Contributions
Abstract: PB1684
Type: Publication Only
Background
Partner and localizer of BRCA2 (PALB2) plays a key role in the DNA damage repair (DDR) and genomic alterations of DDR genes rarely occur in acute myeloid leukemia (AML), while their deregulation at transcriptional level is a known mechanism exploited by leukemic cells in order to sustain the high genetic instability and to continue proliferation.
Aims
We aimed to characterize the role of PALB2 in AML by investigating its genomic alterations and its expression levels, in order to evaluate its potentiality as target of therapies based on a synthetic lethal approach.
Methods
We genotyped 270 AML samples by Single Nucleotide Polymorphism array (SNP 6.0 and Cytoscan HD, Affymetrix). We performed Whole Exome Sequencing (WES, Illumina) of 69 cases to detect single nucleotide variants (MuTect and Varscan 2.0). Gene expression profiling (GEP, Affymetrix) was performed on bone marrow cells of 7 healthy donors (HD) and 60 AML patients. K-means clustering of patients according to the expression of PALB2 was performed.
Results
AML patients carried copy number alterations (CNA) in genes involved in the DDR pathway including PALB2, BRCA1, BRCA2, FANCA and RAD50. Among them, 11 patients (4%) carried a CN loss of PALB2 with a minimal common region of 6.6 Kb, including ex 11-12 encoding for domain of interaction with other DDR related genes. Notably, these patients were also characterized by the co-occurrence of losses of 5q, 17q11, 16p13-p12 and gain of 21q22. Biologically relevant genes targeted by CNAs in PALB2-loss patients were TP53, NF1, BRCA1, STAT3, FANCA, CREBBP, XPO and USP34. Enrichment analysis of differentially altered genes (q <.001) revealed that GO biological processes affected by CNAs included protein folding, apoptotis, mitotic cell cycle, metaphase/anaphase transition, nucleic acid phosphodiester bond hydrolysis, double-strand break repair (p<1e-04). PALB2 was not mutated in our WES dataset. However, DDR genes such as TP53, BRCA1, BRCA2, CHEK2, FANCE were found mutated at least once. Moreover, PALB2 loss significantly associated with TP53 mutations (p=0.015) while KRAS, IDH1/2, TET2 mutations were mutually exclusive. Transcriptional analysis revealed variable PALB2 levels in AML patients (range 52.90-244.37) and its median expression was higher compared with HD (129.26 vs 67.85, respectively; p=.019). We clustered patients according to PALB2 expression and defined 2 clusters: H and L with high and low expression levels of PALB2, respectively (cluster centers 158.86 and 105.41, respectively). Enrichment analysis of differentially expressed genes revealed deregulations of the following GO pathways: mitochondrial translational, regulation of cell proliferation, negative regulation of myeloid cell differentiation and G1/S transition of mitotic cell cycle (p<.013).
Conclusion
We dissected the molecular and transcriptional landscape of AML and we identified alterations in PALB2 and the DDR pathway in a small subgroup of patients. Our data open a new scenario in which PALB2 may drive dependencies to be exploited by targeted therapies in AML: breast cancer patients carrying mutations in PALB2 and BRCA1/2 are candidate for PARP inhibitors treatment, while few clinical trials are available in AML. Therefore, we identified a group of AML patients which may benefit of personalized therapies based on synthetic lethal approaches targeting the DDR pathway.
Supported by: ELN, AIL, AIRC, FP7-NGS-PTL, HARMONY, Fondazione del Monte.
Session topic: 3. Acute myeloid leukemia - Biology & Translational Research
Keyword(s): AML, DNA Damage, Molecular markers, Targeted therapy
Abstract: PB1684
Type: Publication Only
Background
Partner and localizer of BRCA2 (PALB2) plays a key role in the DNA damage repair (DDR) and genomic alterations of DDR genes rarely occur in acute myeloid leukemia (AML), while their deregulation at transcriptional level is a known mechanism exploited by leukemic cells in order to sustain the high genetic instability and to continue proliferation.
Aims
We aimed to characterize the role of PALB2 in AML by investigating its genomic alterations and its expression levels, in order to evaluate its potentiality as target of therapies based on a synthetic lethal approach.
Methods
We genotyped 270 AML samples by Single Nucleotide Polymorphism array (SNP 6.0 and Cytoscan HD, Affymetrix). We performed Whole Exome Sequencing (WES, Illumina) of 69 cases to detect single nucleotide variants (MuTect and Varscan 2.0). Gene expression profiling (GEP, Affymetrix) was performed on bone marrow cells of 7 healthy donors (HD) and 60 AML patients. K-means clustering of patients according to the expression of PALB2 was performed.
Results
AML patients carried copy number alterations (CNA) in genes involved in the DDR pathway including PALB2, BRCA1, BRCA2, FANCA and RAD50. Among them, 11 patients (4%) carried a CN loss of PALB2 with a minimal common region of 6.6 Kb, including ex 11-12 encoding for domain of interaction with other DDR related genes. Notably, these patients were also characterized by the co-occurrence of losses of 5q, 17q11, 16p13-p12 and gain of 21q22. Biologically relevant genes targeted by CNAs in PALB2-loss patients were TP53, NF1, BRCA1, STAT3, FANCA, CREBBP, XPO and USP34. Enrichment analysis of differentially altered genes (q <.001) revealed that GO biological processes affected by CNAs included protein folding, apoptotis, mitotic cell cycle, metaphase/anaphase transition, nucleic acid phosphodiester bond hydrolysis, double-strand break repair (p<1e-04). PALB2 was not mutated in our WES dataset. However, DDR genes such as TP53, BRCA1, BRCA2, CHEK2, FANCE were found mutated at least once. Moreover, PALB2 loss significantly associated with TP53 mutations (p=0.015) while KRAS, IDH1/2, TET2 mutations were mutually exclusive. Transcriptional analysis revealed variable PALB2 levels in AML patients (range 52.90-244.37) and its median expression was higher compared with HD (129.26 vs 67.85, respectively; p=.019). We clustered patients according to PALB2 expression and defined 2 clusters: H and L with high and low expression levels of PALB2, respectively (cluster centers 158.86 and 105.41, respectively). Enrichment analysis of differentially expressed genes revealed deregulations of the following GO pathways: mitochondrial translational, regulation of cell proliferation, negative regulation of myeloid cell differentiation and G1/S transition of mitotic cell cycle (p<.013).
Conclusion
We dissected the molecular and transcriptional landscape of AML and we identified alterations in PALB2 and the DDR pathway in a small subgroup of patients. Our data open a new scenario in which PALB2 may drive dependencies to be exploited by targeted therapies in AML: breast cancer patients carrying mutations in PALB2 and BRCA1/2 are candidate for PARP inhibitors treatment, while few clinical trials are available in AML. Therefore, we identified a group of AML patients which may benefit of personalized therapies based on synthetic lethal approaches targeting the DDR pathway.
Supported by: ELN, AIL, AIRC, FP7-NGS-PTL, HARMONY, Fondazione del Monte.
Session topic: 3. Acute myeloid leukemia - Biology & Translational Research
Keyword(s): AML, DNA Damage, Molecular markers, Targeted therapy