Prospective high-throughput genome profiling of advanced cancers: results of the PERMED-01 clinical trial

International audienceAbstract Background The benefit of precision medicine based on relatively limited gene sets and often-archived samples remains unproven. PERMED-01 (NCT02342158) was a prospective monocentric clinical trial assessing, in adults with advanced solid cancer, the feasibility and impact of extensive molecular profiling applied to newly biopsied tumor sample and based on targeted NGS (t-NGS) of the largest gene panel to date and whole-genome array-comparative genomic hybridization (aCGH) with assessment of single-gene alterations and clinically relevant genomic scores. Methods Eligible patients with refractory cancer had one tumor lesion accessible to biopsy. Extracted tumor DNA was profiled by t-NGS and aCGH. We assessed alterations of 802 “candidate cancer” genes and global genomic scores, such as homologous recombination deficiency (HRD) score and tumor mutational burden. The primary endpoint was the number of patients with actionable genetic alterations (AGAs). Secondary endpoints herein reported included a description of patients with AGA who received a “matched therapy” and their clinical outcome, and a comparison of AGA identification with t-NGS and aCGH versus whole-exome sequencing (WES). Results Between November 2014 and September 2019, we enrolled 550 patients heavily pretreated. An exploitable complete molecular profile was obtained in 441/550 patients (80%). At least one AGA, defined in real time by our molecular tumor board, was found in 393/550 patients (71%, two-sided 90%CI 68–75%). Only 94/550 patients (17%, 95%CI 14–21) received an “AGA-matched therapy” on progression. The most frequent AGAs leading to “matched therapy” included PIK3CA mutations, KRAS mutations/amplifications, PTEN deletions/mutations, ERBB2 amplifications/mutations, and BRCA1/2 mutations. Such “matched therapy” improved by at least 1.3-fold the progression-free survival on matched therapy (PFS2) compared to PFS on prior therapy (PFS1) in 36% of cases, representing 6% of the enrolled patients. Within patients with AGA treated on progression, the use of “matched therapy” was the sole variable associated with an improved PFS2/PFS1 ratio. Objective responses were observed in 19% of patients treated with “matched therapy,” and 6-month overall survival (OS) was 62% (95%CI 52–73). In a subset of 112 metastatic breast cancers, WES did not provide benefit in term of AGA identification when compared with t-NGS/aCGH. Conclusions Extensive molecular profiling of a newly biopsied tumor sample identified AGA in most of cases, leading to delivery of a “matched therapy” in 17% of screened patients, of which 36% derived clinical benefit. WES did not seem to improve these results. Trial registration ID-RCB identifier: 2014-A00966-41; ClinicalTrials.gov identifier: NCT02342158

Caractérisation phénotypique et génomique des patients Becker avec délétion des exons 45-55

International audienceLa dystrophie musculaire de Becker (BMD) est une pathologie liée à l’X qui se caractérise par une dégénérescence des muscles squelettiques et/ou associée à une cardiomyopathie. Les patients Becker BMDdel45-55 présentent une délétion “en phase” des exons 45 à 55 dans le gène DMD. Les introns 44 et 55 qui bordent cette délétion contiennent des séquences régulatrices comme des long-non-coding ARN (lncRNA). Chaque patient BMDdel45-55 présente un point de cassure différent et donc un neo-intron unique avec potentiellement des modifications dans les séquences de lncRNA.L’objectif du projet est d’établir une caractérisation génomique d’une cohorte unique de patients BMDdel45-55 et d’étudier des facteurs impliqués dans leur variabilité phénotypique.Nous avons réalisé (i)une caractérisation phénotypique chez 49 patients, (ii)un séquençage du génome entier chez 19/49 patients et (iii)une étude des lncRNA chez 38/49 patients. Nous avons établi le profil des lncRNA dans des myoblastes immortalisés des sujets sains et DMD avec une délétion des exons 45-52 (Myo-45-52).L’étude phénotypique de notre population identifie une cardiomyopathie dilatée (22%), des difficultés à la marche/course (46%), la fatigabilité (34%). Dans 51% l’âge d’apparition des premiers signes est <18 ans (inconnu 22%). L’étude de la présence de lncRNA au niveau génomique met en évidence plusieurs clusters. L’absence génomique de certains lncRNA s’associe avec un phénotype clinique modéré. L’étude des mêmes lncRNA dans les myoblastes immortalisés a permis d’identifier deux lncRNA non-exprimés dans les Myo-45-52.Notre travail présente une caractérisation phénotypique et génomique de la plus grande cohorte de patients BMDdel45-55. Nous avons identifié des clusters avec un phénotype clinique modéré en fonction du nombre génomique de lncRNA. La caractérisation génomique des candidats pour la thérapie par saut d’exons 45-55 serait favorable dans le design des futures essais cliniques thérapeutiques

Head and Body/Tail Pancreatic Carcinomas Are Not the Same Tumors

International audienceThe association between pancreatic ductal adenocarcinoma (PDAC) location (head vs. Body/Tail (B/T)) and clinical outcome remains controversial. We collected clinicopathological and gene expression data from 249 resected PDAC samples from public data sets, and we compared data between 208 head and 41 B/T samples. The 2-year overall survival (OS) was better for the head than for the B/T PDACs (44 vs. 27%, p = 0.043), especially when comparing tumors with similar TNM classification (T3/4N0M0: 67% vs. 17%, p = 0.002) or from the same molecular class (squamous subtype: 31% vs. 0%, p < 0.0001). Bailey’s molecular subtypes were differentially distributed within the two groups, with the immunogenic subtype being underrepresented in the “B/T” group (p = 0.005). Uni- and multivariate analyses indicated that PDAC anatomic location was an independent prognostic factor. Finally, the supervised analysis identified 334 genes differentially expressed. Genes upregulated in the “head” group suggested lymphocyte activation and pancreas exocrine functions. Genes upregulated in the “B/T” group were related to keratinocyte differentiation, in line with the enrichment for squamous phenotype. We identified a robust gene expression signature (GES) associated with B/T PDAC location, suggesting that head and B/T PDAC are different. This GES could serve as an indicator for differential therapeutic management based on PDAC location