MUTATIONS IN SF3B1 GENE ARE SELECTED INDEPENDENTLY ON ATM/TP53 STATUS AND REDUCE THE TIME TO FIRST TREATMENT IN CLL PATIENTS
(Abstract release date: 05/19/16)
EHA Library. Spunarova M. 06/09/16; 132563; E1014
Mrs. Michaela Spunarova
Contributions
Contributions
Abstract
Abstract: E1014
Type: Eposter Presentation
Background
Significant proportion of chronic lymphocytic leukemia (CLL) patients manifests abnormalities in the DNA damage response pathway (DDR) through defects in TP53 or ATM gene. Interestingly, recurrent mutations in splicing factor 3 subunit b1 (SF3B1) have also been shown to partially impair DDR in CLL patients. Whilst ATM dysfunction seems to typically occur early in CLL pathogenesis, mutations in TP53 and SF3B1 have been reported to be mostly subclonal events originating later during the disease course.
Aims
(a) to assess whether SF3B1 mutations´ occurrence associates with adverse genetic lesions in TP53 and ATM genes, (b) to determine the impact of all three types of defects on time to first treatment (TTFT) and overall survival (OS), and (c) to analyze changes in ATM and SF3B1 mutation status during the disease course.
Methods
We used the yeast functional analysis FASAY coupled to Sanger sequencing for the identification of TP53 mutations (analyzing thus exons 4-10), the next generation sequencing (NGS) on MiSeq instrument (Illumina) for the whole ATM gene screening (62 coding exons with splicing sites), and direct Sanger sequencing for the analysis of mutational hot-spot exons 14-16 in SF3B1 gene. The median coverage in the NGS analysis was ~4000 reads, and we set up a uniform sensitivity of 10% for all three methodologies.
Results
We analyzed unfavorable cohort of 205 patients consisting predominantly (86%) of IGHV unmutated patients, with 64% of the patients being treatment-naïve. The TP53 dysfunction was identified in 53/205 patients (26%), while both ATM and SF3B1 mutations occurred in 49/205 cases (24%). In line with the expectations, we observed the frequent co-occurrence of ATM mutations with del(11q) (P˂0.001), and the strong mutual exclusivity of ATM and TP53 mutations (co-occurring in only one patient). By contrast, there was no significant association or mutual exclusivity between SF3B1 mutations´ presence and ATM or TP53 mutational status, neither among untreated patients nor in the whole cohort. For the TTFT and OS analyses, we firstly employed a hierarchical classification of TP53 and ATM mutations and did not consider SF3B1 mutational status; in addition, we limited this analysis to only IGHV unmutated patients. Compared to TP53-wt/ATM-wt patients having median of 18 months (m), the TTFT was apparently reduced in both TP53-mutated (6 m; P=0.002) and ATM-mutated patients (7 m). However, the latter group exhibited heterogeneous impact of mutations leading to only non-significant TTFT reduction (P=0.130). The OS analysis then showed a prominent (P˂0.001) negative impact of TP53 mutations (38 m) and a borderline significance of ATM mutations (67 m; P=0.058) compared to wt patients (90 m). As a sub-analysis, we assessed the effect of single SF3B1 mutations: these led to reduced TTFT (11 m; P=0.029 compared to 18 m in wt patients), while did not show an impact on OS. The analysis of ATM and SF3B1 throughout the disease course involving at least one relapse then disclosed that (a) 27/28 repeatedly analyzed ATM mutations (median time between analyses 40 m) and (b) 29/30 analyzed SF3B1 mutations (33 m) were identified in both samplings. In addition, 7 out of 72 repeatedly analyzed SF3B1-wt samples showed a new mutation in this gene.
Conclusion
Mutations in SF3B1 occur regardless of the ATM/p53 pathway dysfunction in CLL and can be selected by therapy. Their presence results in early therapy need but not in shorter survival. Supported by projects no. 65269705, TA0 TE02000058 and MUNI/A/1028/2015.
Session topic: E-poster
Keyword(s): ATM, B-CLL, Mutation status, P53
Type: Eposter Presentation
Background
Significant proportion of chronic lymphocytic leukemia (CLL) patients manifests abnormalities in the DNA damage response pathway (DDR) through defects in TP53 or ATM gene. Interestingly, recurrent mutations in splicing factor 3 subunit b1 (SF3B1) have also been shown to partially impair DDR in CLL patients. Whilst ATM dysfunction seems to typically occur early in CLL pathogenesis, mutations in TP53 and SF3B1 have been reported to be mostly subclonal events originating later during the disease course.
Aims
(a) to assess whether SF3B1 mutations´ occurrence associates with adverse genetic lesions in TP53 and ATM genes, (b) to determine the impact of all three types of defects on time to first treatment (TTFT) and overall survival (OS), and (c) to analyze changes in ATM and SF3B1 mutation status during the disease course.
Methods
We used the yeast functional analysis FASAY coupled to Sanger sequencing for the identification of TP53 mutations (analyzing thus exons 4-10), the next generation sequencing (NGS) on MiSeq instrument (Illumina) for the whole ATM gene screening (62 coding exons with splicing sites), and direct Sanger sequencing for the analysis of mutational hot-spot exons 14-16 in SF3B1 gene. The median coverage in the NGS analysis was ~4000 reads, and we set up a uniform sensitivity of 10% for all three methodologies.
Results
We analyzed unfavorable cohort of 205 patients consisting predominantly (86%) of IGHV unmutated patients, with 64% of the patients being treatment-naïve. The TP53 dysfunction was identified in 53/205 patients (26%), while both ATM and SF3B1 mutations occurred in 49/205 cases (24%). In line with the expectations, we observed the frequent co-occurrence of ATM mutations with del(11q) (P˂0.001), and the strong mutual exclusivity of ATM and TP53 mutations (co-occurring in only one patient). By contrast, there was no significant association or mutual exclusivity between SF3B1 mutations´ presence and ATM or TP53 mutational status, neither among untreated patients nor in the whole cohort. For the TTFT and OS analyses, we firstly employed a hierarchical classification of TP53 and ATM mutations and did not consider SF3B1 mutational status; in addition, we limited this analysis to only IGHV unmutated patients. Compared to TP53-wt/ATM-wt patients having median of 18 months (m), the TTFT was apparently reduced in both TP53-mutated (6 m; P=0.002) and ATM-mutated patients (7 m). However, the latter group exhibited heterogeneous impact of mutations leading to only non-significant TTFT reduction (P=0.130). The OS analysis then showed a prominent (P˂0.001) negative impact of TP53 mutations (38 m) and a borderline significance of ATM mutations (67 m; P=0.058) compared to wt patients (90 m). As a sub-analysis, we assessed the effect of single SF3B1 mutations: these led to reduced TTFT (11 m; P=0.029 compared to 18 m in wt patients), while did not show an impact on OS. The analysis of ATM and SF3B1 throughout the disease course involving at least one relapse then disclosed that (a) 27/28 repeatedly analyzed ATM mutations (median time between analyses 40 m) and (b) 29/30 analyzed SF3B1 mutations (33 m) were identified in both samplings. In addition, 7 out of 72 repeatedly analyzed SF3B1-wt samples showed a new mutation in this gene.
Conclusion
Mutations in SF3B1 occur regardless of the ATM/p53 pathway dysfunction in CLL and can be selected by therapy. Their presence results in early therapy need but not in shorter survival. Supported by projects no. 65269705, TA0 TE02000058 and MUNI/A/1028/2015.
Session topic: E-poster
Keyword(s): ATM, B-CLL, Mutation status, P53
Abstract: E1014
Type: Eposter Presentation
Background
Significant proportion of chronic lymphocytic leukemia (CLL) patients manifests abnormalities in the DNA damage response pathway (DDR) through defects in TP53 or ATM gene. Interestingly, recurrent mutations in splicing factor 3 subunit b1 (SF3B1) have also been shown to partially impair DDR in CLL patients. Whilst ATM dysfunction seems to typically occur early in CLL pathogenesis, mutations in TP53 and SF3B1 have been reported to be mostly subclonal events originating later during the disease course.
Aims
(a) to assess whether SF3B1 mutations´ occurrence associates with adverse genetic lesions in TP53 and ATM genes, (b) to determine the impact of all three types of defects on time to first treatment (TTFT) and overall survival (OS), and (c) to analyze changes in ATM and SF3B1 mutation status during the disease course.
Methods
We used the yeast functional analysis FASAY coupled to Sanger sequencing for the identification of TP53 mutations (analyzing thus exons 4-10), the next generation sequencing (NGS) on MiSeq instrument (Illumina) for the whole ATM gene screening (62 coding exons with splicing sites), and direct Sanger sequencing for the analysis of mutational hot-spot exons 14-16 in SF3B1 gene. The median coverage in the NGS analysis was ~4000 reads, and we set up a uniform sensitivity of 10% for all three methodologies.
Results
We analyzed unfavorable cohort of 205 patients consisting predominantly (86%) of IGHV unmutated patients, with 64% of the patients being treatment-naïve. The TP53 dysfunction was identified in 53/205 patients (26%), while both ATM and SF3B1 mutations occurred in 49/205 cases (24%). In line with the expectations, we observed the frequent co-occurrence of ATM mutations with del(11q) (P˂0.001), and the strong mutual exclusivity of ATM and TP53 mutations (co-occurring in only one patient). By contrast, there was no significant association or mutual exclusivity between SF3B1 mutations´ presence and ATM or TP53 mutational status, neither among untreated patients nor in the whole cohort. For the TTFT and OS analyses, we firstly employed a hierarchical classification of TP53 and ATM mutations and did not consider SF3B1 mutational status; in addition, we limited this analysis to only IGHV unmutated patients. Compared to TP53-wt/ATM-wt patients having median of 18 months (m), the TTFT was apparently reduced in both TP53-mutated (6 m; P=0.002) and ATM-mutated patients (7 m). However, the latter group exhibited heterogeneous impact of mutations leading to only non-significant TTFT reduction (P=0.130). The OS analysis then showed a prominent (P˂0.001) negative impact of TP53 mutations (38 m) and a borderline significance of ATM mutations (67 m; P=0.058) compared to wt patients (90 m). As a sub-analysis, we assessed the effect of single SF3B1 mutations: these led to reduced TTFT (11 m; P=0.029 compared to 18 m in wt patients), while did not show an impact on OS. The analysis of ATM and SF3B1 throughout the disease course involving at least one relapse then disclosed that (a) 27/28 repeatedly analyzed ATM mutations (median time between analyses 40 m) and (b) 29/30 analyzed SF3B1 mutations (33 m) were identified in both samplings. In addition, 7 out of 72 repeatedly analyzed SF3B1-wt samples showed a new mutation in this gene.
Conclusion
Mutations in SF3B1 occur regardless of the ATM/p53 pathway dysfunction in CLL and can be selected by therapy. Their presence results in early therapy need but not in shorter survival. Supported by projects no. 65269705, TA0 TE02000058 and MUNI/A/1028/2015.
Session topic: E-poster
Keyword(s): ATM, B-CLL, Mutation status, P53
Type: Eposter Presentation
Background
Significant proportion of chronic lymphocytic leukemia (CLL) patients manifests abnormalities in the DNA damage response pathway (DDR) through defects in TP53 or ATM gene. Interestingly, recurrent mutations in splicing factor 3 subunit b1 (SF3B1) have also been shown to partially impair DDR in CLL patients. Whilst ATM dysfunction seems to typically occur early in CLL pathogenesis, mutations in TP53 and SF3B1 have been reported to be mostly subclonal events originating later during the disease course.
Aims
(a) to assess whether SF3B1 mutations´ occurrence associates with adverse genetic lesions in TP53 and ATM genes, (b) to determine the impact of all three types of defects on time to first treatment (TTFT) and overall survival (OS), and (c) to analyze changes in ATM and SF3B1 mutation status during the disease course.
Methods
We used the yeast functional analysis FASAY coupled to Sanger sequencing for the identification of TP53 mutations (analyzing thus exons 4-10), the next generation sequencing (NGS) on MiSeq instrument (Illumina) for the whole ATM gene screening (62 coding exons with splicing sites), and direct Sanger sequencing for the analysis of mutational hot-spot exons 14-16 in SF3B1 gene. The median coverage in the NGS analysis was ~4000 reads, and we set up a uniform sensitivity of 10% for all three methodologies.
Results
We analyzed unfavorable cohort of 205 patients consisting predominantly (86%) of IGHV unmutated patients, with 64% of the patients being treatment-naïve. The TP53 dysfunction was identified in 53/205 patients (26%), while both ATM and SF3B1 mutations occurred in 49/205 cases (24%). In line with the expectations, we observed the frequent co-occurrence of ATM mutations with del(11q) (P˂0.001), and the strong mutual exclusivity of ATM and TP53 mutations (co-occurring in only one patient). By contrast, there was no significant association or mutual exclusivity between SF3B1 mutations´ presence and ATM or TP53 mutational status, neither among untreated patients nor in the whole cohort. For the TTFT and OS analyses, we firstly employed a hierarchical classification of TP53 and ATM mutations and did not consider SF3B1 mutational status; in addition, we limited this analysis to only IGHV unmutated patients. Compared to TP53-wt/ATM-wt patients having median of 18 months (m), the TTFT was apparently reduced in both TP53-mutated (6 m; P=0.002) and ATM-mutated patients (7 m). However, the latter group exhibited heterogeneous impact of mutations leading to only non-significant TTFT reduction (P=0.130). The OS analysis then showed a prominent (P˂0.001) negative impact of TP53 mutations (38 m) and a borderline significance of ATM mutations (67 m; P=0.058) compared to wt patients (90 m). As a sub-analysis, we assessed the effect of single SF3B1 mutations: these led to reduced TTFT (11 m; P=0.029 compared to 18 m in wt patients), while did not show an impact on OS. The analysis of ATM and SF3B1 throughout the disease course involving at least one relapse then disclosed that (a) 27/28 repeatedly analyzed ATM mutations (median time between analyses 40 m) and (b) 29/30 analyzed SF3B1 mutations (33 m) were identified in both samplings. In addition, 7 out of 72 repeatedly analyzed SF3B1-wt samples showed a new mutation in this gene.
Conclusion
Mutations in SF3B1 occur regardless of the ATM/p53 pathway dysfunction in CLL and can be selected by therapy. Their presence results in early therapy need but not in shorter survival. Supported by projects no. 65269705, TA0 TE02000058 and MUNI/A/1028/2015.
Session topic: E-poster
Keyword(s): ATM, B-CLL, Mutation status, P53
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