Only SF3B1 Mutation involving K700E (And Not Other Codons), Independently Predicts Overall Survival in Myelodysplastic Syndromes

ABSTRACTBackgroundSF3B1 mutations (SF3B1mut) in myelodysplastic syndromes (MDS) frequently involve codon K700E and have a favorable prognosis. The prognostic effect of non-K700E SF3B1mut is uncertain.MethodsWe analyzed the clinical-pathologic features and outcomes of a single-institutional series of 94 SF3B1mut and 415 SF3B1wt newly diagnosed untreated MDS patients and explored the differences between K700E and non-K700E subgroups.FindingsNinety-four (19%) patients had SF3B1mut: median age, 74 years. Fifty-five (60%) patients carried K700E. Recurrent non-K700E mutations (39, 40%) included R625, H662 and K666. Compared to SF3B1mut K700E, non-K700E patients had a lower median ANC (1·8 vs. 2·4, p=0·005) and were frequently “high” R-IPSS (revised International Prognostic Scoring System) [7(19%) vs. 2(4%), p=0·031]. Non-K700E MDS frequently associated with RUNX1 (26% vs. 7%, p=0·012) and exclusively with BCOR, IDH2, and SRSF2 mutations. There was no significant difference in karyotype or SF3B1 variant allele frequency. Most (∼80%) were treated with hypomethylating agents. SF3B1mut had superior overall survival (OS) than SF3B1wt in all MDS categories [not-reached vs. 25·2 months, p=0·0003], low-grade MDS, and MDS with ring sideroblasts (MDS-RS). Compared to SF3B1wt, SF3B1mut K700E had superior outcomes in all MDS categories (25 months vs. not-reached, p=0·0001), low-grade MDS, and MDS-RS, but no significant difference was seen with non-K700E. By multivariate analysis, absence of SF3B1mut K700E (not non-K700E) independently associated with prognosis.InterpretationSF3B1mut MDS show distinct clinical and mutational profiles, with K700E showing a significantly better OS compared to non-K700E mutations and SF3B1wt. Our study highlights the importance of SF3B1 mutation type in MDS risk assessment.Data Sharing StatementThe datasets generated during and/or analyzed during the current study are not publicly available due to patient privacy concerns but are available from the corresponding author on reasonable request.Research in ContextEvidence before this studyWe designed this study based on the collective evidence from a systematic search of the literature for outcomes of patients MDS with SF3B1 mutations (SF3B1mut) from January 2013 to June 2020. Both the International Working Group for the Prognosis of MDS (IWG-PM) proposal and 2016 revisions to the World Health Organization (WHO) Classification of Myelodysplastic Syndromes recognize SF3B1mut MDS with <5% blasts (or ring sideroblasts >5% for WHO) as a distinct sub-category, in the absence of other unfavorable features. This was largely based on favorable prognostic outcomes, a distinct gene expression profile, and association with ring sideroblasts. However, the natural history of SF3B1mut MDS is heterogeneous. A high proportion of SF3B1 mutations occur within codon K700, leading to large-scale mRNA downregulation due to branch point recognition error, while the rest occur outside of this codon. The downstream functional effects of SF3B1 mutations outside of the K700 codon are unclear. The clinical course of SF3B1mut MDS patients likely depends on the type of SF3B1 mutation and other features such as variant allele frequency, concomitant gene mutations, and karyotype. Until now, the effects of the different types of SF3B1 mutations were largely unknown.Added value of this studyIn this study, we report distinctive clinicopathologic characteristics and outcomes of MDS patients with SF3B1 mutations segregated based on mutation type: K700E vs. non-K700E. We show that ∼40% of SF3B1 mutated MDS patients have non-K700E mutations. Non-K700E SF3B1mut MDS have distinct clinico-pathologic features, such as lower ANC and frequent association with mutations in RUNX1, BCOR, IDH2, and SRSF2. There was no significant difference in karyotype or SF3B1 variant allele frequency. Importantly, K700E SF3B1mut MDS had superior overall survival compared to SF3B1wt, in all MDS, low-grade MDS, and MDS with ring sideroblasts, but no significant difference was seen with non-K700E. By multivariate analysis, absence of SF3B1mut K700E, but not non-K700E, independently associated with prognosis.Implications of all the available evidenceTo the best of our knowledge, this is the first study to report these findings from a single-institutional series of MDS primarily treated with hypomethylating agents. Our study highlights the importance of determining the SF3B1 mutation type in MDS risk assessment. These findings are important in light of the recent FDA approval of luspatercept based on the results of the MEDALIST trial that suggested sustained hematological responses in SF3B1mut MDS patients.

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Eprenetapopt (APR-246) and Azacitidine in TP53-Mutant Myelodysplastic Syndromes

Journal of Clinical Oncology ◽

10.1200/jco.20.02341 ◽

2021 ◽

pp. JCO.20.02341 ◽

Cited By ~ 2

Author(s):

David A. Sallman ◽

Amy E. DeZern ◽

Guillermo Garcia-Manero ◽

David P. Steensma ◽

Gail J. Roboz ◽

...

Keyword(s):

Overall Survival ◽

Adverse Events ◽

Allele Frequency ◽

Myelodysplastic Syndromes ◽

Median Overall Survival ◽

Overall Response Rate ◽

Response Rate ◽

Variant Allele ◽

Variant Allele Frequency ◽

Overall Response

PURPOSE Approximately 20% of patients with TP53-mutant myelodysplastic syndromes (MDS) achieve complete remission (CR) with hypomethylating agents. Eprenetapopt (APR-246) is a novel, first-in-class, small molecule that restores wild-type p53 functions in TP53-mutant cells. METHODS This was a phase Ib/II study to determine the safety, recommended phase II dose, and efficacy of eprenetapopt administered in combination with azacitidine in patients with TP53-mutant MDS or acute myeloid leukemia (AML) with 20%-30% marrow blasts (ClinicalTrials.gov identifier: NCT03072043 ). RESULTS Fifty-five patients (40 MDS, 11 AML, and four MDS/myeloproliferative neoplasms) with at least one TP53 mutation were treated. The overall response rate was 71% with 44% achieving CR. Of patients with MDS, 73% (n = 29) responded with 50% (n = 20) achieving CR and 58% (23/40) a cytogenetic response. The overall response rate and CR rate for patients with AML was 64% (n = 7) and 36% (n = 4), respectively. Patients with only TP53 mutations by next-generation sequencing had higher rates of CR (69% v 25%; P = .006). Responding patients had significant reductions in TP53 variant allele frequency and p53 expression by immunohistochemistry, with 21 (38%) achieving complete molecular remission (variant allele frequency < 5%). Median overall survival was 10.8 months with significant improvement in responding versus nonresponding patients by landmark analysis (14.6 v 7.5 months; P = .0005). Overall, 19/55 (35%) patients underwent allogeneic hematopoietic stem-cell transplant, with a median overall survival of 14.7 months. Adverse events were similar to those reported for azacitidine or eprenetapopt monotherapy, with the most common grade ≥ 3 adverse events being febrile neutropenia (33%), leukopenia (29%), and neutropenia (29%). CONCLUSION Combination treatment with eprenetapopt and azacitidine is well-tolerated yielding high rates of clinical response and molecular remissions in patients with TP53-mutant MDS and oligoblastic AML.

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Predictive values of mutational variant allele frequency in overall survival and leukemic progression of myelodysplastic syndromes

Journal of Cancer Research and Clinical Oncology ◽

10.1007/s00432-021-03905-y ◽

2022 ◽

Author(s):

Lingxu Jiang ◽

Li Ye ◽

Liya Ma ◽

Yanling Ren ◽

Xinping Zhou ◽

...

Keyword(s):

Overall Survival ◽

Allele Frequency ◽

Myelodysplastic Syndromes ◽

Variant Allele ◽

Variant Allele Frequency ◽

Predictive Values

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Clinical Utility of Hematopathologist-Triaged NGS Testing When Investigating Patients with Suspected MDS

Blood ◽

10.1182/blood-2021-153594 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 4675-4675

Author(s):

Christina K Ferrone ◽

Amy JM McNaughton ◽

Iran Rashedi ◽

Hubert Tsui ◽

Michael J Rauh

Keyword(s):

Allele Frequency ◽

Conflicts Of Interest ◽

Low Risk ◽

Variant Allele ◽

Low Grade ◽

Variant Allele Frequency ◽

Mutational Status ◽

Morphological Criteria ◽

Significant Difference

Abstract The recognition of MDS is challenging in early stages, where diagnosis may rely solely upon morphological criteria for dysplasia, a non-specific finding prone to inter-observer variation. Patients with equivocal bone marrow (BM) findings may be discharged from Hematology clinics and lost to follow up, or subjected to serial, invasive BM investigations and diagnostic delays. We therefore aimed to demonstrate the importance of hematopathologist-triaged, targeted NGS in identifying clonal cytopenias of undetermined significance (CCUS) in cases where MDS diagnostic criteria are not met based on morphology or cytogenetic analysis. We explored this using three REB-approved cohorts. Our first cohort was retrospective with BM samples ranging from 2010-14, involving cases that were previously suspicious for but non-MDS diagnostic. This included 70 patients from Sunnybrook (SHSC) and Kingston Health Sciences Centres (KHSC): 16 age-matched controls (8 negative lymphoma staging, 8 non-MDS cytopenias); 18 suspicious for MDS; 20 MDS; and 16 MDS/MPN. DNA was extracted and NGS was performed using our custom 48-gene Ion Torrent AmpliSeq myeloid panel (ThermoFisher). We identified suspected mutations in 2/16 (13%) controls (i.e. CHIP), 12/18 (67%) suspicious cases, 17/20 (85%) MDS cases, and 16/16 (100%) MDS/MPN cases. The mean and median number of mutations per suspicious patient (respectively 0.89 and 1; most commonly in SF3B1, TET2, RUNX1, and ASXL1) were lower than MDS (1.85 and 2; p=0.011) and MDS/MPN (3.13 and 3; p<0.0001). There was a significant difference in the average variant allele frequency (VAF) per patient (those with ≥1 mutation) between control and suspicious groups (p=0.022), however, there were no significant differences in the average VAF between suspicious, MDS, and MDS/MPN cases. Furthermore, of the 16 patients with BM suspicious for MDS, 7 went on to get MDS. 4 of these patients had at least 1 clinically relevant somatic variant, while 3 had none. Of those with at least 1 variant, 3 had IPSS-level cytopenias at the time, indicating that had their mutational status been known at the time of their assessment, they would have been diagnosed with the provisional CCUS entity (while the rest would be classified as CHIP). To supplement these findings, we are amassing a prospective cohort involving cases at SHSC where patients have either idiopathic cytopenias (ICUS), or confirmed MDS diagnoses with one or more previously non-diagnostic BM. To date, we have performed sequencing for 36 of these patients, including 23 ICUS and 13 diagnosed MDS cases. Of the ICUS cases, 10 (44%) had at least 1 variant (mean # variant/patient = 1, mean variant allele frequency (VAF) = 34.0%) consistent with CCUS, while 12/13 (92%) of MDS patients had at least 1 variant (mean # variants/patient = 2, mean VAF = 42.3%). These findings are consistent with CCUS being common in suspicious MDS cases, with similar clonal size but lesser mutational burden than diagnosed MDS. In addition to these preliminary findings, 15/36 patients have serial samples that we are currently processing for NGS (among other cases we are accruing to present at the ASH meeting). By exploring serial cases with molecular results pre- and post- MDS diagnosis, we aim to further elucidate which features of CCUS may predict progression to MDS. Finally, we assessed clonality in cases suspicious for myeloid malignancy in our existing prospective myeloid NGS cohort at KHSC (Ferrone et al, JMD 2021). In this cohort of 168 patients, when focusing on cytopenias yet to be diagnosed, 71 patients had suspected MDS, MPN, or MDS/MPN prior to NGS (completed using the Oncomine Myeloid Assay; ThermoFisher). 36/71 (51%) were found to have variants that indicate clonality. This facilitated diagnoses of either myeloid malignancies or pre-malignant states, with nine cases in total of ICUS resulting in the identification of variants that were non-diagnostic of MDS (mainly in TET2), but indicative of CHIP (n=2) or CCUS (n=7). Furthermore, for the limited number with available follow up data, we found no significant difference in survival between individuals with low-grade MDS (n=10) and CCUS (n=6) (p=0.457). This evidence is in keeping with recent findings that the clinical features of CCUS may be consistent with low-risk MDS, emphasizing the importance of closely monitoring these patients, and even the possibility of assessing and treating them similarly to those with low-risk MDS. Disclosures No relevant conflicts of interest to declare.

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TP53 mutation variant allele frequency is a potential predictor for clinical outcome of patients with lower-risk myelodysplastic syndromes

Oncotarget ◽

10.18632/oncotarget.9200 ◽

2016 ◽

Vol 7 (24) ◽

pp. 36266-36279 ◽

Cited By ~ 23

Author(s):

Monika Belickova ◽

Jitka Vesela ◽

Anna Jonasova ◽

Barbora Pejsova ◽

Hana Votavova ◽

...

Keyword(s):

Clinical Outcome ◽

Allele Frequency ◽

Myelodysplastic Syndromes ◽

Lower Risk ◽

Tp53 Mutation ◽

Variant Allele ◽

Variant Allele Frequency ◽

Potential Predictor

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Impact of Mutation Variant Allele Frequency on Phenotype, Outcomes, and Patient Management in Myelodysplastic Syndromes

Clinical Lymphoma Myeloma & Leukemia ◽

10.1016/j.clml.2015.07.092 ◽

2015 ◽

Vol 15 ◽

pp. S43-S44

Author(s):

David Sallman ◽

Rami Komrokji ◽

Christine Vaupel ◽

Thomas Cluzeau ◽

Kathy L. McGraw ◽

...

Keyword(s):

Allele Frequency ◽

Myelodysplastic Syndromes ◽

Patient Management ◽

Variant Allele ◽

Variant Allele Frequency

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Only Hotspot SF3B1 K700E Mutation Is an Independent Predictor of Overall Survival in Myelodysplastic Syndromes

Blood ◽

10.1182/blood-2020-141446 ◽

2020 ◽

Vol 136 (Supplement 1) ◽

pp. 24-25

Author(s):

Rashmi Kanagal-Shamanna ◽

Guillermo Montalban Bravo ◽

Koji Sasaki ◽

Carlos E. Bueso-Ramos ◽

Elias Jabbour ◽

...

Keyword(s):

Overall Survival ◽

Board Of Directors ◽

Research Funding ◽

P Value ◽

Aberrant Splice ◽

Low Grade ◽

Advisory Committees ◽

Pathologic Features ◽

Significant Difference ◽

Advisory Role

SF3B1 mutated (SF3B1mut) MDS is associated with increased ring sideroblasts (RS) and favorable outcome. IWG-PM proposed that SF3B1mut MDS be considered a distinct entity in the absence of other unfavorable features. However, not all SF3B1mut MDS have similar clinical course. Hotspot K700E SF3B1mut leads to aberrant splice junctions and large-scale mRNA downregulation by activating a cryptic splice site. The functional effects of SF3B1mut outside of K700E is not clear. The outcome can also be altered by concomitant gene mutations and karyotype. In this study, we studied the clinical-pathologic features and outcome in a single-institutional series of 94 SF3B1mut and 415 SF3B1wt MDS, and explored the differences between K700E and non-K700E subgroups. All untreated MDS patients diagnosed over a 3-year duration who underwent NGS were selected. Overall survival was calculated from diagnosis to death/ last follow-up. Univariate (UVA) Cox proportional hazards regression was used to identify any association of variables with outcome followed by multivariate modeling (MVA) (p-value 0.200 cutoff). Of 509 patients, 94 (19%) had SF3B1mut: 59 men, 35 women; median age: 74 (39-92) years. Baseline characteristics: Table 1. Compared to SF3B1wt, SF3B1mut had a significantly higher median age (74 vs. 70, p=0.0008), MCV (105 vs. 96, p<0.0001), platelet count (188 vs. 78, p<0.0001) and lower BM blasts (2 vs. 4, p=0.003). SF3B1mut were less frequently therapy-related (18% vs. 34%, p=0.002), significantly enriched in R-IPSS VL/L and WHO MDS-RS and MDS with iso del(5q). Majority (~66%) had concomitant mutations: TET2 (25%), DNMT3A (21%), RUNX1 (15%), TP53 (10%), ASXL1 (7%), BCOR (4%), IDH1/2 (4%), SRSF2 (3%), RAS (3%) and EZH2 (3%) (Fig 1B). ~10% showed complex karyotype (CK). Among SF3B1mut, hotspot K700E mutation was seen in 55 (~60%). Non K700E mutations (n=39, 40%) frequently involved codons: H662, K666 and R625, seen in 8 patients each (Fig 1A). SF3B1 K700E showed a higher median RS% (50% vs. 34%; p=0.038), ANC (2.4 vs. 1.8, p=0.005) and a trend for higher platelet (196 vs. 124, p=0.05). SF3B1mut were less likely MDS-EB than non-K700E (22% vs. 49%, p=0.008). All 4 SF3B1mut patients that fit WHO criteria for MDS with isolated del(5q) had K700E (Table). The frequency of RUNX1 mutation was significantly higher in non-K700E cases (26% vs. 7.3%, p=0.012); mutations in BCOR (p=0.02), IDH2 (p=0.07) and SRSF2 (p=0.07) were exclusively noted in non-K700E cases (Fig 1C). There was no significant difference in TP53mut or CHIP-associated mutations DNMT3A, ASXL1 and TET2 or SF3B1 VAF. There was no significant differences in diploid vs. CK. However, K700E had lower CCCS categories (0/1, n=39; 2/3/4, n=10 vs. 0/1, n=19; 2/3/4, n=17); p=0.011). Majority were treated with HMA [16/17 (94%) K700E; 15/19 (79%) non-K700, 217/ 277 (78%) SF3B1wt]. SF3B1mut had better OS than SF3B1wt in all MDS (NR vs. 25.2 months, p=0.0003; fig 1D), low-grade MDS (NR vs. 41.3 months, p=0.0015; fig 1E) and MDS-RS (NR vs. 22.3 months, p=0.0004; fig 1F). Four (7.3%) K700E died compared to 9 (23%; p=0.036) non-K700E. The outcome of non-K700E was similar to SF3B1wt, in all MDS, low-grade MDS and MDS-RS (median OS, NR for both; p=0.021). By UVA, the following associated with worse outcome: higher BM blasts, lower hemoglobin, platelet and MCV, prior chemo-radiation, CK, higher R-IPSS, absence of mutations in SF3B1 K700E, TET2 and U2AF1 and presence of TP53mut. Non-K700E did not associate with OS. By MVA, lower hemoglobin, higher R-IPSS, absence of SF3B1 K700E and presence of TP53mut were independent predictors of worse OS. Within MDS-RS categories, independent prognostic factors of worse OS included lower platelet, presence of mutations in non-K700E SF3B1mut, ASXL1, SRSF2 and TP53. TP53mut/CK was seen in 10% SF3B1mut MDS. No survival differences were noted between SF3B1mut with or without TP53mut/CK (median OS, NR) and SF3B1wt without TP53mut/CK (44.3 months), but TP53mut/CK with SF3B1wt MDS had a worse outcome (median OS, 12.9 months, HR 1.46, p=0.001; fig 1G). Same findings were noted within low-grade MDS and MDS-RS, suggesting SF3B1mut negates the poor prognostic effect of TP53mut/CK. About 40% SF3B1mut MDS show non K700E mutations. K700E and non K700E SF3B1mut MDS show distinct clinical and mutational profiles, with K700E showing a significantly better OS compared to non K700E and SF3B1wt. Only SF3B1 K700E independently predicted for worse OS in MDS. Figure Disclosures Sasaki: Pfizer Japan: Consultancy; Daiichi Sankyo: Consultancy; Novartis: Consultancy, Research Funding; Otsuka: Honoraria. Jabbour:Genentech: Other: Advisory role, Research Funding; BMS: Other: Advisory role, Research Funding; Pfizer: Other: Advisory role, Research Funding; AbbVie: Other: Advisory role, Research Funding; Takeda: Other: Advisory role, Research Funding; Adaptive Biotechnologies: Other: Advisory role, Research Funding; Amgen: Other: Advisory role, Research Funding. Kantarjian:Amgen: Honoraria, Research Funding; Ascentage: Research Funding; BMS: Research Funding; Daiichi-Sankyo: Honoraria, Research Funding; Immunogen: Research Funding; Jazz: Research Funding; Novartis: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; Sanofi: Research Funding; Actinium: Honoraria, Membership on an entity's Board of Directors or advisory committees; Adaptive biotechnologies: Honoraria; Aptitute Health: Honoraria; BioAscend: Honoraria; Delta Fly: Honoraria; Janssen: Honoraria; Oxford Biomedical: Honoraria; Abbvie: Honoraria, Research Funding. Garcia-Manero:Astex Pharmaceuticals: Consultancy, Honoraria, Research Funding; AbbVie: Honoraria, Research Funding; Bristol-Myers Squibb: Consultancy, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Merck: Research Funding; Onconova: Research Funding; Genentech: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Helsinn Therapeutics: Consultancy, Honoraria, Research Funding; Acceleron Pharmaceuticals: Consultancy, Honoraria; H3 Biomedicine: Research Funding; Amphivena Therapeutics: Research Funding; Novartis: Research Funding; Jazz Pharmaceuticals: Consultancy.

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Impact of TP53 mutation variant allele frequency on phenotype and outcomes in myelodysplastic syndromes

Leukemia ◽

10.1038/leu.2015.304 ◽

2015 ◽

Vol 30 (3) ◽

pp. 666-673 ◽

Cited By ~ 81

Author(s):

D A Sallman ◽

R Komrokji ◽

C Vaupel ◽

T Cluzeau ◽

S M Geyer ◽

...

Keyword(s):

Allele Frequency ◽

Myelodysplastic Syndromes ◽

Tp53 Mutation ◽

Variant Allele ◽

Variant Allele Frequency

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Examination of the predicted prevalence of Gitelman syndrome by ethnicity based on genome databases

Scientific Reports ◽

10.1038/s41598-021-95521-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Atsushi Kondo ◽

China Nagano ◽

Shinya Ishiko ◽

Takashi Omori ◽

Yuya Aoto ◽

...

Keyword(s):

Allele Frequency ◽

Carrier Frequency ◽

Japanese Population ◽

Autosomal Recessive ◽

Disease Prevalence ◽

Gitelman Syndrome ◽

Variant Allele ◽

Variant Allele Frequency ◽

Genome Databases ◽

Heterozygous Carriers

AbstractGitelman syndrome is an autosomal recessive inherited salt-losing tubulopathy. It has a prevalence of around 1 in 40,000 people, and heterozygous carriers are estimated at approximately 1%, although the exact prevalence is unknown. We estimated the predicted prevalence of Gitelman syndrome based on multiple genome databases, HGVD and jMorp for the Japanese population and gnomAD for other ethnicities, and included all 274 pathogenic missense or nonsense variants registered in HGMD Professional. The frequencies of all these alleles were summed to calculate the total variant allele frequency in SLC12A3. The carrier frequency and the disease prevalence were assumed to be twice and the square of the total allele frequency, respectively, according to the Hardy–Weinberg principle. In the Japanese population, the total carrier frequencies were 0.0948 (9.5%) and 0.0868 (8.7%) and the calculated prevalence was 0.00225 (2.3 in 1000 people) and 0.00188 (1.9 in 1000 people) in HGVD and jMorp, respectively. Other ethnicities showed a prevalence varying from 0.000012 to 0.00083. These findings indicate that the prevalence of Gitelman syndrome in the Japanese population is higher than expected and that some other ethnicities also have a higher prevalence than has previously been considered.

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