Sabrina Bedja

BACKGROUND: Patient Derived Organoids (PDOs) emerged as the best technology to develop ex vivo tumor avatars. Whether drug testing on PDOs to identify efficient therapies will bring clinical utility by improving patient survival remains unclear. To test this hypothesis in the frame of clinical trials, PDO technology faces three main challenges to be implemented in routine clinical practices: i) generating PDOs with a limited amount of tumor material; ii) testing a wide panel of anti-cancer drugs; and iii) obtaining results within a time frame compatible with patient disease management. We aimed to address these challenges in a prospective study in patients with colorectal cancer (CRC). METHODS: Fresh surgical or core needle biopsies were obtained from patients with CRC. PDOs were established and challenged with a panel of 25 FDA-approved anti-cancer drugs (chemotherapies and targeted therapies) to establish a scoring method ('chemogram') identifying in vitro responders. The results were analyzed at the scale of the cohort and individual patients when the follow-up data were available. RESULTS: A total of 25 PDOs were successfully established, harboring 94% concordance with the genomic profile of the tumor they were derived from. The take-on rate for PDOs derived from core needle biopsies was 61.5%. A chemogram was obtained with a 6-week median turnaround time (range, 4-10 weeks). At least one hit (mean 6.16) was identified for 92% of the PDOs. The number of hits was inversely correlated to disease metastatic dissemination and the number of lines of treatment the patient received. The chemograms were compared to clinical data obtained from 8 patients and proved to be predictive of their response with 75% sensitivity and specificity. CONCLUSIONS: We show that PDO-based drug tests can be achieved in the frame of routine clinical practice. The chemogram could provide clinicians with a decision-making tool to tailor patient treatment. Thus, PDO-based functional precision oncology should now be tested in interventional trials assessing its clinical utility for patients who do not harbor activable genomic alterations or have developed resistance to standard of care treatments.

We report the outcome of chloroquine treatment and the prevalence of mutations at codon 86 of the pfmdr1 gene, at codon 76 of the pfcrt gene, and at codon 108 of the pfdhfr gene in clinical isolates of Plasmodium falciparum collected from 30 children under 10 years of age living in the Comoros Union. This in vivo study was carried out in February and March 2001 in Moroni. Chloroquine treatment failed in 23 children (76.6%; 95% confidence interval: 57.7 to 90.1%). Subsequent genotyping showed that all P. falciparum isolates (100%) harboured a tyrosine residue at position 86 in pfMDR1. 83.3% (25/30) of these isolates harboured a mutation at position 76 in pfCRT and half (15/30) of these isolates also harboured a mutation at position 108 in pfDHFR. Chloroquine resistance is a real concern in the Comoros Union. The prevalence of pfDHFR mutant parasites is alarming. The alternative drugs proposed as a replacement for chloroquine as first-line treatment in Comoros, and the strategy to monitor the drug susceptibility of Plasmodium sp in this part of the Indian Ocean sub-region are discussed.

Over the last ten years, Patient-Derived Organoids (PDOs) emerged as the most reliable technology to generate ex-vivo tumor avatars. PDOs retain the main characteristics of their original tumor, making them a system of choice for pre-clinical and clinical studies. In particular, PDOs are attracting interest in the field of Functional Precision Medicine (FPM), which is based upon an ex-vivo drug test in which living tumor cells (such as PDOs) from a specific patient are exposed to a panel of anti-cancer drugs. Currently, the Adenosine Triphosphate (ATP) based cell viability assay is the gold standard test to assess the sensitivity of PDOs to drugs. The readout is measured at the end of the assay from a global PDO population and therefore does not capture single PDO responses and does not provide time resolution of drug effect. To this end, in this study, we explore for the first time the use of powerful large foundation models for the automatic processing of PDO data. In particular, we propose a novel imaging-based high-throughput screening method to assess real-time drug efficacy from a time-lapse microscopy video of PDOs. The recently proposed SAM algorithm for segmentation and DI-NOv2 model are adapted in a comprehensive pipeline for processing PDO microscopy frames. Moreover, an attention mechanism is proposed for fusing temporal and spatial features in a multiple instance learning setting to predict ATP. We report better results than other non-time-resolved methods, indicating that the temporality of data is an important factor for the prediction of ATP. Extensive ablations shed light on optimizing the experimental setting and automating the prediction both in real-time and for forecasting.

•KRAS mutations in PDAC have distinct impacts on tumor initiation and outcomes.•This study compared characteristics and outcomes of PDAC based on codon-specific KRAS mutants (G12 versus others).•No significant differences in main characteristics, except for BRAF, were observed between KRASG12 and KRASother.•KRASG12 patients had worse overall survival compared to KRASother patients in PDAC, but similar response to treatments.•This study indicates the importance of codon-specific KRAS mutations in prognosis. BackgroundHow distinct KRAS alterations in pancreatic adenocarcinoma (PDAC) influence tumor initiation and outcomes remains unclear. Moreover, KRAS is now partly targetable with novel specific inhibitors targeting KRASG12 (G12C or G12D), but specific outcomes of these subgroups of patients is poorly described. In this study, we compared clinical/genomic characteristics and outcomes of PDAC depending on codon-specific KRAS mutant (G12 versus others), as well as gene expression profiles and in vitro drug sensibility using organoids.Patients and methodsAll metastatic patients with PDAC and available molecular profile from 2015 to 2022 were eligible, and patients with KRAS mutation were included. Transcriptomic data from 69 KRAS-mutated tumors were also analyzed.ResultsOverall, 263 patients were included—239 KRASG12 (91%) and 24 (9%) KRASother. There was no difference between KRASG12 and KRASother regarding clinicopathological characteristics and potentially actionable alterations, except for BRAF that was found in 13% of KRASother (P = 0.01). G protein subunit alpha S (GNAS) was found more altered in KRASother tumors (P = 0.002) suggesting potential intraductal papillary mucinous neoplasm precursors. The median overall survival from metastatic diagnosis was 16.7 months [95% confidence interval (CI) 14.3-18.3 months] in KRASG12 and 24.9 months (95% CI 17.4-43.4 months) in KRASother [hazard ratio (ref: KRASG12) = 0.56 (0.34-0.94), P = 0.04 adjusted]. The first-line treatment response was not different between groups (overall response rate and progression-free survival), as confirmed with a similar organoid in vitro sensibility. Transcriptomic analyses showed a significant and exclusive up-regulation of immune pathways in KRASG12 tumors.ConclusionsCodon-specific KRAS mutations are not equal and we report that KRASG12 patients have a worst prognosis than KRASother patients in PDAC. These results warrant to be confirmed in larger-scale studies. How distinct KRAS alterations in pancreatic adenocarcinoma (PDAC) influence tumor initiation and outcomes remains unclear. Moreover, KRAS is now partly targetable with novel specific inhibitors targeting KRASG12 (G12C or G12D), but specific outcomes of these subgroups of patients is poorly described. In this study, we compared clinical/genomic characteristics and outcomes of PDAC depending on codon-specific KRAS mutant (G12 versus others), as well as gene expression profiles and in vitro drug sensibility using organoids. All metastatic patients with PDAC and available molecular profile from 2015 to 2022 were eligible, and patients with KRAS mutation were included. Transcriptomic data from 69 KRAS-mutated tumors were also analyzed. Overall, 263 patients were included—239 KRASG12 (91%) and 24 (9%) KRASother. There was no difference between KRASG12 and KRASother regarding clinicopathological characteristics and potentially actionable alterations, except for BRAF that was found in 13% of KRASother (P = 0.01). G protein subunit alpha S (GNAS) was found more altered in KRASother tumors (P = 0.002) suggesting potential intraductal papillary mucinous neoplasm precursors. The median overall survival from metastatic diagnosis was 16.7 months [95% confidence interval (CI) 14.3-18.3 months] in KRASG12 and 24.9 months (95% CI 17.4-43.4 months) in KRASother [hazard ratio (ref: KRASG12) = 0.56 (0.34-0.94), P = 0.04 adjusted]. The first-line treatment response was not different between groups (overall response rate and progression-free survival), as confirmed with a similar organoid in vitro sensibility. Transcriptomic analyses showed a significant and exclusive up-regulation of immune pathways in KRASG12 tumors. Codon-specific KRAS mutations are not equal and we report that KRASG12 patients have a worst prognosis than KRASother patients in PDAC. These results warrant to be confirmed in larger-scale studies.