TY - JOUR
T1 - Discovery and validation of a transcriptional signature identifying homologous recombination-deficient breast, endometrial and ovarian cancers
AU - Beinse, Guillaume
AU - Just, Pierre Alexandre
AU - Le Frere Belda, Marie Aude
AU - Laurent-Puig, Pierre
AU - Jacques, Sebastien
AU - Koual, Meriem
AU - Garinet, Simon
AU - Leroy, Karen
AU - Delanoy, Nicolas
AU - Blons, Helene
AU - Gervais, Claire
AU - Durdux, Catherine
AU - Chapron, Charles
AU - Goldwasser, François
AU - Terris, Benoit
AU - Badoual, Cecile
AU - Taly, Valerie
AU - Bats, Anne Sophie
AU - Borghese, Bruno
AU - Alexandre, Jérôme
N1 - Publisher Copyright:
© 2022, The Author(s), under exclusive licence to Springer Nature Limited.
PY - 2022/10/5
Y1 - 2022/10/5
N2 - Background: Molecular alterations leading to homologous recombination deficiency (HRD) are heterogeneous. We aimed to identify a transcriptional profile shared by endometrial (UCEC), breast (BRCA) and ovarian (OV) cancers with HRD. Methods: Genes differentially expressed with HRD genomic score (continuous gHRD score) in UCEC/BRCA/OV were identified using edgeR, and used to train a RNAseq score (ridge-regression model) predictive of the gHRD score (PanCanAtlas, N = 1684 samples). The RNAseq score was applied in independent gynaecological datasets (CARPEM/CPTAC/SCAN/TCGA, N = 4038 samples). Validations used ROC curves, linear regressions and Pearson correlations. Overall survival (OS) analyses used Kaplan–Meier curves and Cox models. Results: In total, 656 genes were commonly up/downregulated with gHRD score in UCEC/BRCA/OV. Upregulated genes were enriched for nuclear/chromatin/DNA-repair processes, while downregulated genes for cytoskeleton (gene ontologies). The RNAseq score correlated with gHRD score in independent gynaecological cancers (R² = 0.4–0.7, Pearson correlation = 0.64–0.86, all P < 10−11), and was predictive of gHRD score >42 (RNAseq HRD profile; AUC = 0.95/0.92/0.78 in UCEC/BRCA/OV). RNAseq HRD profile was associated (i) with better OS in platinum-treated advanced TP53-mutated-UCEC (P < 0.001) and OV (P = 0.013), and (ii) with poorer OS (P < 0.001) and higher benefit of adjuvant chemotherapy in Stage I–III BRCA (interaction test, P < 0.001). Conclusions: UCEC/BRCA/OV with HRD-associated genomic scars share a common transcriptional profile. RNAseq signatures might be relevant for identifying HRD-gynaecological cancers, for prognostication and for therapeutic decision.
AB - Background: Molecular alterations leading to homologous recombination deficiency (HRD) are heterogeneous. We aimed to identify a transcriptional profile shared by endometrial (UCEC), breast (BRCA) and ovarian (OV) cancers with HRD. Methods: Genes differentially expressed with HRD genomic score (continuous gHRD score) in UCEC/BRCA/OV were identified using edgeR, and used to train a RNAseq score (ridge-regression model) predictive of the gHRD score (PanCanAtlas, N = 1684 samples). The RNAseq score was applied in independent gynaecological datasets (CARPEM/CPTAC/SCAN/TCGA, N = 4038 samples). Validations used ROC curves, linear regressions and Pearson correlations. Overall survival (OS) analyses used Kaplan–Meier curves and Cox models. Results: In total, 656 genes were commonly up/downregulated with gHRD score in UCEC/BRCA/OV. Upregulated genes were enriched for nuclear/chromatin/DNA-repair processes, while downregulated genes for cytoskeleton (gene ontologies). The RNAseq score correlated with gHRD score in independent gynaecological cancers (R² = 0.4–0.7, Pearson correlation = 0.64–0.86, all P < 10−11), and was predictive of gHRD score >42 (RNAseq HRD profile; AUC = 0.95/0.92/0.78 in UCEC/BRCA/OV). RNAseq HRD profile was associated (i) with better OS in platinum-treated advanced TP53-mutated-UCEC (P < 0.001) and OV (P = 0.013), and (ii) with poorer OS (P < 0.001) and higher benefit of adjuvant chemotherapy in Stage I–III BRCA (interaction test, P < 0.001). Conclusions: UCEC/BRCA/OV with HRD-associated genomic scars share a common transcriptional profile. RNAseq signatures might be relevant for identifying HRD-gynaecological cancers, for prognostication and for therapeutic decision.
UR - http://www.scopus.com/inward/record.url?scp=85132812711&partnerID=8YFLogxK
U2 - 10.1038/s41416-022-01900-9
DO - 10.1038/s41416-022-01900-9
M3 - Article
C2 - 35752712
AN - SCOPUS:85132812711
SN - 0007-0920
VL - 127
SP - 1123
EP - 1132
JO - British Journal of Cancer
JF - British Journal of Cancer
IS - 6
ER -