A 6-GENE EXPRESSION SIGNATURE IN MANTLE CELL LYMPHOMA: RESULTS FROM THE FONDAZIONE ITALIANA LINFOMI (FIL)-MCL-0208 TRIAL
(Abstract release date: 05/19/16)
EHA Library. Bomben R. 06/09/16; 132926; E1377
Dr. Riccardo Bomben
Contributions
Contributions
Abstract
Abstract: E1377
Type: Eposter Presentation
Background
The aggressive clinical behavior of mantle cell lymphoma (MCL) is mainly attributed to the t(11;14)(q13;q32) traslocation and cyclin D1 (CCND1) overexpression. Nevertheless, a certain degree of clinical/biological heterogeneity has been reported.
Aims
To identify MCL subsets with peculiar clinical/biological features in the context of a cohort of homogeneously treated MCL patients.
Methods
The study used gene expression profiling (GEP) and quantitative real-time PCR (qRT-PCR) validations in peripheral blood (PB, n=46) and formalin fixed paraffin embedded (FFPE, n=42) samples from 82 MCL cases enrolled in the Fondazione Italiana Linfomi (FIL)-MCL-0208 randomized clinical trial (high-dose therapy followed by autologous transplantation).
Results
i) Unsupervised and supervised analyses. GEP from 27 PB samples were analyzed by principal component analysis (PCA) and divided in two subgroups named PCA1 (14 cases) and PCA2 (13 cases). Supervised analysis, according to PCA classification, identified a gene expression signature of 902 probes (700 up-regulated). Gene Set Enrichment Analysis (GSEA) demonstrated a significant enrichment of five B Cell Receptor (BCR)-related gene sets, these genes being constitutively over-expressed in PCA2 samples. ii) Identification of a “PCA2-type” gene signature. By merging the lists of differentially expressed genes and the BCR signaling related genes according to GSEA, a group of 14 genes, all overexpressed in PCA2 cases, was obtained. Among these genes, 6 genes, AKT3, BCL2, BTK, CD79B, PIK3CD, and SYK, were selected for further validations. iii) Generation of a 6-gene prediction model. These 6 genes were analyzed by qRT-PCR and utilized to generate a prediction model by using 17 cases as training cohort and 10 cases as validation cohort (all from PB samples). By this approach, 10/10 cases of the validation cohort were correctly assigned according to the PCA2/PCA1 classification. qRT-PCR was then utilized to classify 19 additional cases (10 PCA2 cases) not employed in GEP. Overall, in the 46 cases, 23 cases were classified as PCA2 by the GEP/qRT-PCR approach. iv) Clinical/biological correlations. No association was found between the 6-gene signature and IGHV status (33/41 unmutated IGHV cases) and the overexpression of SOX11 (15/27 cases over the median value). Moreover, no association was found with the presence of the main recurrent mutations of the ATM, BIRC3, CCND1, KMTD2, NOTCH1, TP53, TRAF2, WHSC1 genes. Finally, an “ad-interim” analysis of progression free survivals (PFS) suggested a shorter PFS (2-years PFS 76% vs 44%, p=0.04) for PCA2 cases. v) Application of the 6-gene signature to FFPE samples. By testing the 6-gene signature, by qRT-PCR in FFPE samples, 22 and 20 cases were classified PCA1 or PCA2, respectively. Again, in this independent series, PCA2 group demonstrated a trend for shorter PFS (2-years PFS 95% vs 80%, p=0.15). Merging together cases analyzed using PB and FFPE material, PCA2 patients had a shorter PFS (2-years PFS 85% vs 61%, p=0.02). vi) 6-gene signature and sensitivity to the BCR inhibitor ibrutinib. We investigated the proliferation rate of the MCL cell lines Rec-1, Jeko-1, Mino, JVM-2, JVM-13, and Z-138 in presence or in absence of ibrutinib 10 nM for 7 days. By qRT-PCR sensitive cell lines showed higher expression levels of the selected six genes than the resistant counterpart, and were classified as PCA2.
Conclusion
A novel 6-gene expression signature related to the BCR pathway has been found to characterize MCL cells with peculiar clinical/biological features and sensitivity to BCR inhibitors.
Session topic: E-poster
Keyword(s): Gene array, Mantle cell lymphoma, Real time PCR
Type: Eposter Presentation
Background
The aggressive clinical behavior of mantle cell lymphoma (MCL) is mainly attributed to the t(11;14)(q13;q32) traslocation and cyclin D1 (CCND1) overexpression. Nevertheless, a certain degree of clinical/biological heterogeneity has been reported.
Aims
To identify MCL subsets with peculiar clinical/biological features in the context of a cohort of homogeneously treated MCL patients.
Methods
The study used gene expression profiling (GEP) and quantitative real-time PCR (qRT-PCR) validations in peripheral blood (PB, n=46) and formalin fixed paraffin embedded (FFPE, n=42) samples from 82 MCL cases enrolled in the Fondazione Italiana Linfomi (FIL)-MCL-0208 randomized clinical trial (high-dose therapy followed by autologous transplantation).
Results
i) Unsupervised and supervised analyses. GEP from 27 PB samples were analyzed by principal component analysis (PCA) and divided in two subgroups named PCA1 (14 cases) and PCA2 (13 cases). Supervised analysis, according to PCA classification, identified a gene expression signature of 902 probes (700 up-regulated). Gene Set Enrichment Analysis (GSEA) demonstrated a significant enrichment of five B Cell Receptor (BCR)-related gene sets, these genes being constitutively over-expressed in PCA2 samples. ii) Identification of a “PCA2-type” gene signature. By merging the lists of differentially expressed genes and the BCR signaling related genes according to GSEA, a group of 14 genes, all overexpressed in PCA2 cases, was obtained. Among these genes, 6 genes, AKT3, BCL2, BTK, CD79B, PIK3CD, and SYK, were selected for further validations. iii) Generation of a 6-gene prediction model. These 6 genes were analyzed by qRT-PCR and utilized to generate a prediction model by using 17 cases as training cohort and 10 cases as validation cohort (all from PB samples). By this approach, 10/10 cases of the validation cohort were correctly assigned according to the PCA2/PCA1 classification. qRT-PCR was then utilized to classify 19 additional cases (10 PCA2 cases) not employed in GEP. Overall, in the 46 cases, 23 cases were classified as PCA2 by the GEP/qRT-PCR approach. iv) Clinical/biological correlations. No association was found between the 6-gene signature and IGHV status (33/41 unmutated IGHV cases) and the overexpression of SOX11 (15/27 cases over the median value). Moreover, no association was found with the presence of the main recurrent mutations of the ATM, BIRC3, CCND1, KMTD2, NOTCH1, TP53, TRAF2, WHSC1 genes. Finally, an “ad-interim” analysis of progression free survivals (PFS) suggested a shorter PFS (2-years PFS 76% vs 44%, p=0.04) for PCA2 cases. v) Application of the 6-gene signature to FFPE samples. By testing the 6-gene signature, by qRT-PCR in FFPE samples, 22 and 20 cases were classified PCA1 or PCA2, respectively. Again, in this independent series, PCA2 group demonstrated a trend for shorter PFS (2-years PFS 95% vs 80%, p=0.15). Merging together cases analyzed using PB and FFPE material, PCA2 patients had a shorter PFS (2-years PFS 85% vs 61%, p=0.02). vi) 6-gene signature and sensitivity to the BCR inhibitor ibrutinib. We investigated the proliferation rate of the MCL cell lines Rec-1, Jeko-1, Mino, JVM-2, JVM-13, and Z-138 in presence or in absence of ibrutinib 10 nM for 7 days. By qRT-PCR sensitive cell lines showed higher expression levels of the selected six genes than the resistant counterpart, and were classified as PCA2.
Conclusion
A novel 6-gene expression signature related to the BCR pathway has been found to characterize MCL cells with peculiar clinical/biological features and sensitivity to BCR inhibitors.
Session topic: E-poster
Keyword(s): Gene array, Mantle cell lymphoma, Real time PCR
Abstract: E1377
Type: Eposter Presentation
Background
The aggressive clinical behavior of mantle cell lymphoma (MCL) is mainly attributed to the t(11;14)(q13;q32) traslocation and cyclin D1 (CCND1) overexpression. Nevertheless, a certain degree of clinical/biological heterogeneity has been reported.
Aims
To identify MCL subsets with peculiar clinical/biological features in the context of a cohort of homogeneously treated MCL patients.
Methods
The study used gene expression profiling (GEP) and quantitative real-time PCR (qRT-PCR) validations in peripheral blood (PB, n=46) and formalin fixed paraffin embedded (FFPE, n=42) samples from 82 MCL cases enrolled in the Fondazione Italiana Linfomi (FIL)-MCL-0208 randomized clinical trial (high-dose therapy followed by autologous transplantation).
Results
i) Unsupervised and supervised analyses. GEP from 27 PB samples were analyzed by principal component analysis (PCA) and divided in two subgroups named PCA1 (14 cases) and PCA2 (13 cases). Supervised analysis, according to PCA classification, identified a gene expression signature of 902 probes (700 up-regulated). Gene Set Enrichment Analysis (GSEA) demonstrated a significant enrichment of five B Cell Receptor (BCR)-related gene sets, these genes being constitutively over-expressed in PCA2 samples. ii) Identification of a “PCA2-type” gene signature. By merging the lists of differentially expressed genes and the BCR signaling related genes according to GSEA, a group of 14 genes, all overexpressed in PCA2 cases, was obtained. Among these genes, 6 genes, AKT3, BCL2, BTK, CD79B, PIK3CD, and SYK, were selected for further validations. iii) Generation of a 6-gene prediction model. These 6 genes were analyzed by qRT-PCR and utilized to generate a prediction model by using 17 cases as training cohort and 10 cases as validation cohort (all from PB samples). By this approach, 10/10 cases of the validation cohort were correctly assigned according to the PCA2/PCA1 classification. qRT-PCR was then utilized to classify 19 additional cases (10 PCA2 cases) not employed in GEP. Overall, in the 46 cases, 23 cases were classified as PCA2 by the GEP/qRT-PCR approach. iv) Clinical/biological correlations. No association was found between the 6-gene signature and IGHV status (33/41 unmutated IGHV cases) and the overexpression of SOX11 (15/27 cases over the median value). Moreover, no association was found with the presence of the main recurrent mutations of the ATM, BIRC3, CCND1, KMTD2, NOTCH1, TP53, TRAF2, WHSC1 genes. Finally, an “ad-interim” analysis of progression free survivals (PFS) suggested a shorter PFS (2-years PFS 76% vs 44%, p=0.04) for PCA2 cases. v) Application of the 6-gene signature to FFPE samples. By testing the 6-gene signature, by qRT-PCR in FFPE samples, 22 and 20 cases were classified PCA1 or PCA2, respectively. Again, in this independent series, PCA2 group demonstrated a trend for shorter PFS (2-years PFS 95% vs 80%, p=0.15). Merging together cases analyzed using PB and FFPE material, PCA2 patients had a shorter PFS (2-years PFS 85% vs 61%, p=0.02). vi) 6-gene signature and sensitivity to the BCR inhibitor ibrutinib. We investigated the proliferation rate of the MCL cell lines Rec-1, Jeko-1, Mino, JVM-2, JVM-13, and Z-138 in presence or in absence of ibrutinib 10 nM for 7 days. By qRT-PCR sensitive cell lines showed higher expression levels of the selected six genes than the resistant counterpart, and were classified as PCA2.
Conclusion
A novel 6-gene expression signature related to the BCR pathway has been found to characterize MCL cells with peculiar clinical/biological features and sensitivity to BCR inhibitors.
Session topic: E-poster
Keyword(s): Gene array, Mantle cell lymphoma, Real time PCR
Type: Eposter Presentation
Background
The aggressive clinical behavior of mantle cell lymphoma (MCL) is mainly attributed to the t(11;14)(q13;q32) traslocation and cyclin D1 (CCND1) overexpression. Nevertheless, a certain degree of clinical/biological heterogeneity has been reported.
Aims
To identify MCL subsets with peculiar clinical/biological features in the context of a cohort of homogeneously treated MCL patients.
Methods
The study used gene expression profiling (GEP) and quantitative real-time PCR (qRT-PCR) validations in peripheral blood (PB, n=46) and formalin fixed paraffin embedded (FFPE, n=42) samples from 82 MCL cases enrolled in the Fondazione Italiana Linfomi (FIL)-MCL-0208 randomized clinical trial (high-dose therapy followed by autologous transplantation).
Results
i) Unsupervised and supervised analyses. GEP from 27 PB samples were analyzed by principal component analysis (PCA) and divided in two subgroups named PCA1 (14 cases) and PCA2 (13 cases). Supervised analysis, according to PCA classification, identified a gene expression signature of 902 probes (700 up-regulated). Gene Set Enrichment Analysis (GSEA) demonstrated a significant enrichment of five B Cell Receptor (BCR)-related gene sets, these genes being constitutively over-expressed in PCA2 samples. ii) Identification of a “PCA2-type” gene signature. By merging the lists of differentially expressed genes and the BCR signaling related genes according to GSEA, a group of 14 genes, all overexpressed in PCA2 cases, was obtained. Among these genes, 6 genes, AKT3, BCL2, BTK, CD79B, PIK3CD, and SYK, were selected for further validations. iii) Generation of a 6-gene prediction model. These 6 genes were analyzed by qRT-PCR and utilized to generate a prediction model by using 17 cases as training cohort and 10 cases as validation cohort (all from PB samples). By this approach, 10/10 cases of the validation cohort were correctly assigned according to the PCA2/PCA1 classification. qRT-PCR was then utilized to classify 19 additional cases (10 PCA2 cases) not employed in GEP. Overall, in the 46 cases, 23 cases were classified as PCA2 by the GEP/qRT-PCR approach. iv) Clinical/biological correlations. No association was found between the 6-gene signature and IGHV status (33/41 unmutated IGHV cases) and the overexpression of SOX11 (15/27 cases over the median value). Moreover, no association was found with the presence of the main recurrent mutations of the ATM, BIRC3, CCND1, KMTD2, NOTCH1, TP53, TRAF2, WHSC1 genes. Finally, an “ad-interim” analysis of progression free survivals (PFS) suggested a shorter PFS (2-years PFS 76% vs 44%, p=0.04) for PCA2 cases. v) Application of the 6-gene signature to FFPE samples. By testing the 6-gene signature, by qRT-PCR in FFPE samples, 22 and 20 cases were classified PCA1 or PCA2, respectively. Again, in this independent series, PCA2 group demonstrated a trend for shorter PFS (2-years PFS 95% vs 80%, p=0.15). Merging together cases analyzed using PB and FFPE material, PCA2 patients had a shorter PFS (2-years PFS 85% vs 61%, p=0.02). vi) 6-gene signature and sensitivity to the BCR inhibitor ibrutinib. We investigated the proliferation rate of the MCL cell lines Rec-1, Jeko-1, Mino, JVM-2, JVM-13, and Z-138 in presence or in absence of ibrutinib 10 nM for 7 days. By qRT-PCR sensitive cell lines showed higher expression levels of the selected six genes than the resistant counterpart, and were classified as PCA2.
Conclusion
A novel 6-gene expression signature related to the BCR pathway has been found to characterize MCL cells with peculiar clinical/biological features and sensitivity to BCR inhibitors.
Session topic: E-poster
Keyword(s): Gene array, Mantle cell lymphoma, Real time PCR
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