The results of this pre-clinical project will impact the possibility to set up a clinical trial investigating AZD7648 + doxorubicin in sarcoma patients with advanced disease.