Germline and Somatic Variants of CSF3R Define Distinct Myeloid Neoplasia Syndromes

Abstract Somatic and germline (GL) variants of CSF3R are found in myeloid neoplasia (MN) and severe congenital neutropenia (SCN). In particular, somatic gain-of-function mutations in the juxtamembrane region of the receptor occur in chronic neutrophilic leukemia (CNL) or secondary AML. Another hotspot for somatic nonsense variants frequently mutated in these categories of pts involves the intracellular domain which regulates inhibitory growth pathways. We hypothesized that the somatic CSF3R variants could reveal previously unrecognized GL SCN mutations. When we studied a cohort of 2,610 pts with MN, we identified a total of 68 CSF3R variants (CSF3RMT). Using a bioanalytic pipeline, we assigned pathogenicity and type of origin (somatic vs. GL) to these variants, particularly those not previously described. In total, we found 32 GL (CSF3RGL) and 36 somatic (CSF3RS) mutations. Of the GL variants, 4 were previously described in pts with SCN consistent with heterozygous loss of function of the CSF3R gene. However, 15 additional alterations were located in similar regions and were predicted to be pathogenic while 13 variants were previously never described. Most of the CSF3RGL mutations were identified in pts with AML and MDS (88%). Interestingly, 2 (6%) pts had co-existing idiopathic neutropenia that progressed to secondary MDS. Another pt had aplastic anemia that eventually progressed to secondary AML. CSF3RGL were most often located in either the intracellular domain (44%) or the extracellular domain (34%) while none of the CSF3RGL mutations were found in the juxtamembrane region (Fig1). AML was detected in 21% of the pts with a CSF3RGL intracellular domain mutation and 18% of the pts with extracellular domain mutations. Of the germline missense variants, E808K (28%), R698C (9%), and E149D (9%) were the most frequently detected. Among the pts with E808K, 22% developed AML. The previously non-reported variants were detected in either the intracellular (50%) or the extracellular domain (50%). Missense variants were detected in 9/10 of the novel mutations in the following locations: L723V (20%), R428K (10%), G731R (10%), V406fs (10%), G687S (10%), P682H (10%), T154I (10%), and S413L (10%). One truncating mutation was found (c.1865-6delC) and it was located in intron 14 and has unknown impact on CSF3R function. Complex karyotype was noted in 19 % of the cases with CSF3RGL. DNMT3A (19%), NRAS (13%), FLT3 (9%), and BCOR (9%), were the most commonly found co-mutations. CSF3R S mutations were all heterozygous and found in 18 pts with AML and 18 pts with MDS and other MN. Overall, these lesions mapped within the intracellular proximal and distal domains (53%), the extracellular domain (14%) the juxtamembrane domain (25%), and the transmembrane domain (8%). Of note, MDS/MPN pts with CSF3RS mutations (11%) had lesions distributed between the intracellular, juxtamembrane and extracellular domains while none of the AML pts had mutations in the extracellular domain. Of all mutations, 36% were truncating events previously described in the context of post SCN AML while 61% were missense mutations. T618I was the most frequent CSF3RS detected (25%), followed by Q749X (11%), Q741X (9%), Q743X (6%). Juxtamembrane hits (CNL-like lesion) were all in the same canonical region (T618I). In contrast, somatic hits otherwise typical for post SCN AML were found in 33% of CSF3RS alterations and included the following: Q749X(4), Q741X (3), Q739X (2), S742X, Q743X, and E405K (not typical for post SCN AML). Taken together the combined allelic burden of these variants did not exceed that of general population (OR: 0.9503) suggesting that they are not significant risk alleles. Of note is that none of these variants were found to be in biallelic (somatic/GL) configurations. Complex karyotype was found in 19% of the pts with CSF3RS followed by del7q in 13% of cases. Importantly, an antecedent history of neutropenia was noted only in 14% of the pts carrying CSF3RS. Regarding associated mutations, ASXL1 (43%), RUNX1 (23%), SETBP1 (23%), TET2 (23%), DNMT3A (17%), SRSF2 (16%), EZH2 (14%), IDH2 (11%), and NRAS (11%) were the most common co-mutations. We have investigated CSF3RS mutations for the presence of GL alterations, but compound heterozygous configurations were not identified. We concluded that CSF3R mutations typically associated with SCN transformation to myeloid neoplasia can occur without GL variants associated with this defect. Figure 1 Figure 1. Disclosures Balasubramanian: Servier Pharmaceuticals: Research Funding. Patel: Apellis: Consultancy, Other: educational talks, Speakers Bureau; Alexion: Consultancy, Other: educational talks, Speakers Bureau. Advani: Kite Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Research Funding; Glycomimetics: Membership on an entity's Board of Directors or advisory committees, Research Funding; Seattle Genetics: Membership on an entity's Board of Directors or advisory committees, Research Funding; OBI: Research Funding; Immunogen: Research Funding; Amgen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Pfizer: Honoraria, Research Funding; Macrogenics: Research Funding. Carraway: AbbVie: Other: Independent review committee; Agios: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Stemline: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Takeda: Other: Independent review committee; Astex: Other: Independent review committee; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Celgene, a Bristol Myers Squibb company: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Maciejewski: Novartis: Consultancy; Regeneron: Consultancy; Bristol Myers Squibb/Celgene: Consultancy; Alexion: Consultancy.

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Genomic Landscape of PHD Finger Protein 6 (PHF6) Mutant Myeloid Neoplasia

Blood ◽

10.1182/blood-2021-153554 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 1154-1154

Author(s):

Laila Terkawi ◽

Carmelo Gurnari ◽

Sunisa Kongkiatkamon ◽

Simona Pagliuca ◽

Minako Mori ◽

...

Keyword(s):

Transcriptional Regulation ◽

Board Of Directors ◽

Research Funding ◽

Binding Capacity ◽

Review Committee ◽

Advisory Committees ◽

Arginine Residues ◽

Independent Review ◽

Myeloid Neoplasia ◽

The Impact

Abstract Clinical impact and mechanistic contributions to leukemogenesis are difficult to assign to less common somatic mutations. However, the genetics of inherited syndromes can often be helpful in discerning the biological functions and mechanistic consequences of genes in other diseases. PHF6 (Xq26.2) encodes a protein consisting of two PHD-type zinc finger domains with activity in transcriptional regulation. PHF6 translocations were originally described in T-ALL and its mutations were later observed also in CML and adult AML. Germline (GL) PHF6MT cause Börjeson-Forssman-Lehmann syndrome (BFLS), an X-linked disorder characterized by intellectual disability and, to date, only a few BFLS cases were found to develop lymphoma or T-ALL. While regularly encountered in myeloid neoplasia (MN), the impact and functional meaning of PHF6 are not well established. To determine the incidence, distribution and molecular context of PHF6MT we studied a large cohort of patients with MN (n=8617) collected from our institution and public series. 1 Overall, 73% of patients were AML (pAML 69%; sAML 4%), MDS (22%) and MDS/MPN (5%) with a median age at diagnosis of 67 ys (18-100). We detected 149 patients (2%) carrying at least 1 PHF6MT with 11 harboring more than 1 hit. Four patients carried -X in addition to PHF6MT (2 males; 2 females). Majority of patients (68%) carried frameshift del/ins and nonsense. Mutations were scattered across all coding region with a slightly enrichment (47%) in the second PHD domain (239-330 aa) including the frequent R274Q/X (n=17). Common hits mainly affected arginine residues essential for DNA binding capacity (R129X n=9, R116X=7, R319X=5, R225X=3) followed by other hits (I314T=6, Y301X and C20fs=4 each). Of note, R116X, R225X, R274X, C280Y, H329R and Y303* lesions overlapped with the T-ALL PHF6MT spectrum while no overlap was found with GL mutations found in BFLS. Overall, 75% of all PHF6MT carriers were males and carried mostly (80%) truncating lesions. Compared to mutational frequencies observed in other X-linked genes, truncating PHF6MT behaved similarly to those in ZRSR2 (78%), STAG2 (73%) and BCOR (62%). Conversely, BCORL1MT, KDM6AMT and PIGAMT were evenly distributed between genders. When evaluating mutational characteristics in males and females, no differences were found in sex-adjusted median variant allelic burden of PHF6MT (54.8 vs 51%) nor its mRNA expression levels suggesting locus inactivation. PHF6MT tended to be older than PHF6WT patients (72 vs 68 ys; P= .05) and had mostly (63%) AML followed by MDS (23%) and MDS/MPN (14%). OS was similar between PHF6MT and PHF6WT patients (P= .16). Expression analyses showed that PHF6 loss leads to deregulation of chromatin and transcriptional factor genes. Indeed, in our cohort the most comutated genes were transcriptional factors and chromatin modifiers genes such as RUNX1 (26/149, 17%), ASXL1 (23/149, 15%) and TET2 (17/149, 11%). Of note, this group characterized by the triple ASXL1, RUNX1, TET2 mutational configuration clustered in one of the genomic groups previously identified (GC-3) 1 but the presence of these lesions did not worsen the OS as compared to PHF6MT without this mutational constellation. A low frequency of SF3B1MT (4%) was also noted confirming the enrichment of PHF6MT in AML rather than in low risk MDS. Further, 12% (14 males; 4 females) of PHF6MT patients had X-mutation mosaicism as shown by concomitant hits in BCOR (n=8), ZRSR2 (4), STAG2 (5), KDM6A (1). PHF6MT were equally founder lesions (30%; 44/149) and subclonal (34%; 50/149) whereas the rest was indistinguishable by VAF discrimination (co-dominant). The most common subclonal mutations were U2AF1 (14%, 6/44), IDH1/2 (9%, 4/44) and RUNX1 (7%, 3/44). When PHF6MT were subclonal, the founder hits were in TET2 (14%, 7/50), DNMT3A and RUNX1 (12%, each 6/50) genes. Given the high frequency of RUNX1MT in PHF6MT we investigated whether RUNX1 and PHF6 might be correlated. Transcriptomic analysis of 6246 patients (from 9 public studies) 2 showed a direct linear correlation (AdjR2= .03, P=5.55e-05) between the expression of the two genes. Our study is the largest to date to investigate the genetic landscape of PHF6MT in MN and highlights a strong connection of PHF6 with transcriptional regulation and chromatin genes. Ongoing scDNA-seq will clarify whether these mutations were acquired in distinct clones helping in dissecting the clonal hierarchy of PHF6MT cases. Disclosures Carraway: Celgene, a Bristol Myers Squibb company: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Agios: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Stemline: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AbbVie: Other: Independent review committee; Takeda: Other: Independent review committee; Astex: Other: Independent review committee; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Advani: Seattle Genetics: Membership on an entity's Board of Directors or advisory committees, Research Funding; Kite Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Research Funding; Glycomimetics: Membership on an entity's Board of Directors or advisory committees, Research Funding; Macrogenics: Research Funding; Immunogen: Research Funding; OBI: Research Funding; Amgen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Pfizer: Honoraria, Research Funding. Maciejewski: Regeneron: Consultancy; Novartis: Consultancy; Alexion: Consultancy; Bristol Myers Squibb/Celgene: Consultancy.

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Deficiency of RPS14 Beyond the Haploinsufficient Loss in Del(5q)

Blood ◽

10.1182/blood-2021-151926 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 2591-2591

Author(s):

Vera Adema ◽

Sunisa Kongkiatkamon ◽

Laura Palomo ◽

Wencke Walter ◽

Stephan Hutter ◽

...

Keyword(s):

Gene Expression ◽

Board Of Directors ◽

Linear Model ◽

Research Funding ◽

Review Committee ◽

Advisory Committees ◽

Tp53 Mutations ◽

Model Based ◽

Independent Review ◽

Cluster 2

Abstract The prevailing theory in del(5q) is that haploinsuffciency (HI) stemming from deletion and not simply LOH (loss of heterozygosity) is the culprit in clonal evolution. To date no haploinsufficient gene has been found to be the leukemogenic factor conveying growth advantage, but various other genes have been found to be important for phenotypic features or for propensity to acquire subsequent specific lesions. RPS14 is an example of such a gene, particularly in patients (pts) with isolated del(5q), responsible for macrocytic anemia and erythroid dysplasia and a propensity for acquisition of TP53 mutations. We hypothesized that RPS14 downmodulation and its consequences may be more common than del(5q) and it is frequent pathophysiologic feature in MDS. We first analyzed the genomic and expression profile of 170 pts with del(5q) and 825 diploid for 5q. We developed a new analytic pipeline to identify the most HI genes present in a large number of del(5q) pts. Genes within CDR (common deleted region) were classified as HI from the linear model fit if (i) clonality vs. gene expression slope from the isolated del(5q) was negative and FDR<.05; and (ii) effect of del(5q) at 50% clonality vs. other cases was negative and FDR<.05. A total of 62 genes met these criteria for linear-model based genes HI status, with a further 5 genes dropping due to low expression. Gene expression for these 57 HI genes among del(5q) samples was adjusted to 50%-clonality using the slopes from the estimated linear model to remove clonal heterogeneity. After applying model-based sparse clustering approach on all cohort, we obtained 7 clusters (Figure 1). As expected, del(5q) cases clustered together and showed consistent HI of 5q marker gene expression. Cluster-1 (n=146) included almost all del(5q) cases, except for 8 "mis-categorized" patients. It was characterized by low risk MDS (LR-MDS), presence of anemia/neutropenia and low mutational burden, with TP53 being the most commonly mutated gene and the only cluster with CSNK1A1 mutations. The remaining non-del(5q) patients were grouped in 6 clusters. Diploid cluster-2 (n=133) featured a normal karyotype, frequent ASXL1 and TET2 mutations, and profound down-modulation of RPS14 in all the patients included in the cluster (vs. other diploid pts). While the median RPS14 expression in cluster-1 (del(5q) cluster, with 50% adjusted clonality) was 7.29 (range 4.68-8.82 Log 2CPM), cluster-2 exhibited a median RPS14 expression of 6.12 Log 2CPM (range: 4.91-7.31 Log 2CPM). Clusters-3, -4, -5 (n=138, 90, 94, respectively) included most of the high risk MDS (HR-MDS). Cluster-3 was enriched for thrombocytopenia and SRSF2 mutations; cluster-4 for anemia, thrombocytopenia and ASXL1 and SRSF2 mutations. Cluster-5 was characterized by pancytopenia and frequent ASXL1 mutations and CK (complex karyotype). Cluster-6 (n=66) and -7 (n=233) contained the majority of non-del(5q) LR-MDS. When we analyzed the RPS14 expression in these clusters based on the RPS14 expression in cluster 2 we found 13% (n=18), 21% (n=19), 9% (n=8), 14% (n=9), 7% (n=16) of low RPS14 expressors in cluster-3, -4, -5, -6, -7, respectively. Cluster-2 showed a similar percentage of patients with anemia, and thrombocytopenia vs. Cluster-1 (69 vs. 50%, 23 vs. 30%; respectively). The mutational profile included a higher frequency of mutations for SRSF2 (29 vs. 0%), NRAS/KRAS (22% vs. 4%), ASXL1 (40 vs. 15%), TET2 (35 vs. 15%), and JAK2 (17 vs. 6%). These results indicate a more proliferative molecular spectrum of RPS14 downregulated cluster-2 than del(5q)-cluster-1, but RPS14 downmodulation did not lead to acquisition of TP53 mutations (4% vs. 76%). Considering all non-del(5q) RPS14 low expressors (n=186), only 3% of the cases had TP53 mutations. Since TP53 and CSNK1A1 mutations were characteristic of cluster-1 we studied interactions with HI RPS14. HI RPS14 in del(5q) and diploid low expressors showed a decreased expression of CDKN1A (P<.001) in comparison to the non-HI or low RPS14. We also found that CSNK1A1 mutations were not found outside of del(5q) pts, CSNK1A1 low expressors coincided with RPS14 low expressors. In conclusion, RPS14 expression defect is more widespread than del(5q) in MDS. However, only del(5q) RPS14 HI pts are prone to harbor TP53 and CSNK1A1 mutations; a group of diploid pts with low RPS14 and CSNK1A1 expressions might mimic some del5q features and could potentially respond to similar treatments. Figure 1 Figure 1. Disclosures Diez-Campelo: Takeda Oncology: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; BMS: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau. Carraway: AbbVie: Other: Independent review committee; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Takeda: Other: Independent review committee; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Agios: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Astex: Other: Independent review committee; Stemline: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Celgene, a Bristol Myers Squibb company: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Maciejewski: Bristol Myers Squibb/Celgene: Consultancy; Regeneron: Consultancy; Novartis: Consultancy; Alexion: Consultancy.

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A Novel Machine Learning-Derived Molecular Classification Scheme with Prognostic Significance

Blood ◽

10.1182/blood-2021-152443 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 3666-3666

Author(s):

Tariq Kewan ◽

Arda Durmaz ◽

Hassan Awada ◽

Carmelo Gurnari ◽

Waled Bahaj ◽

...

Keyword(s):

Machine Learning ◽

Board Of Directors ◽

Research Funding ◽

Prognostic Significance ◽

Molecular Classification ◽

Molecular Architecture ◽

Review Committee ◽

Advisory Committees ◽

Independent Review ◽

Normal Cytogenetics

Abstract The gold standard for the diagnosis of MDS relies on morphologic alterations hampered by a great deal of subjectivity. Cytogenetic and clinical features allow for clinical classifications predictive of survival. However, with a few exceptions (SF3B1MT, del5q, and certain balanced translocations), neither classic histo-morphology nor prognostic scoring systems (e.g., IPSS-R) are reflective of pathogenic underpinnings. To date supervised analyses of mutational data did not succeed to produce profiles specific or predictive of traditional disease sub-entities. Large cohorts with clinical annotation and a sufficient follow-up allow for innovative biostatistical approaches to subgroup patients according to molecular profiles. Objective operator-independent subcategorization may be congruent with common pathogenic links, rational applications of targeted therapeutics and better prognostications. We hypothesized that machine-learning (ML) strategies used for analysis of mutational/cytogenetic profiles will enable recognition of invariant disease subcategories according to their molecular configurations. Herein, we compiled a meta-analytic database (our cohorts and publicly available sources) of 3,011 MDS (median age 71yrs) and 6,788 pAML/sAML. Results of deep targeted sequencing of a panel of 55 myeloid mutations were collected together with cytogenetics. We then performed unsupervised analysis of MDS and AML patients using Bayesian Latent Class Analysis (BLCA). A consensus matrix was then clustered using Ward's criteria to generate final cluster assignment based on the highest silhouette value. To identify genomic signatures, we used Random Forest classification and extracted mutations with highest global importance indicated by mean decrease in accuracy. Using BLCA we identified 5 unique genomic clusters (GCs) with 3 distinct prognostic outcomes [low risk (LR), intermediate risk (Int), and high risk (HR)] that were validated by survival analysis (Fig.1A,B). The LR group included GC-1 and was characterized by the highest prevalence of normal cytogenetics (100%) and SF3B1 MT (25%) with co-occurring DNMT3A MT (14%), and absence of ASXL1 MT, ETV6 MT, STAG2 MT, TP53 MT, and complex/abnormal cytogenetics. Int group included GC-2 and GC-4. GC-2 was characterized by a higher percentage of abnormal cytogenetics cases than LR group and absence of STAG2 MT, SRSF2 MT, ASXL1 MT, TP53 MT, and normal/complex cytogenetics. GC-4 had the highest frequency of SRSF2 MT (52%) with co-occurring ASXL1 MT (59%), TET2 MT (40%), normal karyotype, and absence of complex/abnormal cytogenetics. Finally, HR included GC-3 and GC-5. GC-3 included ASXL1 MT (67%) with co-occurring SRSF2 MT (47%), TET2 MT (37%), STAG2 MT (22%), and absence of normal cytogenetics. GC- 5 had the highest frequency of -5/del(5q) (50%), -7/del(7q) (43%), -17/del(17p) (16%) and the highest odds of complex karyotype (92%) as well as TP53 MT (48%). Paralleling the genomic ML-based clustering, the clinical relevance of these subgroups was reflected in significantly different survivals [median (95% CI)]: i) GC-1 [69 (59-80)], ii) GC-2 [35 (29-41)], iii) GC-3 [12 (10-16)], GC-4 [27 (22-34)], and GC-5 [9 (7-11)] months (Fig.1C). We then classified the MDS cohort according to the recently published and validated AML GCs (Awada et al Blood 2021) to investigate overlapping genomic features. Overall, 90% of MDS GC-1 and 67% of MDS GC-2 had the same molecular architecture of AML GC-2 and 70% of MDS GC-5 had the same molecular features of AML GC-4. In addition, 98% of MDS GC-3 and 92% of MDS GC-4 had the same features of AML GC-3 (Fig.1D). In sum, we propose a novel objective molecular classification of MDS and related diseases that allows subgrouping of patients according to shared pathogenesis for a better prognostic resolution without errors derived from subjectivity. The model was then internally and externally validated using a cohort of 200 cases. Results of a validation cohort and online URL site of molecular clustering will be presented at the meeting. Figure 1 Figure 1. Disclosures Balasubramanian: Servier Pharmaceuticals: Research Funding. Patel: Alexion: Consultancy, Other: educational talks, Speakers Bureau; Apellis: Consultancy, Other: educational talks, Speakers Bureau. Carraway: Celgene, a Bristol Myers Squibb company: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Astex: Other: Independent review committee; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Agios: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Takeda: Other: Independent review committee; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AbbVie: Other: Independent review committee; Stemline: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Maciejewski: Regeneron: Consultancy; Novartis: Consultancy; Alexion: Consultancy; Bristol Myers Squibb/Celgene: Consultancy.

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TERT Rare Variants in Myeloid Neoplasia: Lack of Clinical Impact or Role as Risk Alleles

Blood ◽

10.1182/blood-2021-145942 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 1537-1537

Author(s):

Carmelo Gurnari ◽

Adam Wahida ◽

Simona Pagliuca ◽

Tariq Kewan ◽

Waled Bahaj ◽

...

Keyword(s):

Board Of Directors ◽

Rare Variants ◽

Review Committee ◽

Advisory Committees ◽

Available N ◽

Risk Alleles ◽

Independent Review ◽

Myeloid Neoplasia ◽

Coding Variants

Abstract Dyskeratosis congenita is a prototypic inherited telomeropathy. Telomere length (TL) shortening has also been described in aplastic anemia (AA) and attributed in occasional patients to the presence of mostly heterozygous germline alterations in telomerase machinery genes (most commonly in the reverse transcriptase gene, TERT). Among various heterozygous variants described, certain TERT variants associated with shortened TL (e.g. H412Y and A202T) showed later a higher prevalence in general population questioning their pathogenicity and role as risk alleles. Nevertheless, shortened TL has been shown to correlate with poor outcomes in AA and myelodysplastic syndromes (MDS) along with a higher progression rate to acute myeloid leukemia, and increased non-relapse mortality after HSCT. A high prevalence (41/1514; 2.7%) of non-recurrent germline TERT rare variants, has been found in patients with MDS undergoing HSCT (Reilly et al Blood 2021) without any clinically apparent diagnosis of a telomere biology disorder. Despite their classification as VUS, these alterations were shown to result in impairment of telomere elongation in vitro and reduced TL in vivo. Clinically, VUS carriers were also characterized by younger age at MDS presentation (median 52 years) and shorter survival due to a higher incidence of non-relapse mortality. We hypothesized that should such rare variants (traditionally thought as VUS) represent founder lesions and constitute risk alleles, one would expect to find some recurrence of these lesions in other cohorts of patients with myeloid neoplasia (MN). To test this hypothesis we screened a large meta-analytic cohort of MN patients (n=2560) including our patients (The Cleveland Clinic Foundation and MLL-Munich Leukemia laboratory) and a public series (The BEAT AML Master Trial and TCGA among others) for the presence of TERT coding variants. When whole genome sequencing was available (n=1432) TelomereHunter tool was used to estimate TL in carriers of TERT rare variants and wild-type (WT) cohorts. Overall, we identified 73 TERT coding variants. Based on maximum gnomAD population allele frequency (AF) <0.001 and ACMG and pathogenicity scores according to the classifiers of VarSome (https://varsome.com), we found 37/2560 (1.4%) variants which were categorized as rare and VUS. Of note, only 6 patients harbored established TERT pathogenic variants while the rest were common and VUS. Alterations occurred in the RTD (52%), TRBD-Linker region (29%) and CTE domain (19%). When compared to the aforementioned HSCT cohort described by Reilly et al, TERT rare VUS had a lower frequency and did not overlap with any of the VUS reported in this study, except for 2 patients harboring one variant each in amino acid locations 741 and 1041. Assessment of TL, possible in 12 patients carrying TERT rare variants, did not reveal differences compared to TERT WT cases. Interestingly, none of these rare variants were also observed in a control cohort of patients with AA (n=268). In terms of clinical features, MN patients with TERT rare variants harbored more somatic hits in DNMT3A and SF3B1 (26% each), and FLT3 (15%) with a diverse spectrum of additional molecular lesions, including germline VUS of other genes (4 patients harbored concomitant VUS in BRCA1, FANCG, and SAMD9, with another patient carrying a likely benign SAMD9L variant) (Fig1). When compared to WT counterparts, patients harboring TERT rare variants had a similar median age at MN diagnosis (70 vs. 66, P= 0.38) and similar survival outcomes (P= 0.96). Importantly, HSCT outcomes were ascertained only in 7 cases because of the real-life nature of our cohort which compiles MN patients of any subtype and age, thereby not biased by transplant referral like in the aforementioned study focusing only on MDS patients undergone HSCT. Finally, principal causes of death were primary disease (63%), presence of another malignancy (19%) and infections (13%) and, of note, no patient died of non-infectious pulmonary causes. In sum, our study, while confirming a relatively high (albeit not significant vs. controls) combined TERT VUS population burden in MN, also strongly indicates that rare TERT VUS are non-recurrent. Therefore, they cannot be considered risk alleles individually nor can their biological (combined or individual) impact in terms of non-transplant outcomes, irrespective of their in vitro functional effects. Figure 1 Figure 1. Disclosures Carraway: Celgene, a Bristol Myers Squibb company: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Stemline: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Agios: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AbbVie: Other: Independent review committee; Takeda: Other: Independent review committee; Astex: Other: Independent review committee; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Maciejewski: Bristol Myers Squibb/Celgene: Consultancy; Alexion: Consultancy; Novartis: Consultancy; Regeneron: Consultancy.

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The Drive to Acquire Biallelic Hits Inversely Correlates with the Functional Impact of the Primary TP53 Lesion: The Complexity of TP53 Role Assessment

Blood ◽

10.1182/blood-2021-152848 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 3322-3322

Author(s):

Waled Bahaj ◽

Carmelo Gurnari ◽

Tariq Kewan ◽

Suresh Kumar Balasubramanian ◽

Simona Pagliuca ◽

...

Keyword(s):

Board Of Directors ◽

Research Funding ◽

Clinical Impact ◽

Dominant Negative ◽

Rapid Progression ◽

Compound Heterozygous ◽

Review Committee ◽

Advisory Committees ◽

Tp53 Mutations ◽

Independent Review

Abstract While the clinical impact and the mechanistic contribution of TP53 mutations have been a subject of intense research, many questions about its role in myeloid neoplasia (MN) remain unanswered. Previous molecular studies have confirmed the assertion that biallelic inactivation confers less favorable prognosis as opposed to monoallelic hits. These evidences agree with the observation that carriers of Li-Fraumeni syndrome do not always exhibit a complete penetrance of the recessive TP53 lesion. Thus, the presence of a residual function of TP53 appears to be somehow protective until it is offset by additional damage of contralateral allele or compound heterozygous hits in synergistic pro-leukemogenic pathways. TP53 can be affected by lesions of diverse configurations (e.g. biallelic, homo/hemizygous) targeting different locations [missense mutation (ms) in various hotspots vs truncations], and their assessment in terms of clinical consequences is complex. Only large cohorts of patients allow to discern the often discrete nuances of TP53 effects in individual inactivation patterns. We have compiled molecular and clinical data of a meta-analytic cohort (CCF and public datasets) of 1,011 patients with TP53 alterations, along with 3,419 cases found to be TP53 wild type (WT). A total of 1,258 TP53 mutations/deletions were found, 66% classified as biallelic and 37% as monoallelic hits (including single deletions). We investigated the closest hotspot ms mutations, hypothesizing that lesions mapping sequences in proximity will have the same phenotypic impact. Next, we arranged ms mutations into 6 main sites with each one containing lesions mapping within 5 amino acidic positions from the canonical hotspot location. These sites were mutated in 58% of patients with presence of truncating hits in 27% of cases. When ms mutation sites were compared to each other, a less dismal survival was observed for only the R175H hotspot (p .03). Most hotspots are known to exhibit dominant-negative effects (likely due to tetramer protein configurations) and thus, inhibit >50% of the TP53 activity as opposed to truncations which should inactivate ~50%. Consequently, one would expect that hotspot mutations produce a more aggressive phenotype. However, patients with ms hits had similar survival as those with truncating mutations (p=.6), likely because truncations were more often biallelic than ms mutation (81% vs 65%, p=.006). Indeed, we can stipulate that the strength (functional impairment) conveyed by a mutation will inversely correlate with the propensity to acquire biallelic hits. Therefore, we hypothesized that truncations (inactivating less TP53) would require an additional hit if compared to the stronger dominant-negative ms lesions. Notably, double hits were identified in 81% of cases carrying truncating mutations vs. 66% in those with ms canonical sites mutations (p<.009). Carriers of biallelic mutations had worse prognosis than those with monoallelic hits in adjusted multivariate analysis (HR 2.2 95% CI 1.8-2.7 p<.001). However, unlike in previous reports, in our large cohort containing several MN types, monoallelic hits were not survival neutral, but worsened the prognosis as compared to WT patients (p<.001). This finding implies a strong driver effect for TP53 lesions, which are characterized by a rapid progression even in the monoallelic configuration. Similarly, monoallelic hits were associated with a higher mutational burden compared to biallelic ones (1.22 vs 0.91 co-mutations/patient, p=.02), which likely compensated the need for further TP53 inactivation. When focusing on the accompanying genomic landscape of our cohort, we found that 45% of cases had TP53 mutations as the sole molecular lesion vs 55% of patients who also harbored co-occurring somatic events. In particular, complex karyotype was more frequent among patients without co-occurring mutations (79% vs 57%, p<.001). As of associations with disease subtypes, primary AML cases had a lower burden of co-mutations (p<.001) while the highest percentages were registered in LR-MDS (p=.005). In summary, our study demonstrates the complexity of assigning a correct clinical impact to TP53 mutations, which are characterized by a high degree of genomic heterogeneity. In addition to the genetic context, TP53 role may also vary in different subtypes of MN (e.g., AML vs MDS) shaping in a different fashion individual patients' trajectories. Disclosures Balasubramanian: Servier Pharmaceuticals: Research Funding. Saunthararajah: EpiDestiny: Consultancy, Current holder of individual stocks in a privately-held company, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties. Hamilton: Syndax: Membership on an entity's Board of Directors or advisory committees; Equilium: Membership on an entity's Board of Directors or advisory committees. Carraway: Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AbbVie: Other: Independent review committee; Takeda: Other: Independent review committee; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Agios: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Celgene, a Bristol Myers Squibb company: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Stemline: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Astex: Other: Independent review committee. Maciejewski: Novartis: Consultancy; Regeneron: Consultancy; Bristol Myers Squibb/Celgene: Consultancy; Alexion: Consultancy.

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Myelodysplastic Syndromes: A More Global 5-Hydroxymethylcytosine Deficiency Disorder Than Suggested By the Presence of TET2 Mutations

Blood ◽

10.1182/blood-2021-145949 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 3665-3665

Author(s):

Carmelo Gurnari ◽

Simona Pagliuca ◽

Yihong Guan ◽

Courtney E. Hershberger ◽

Ying Ni ◽

...

Keyword(s):

Board Of Directors ◽

High Frequency ◽

Research Funding ◽

Regression Analyses ◽

Review Committee ◽

Advisory Committees ◽

Mutational Burden ◽

Impact On Survival ◽

Independent Review

Abstract The high frequency of TET2 mutations in myelodysplastic syndromes (MDS) and the sole function of TET-dioxygenases as 5-hydroxymethylcytosine (5-hmC) hydroxylases emphasize the key role of this gene in disease pathogenesis. However, the broad down-regulation of 5-hmC argues for a role of DNA demethylation in MDS beyond TET2 lesions, which albeit the high frequency, do not convey any impact on survival outcomes. In fact, decrease in 5-hmC levels is by far more widely spread than TET2 lesions pointing towards other pathways affecting TET2 activity, thereby obscuring a precise determination of its mutational and clinical consequences. Herein, we investigated TETs expression to identify factors explaining the widespread deficiency of 5-hmC in MDS possibly determining clinical phenotypes and prognosis. An integrative data analysis of genomic studies (whole genome and deep targeted NGS), RNA-sequencing and 5-hmC quantification was performed on 1,665 patients with MDS and 91 healthy controls (HC). Meta-analytic studies of 5-hmC levels in myeloid neoplasia (n=598) and data of RNA-sequencing of fractionated CD34 (GSE63569) were also included as confirmatory cohorts. We started by analyzing the clinical impact of TET2 mutations carried by 23% of our study population. No impact on survival was found in carriers of TET2 lesions including those with biallelic, truncating or missense mutations compared to wild-type (WT) (Fig1A). By using 5-hmC levels as a functional readout of TET activity, we found a TET deficiency in about 70% of patients, a proportion higher than one would conclude by considering the mere presence of TET2 mutations (Fig1B). To explain the decrease in 5-hmC levels in WT cases, we next examined transcriptome modifications. Analysis of the expression of TET family of genes showed that MDS patients had lower TET2 mRNA levels in total and in CD34+ cells as compared to HC, irrespective of their TET2 status. Therefore, we reasoned that TET2 deficiency is more ubiquitously involved in MDS pathogenesis than what would be expected by the only estimation of mutant cases. Indeed, "low expressor" status (defined by TET2 expression < 25%ile of HC) was found in 74% of MDS. Along with variable 5-hmC levels, concomitant differences in TET1/TET3 expression were also investigated. While TET1 levels were too low to be evaluated, TET3 expression levels were markedly higher in all and in WT MDS compared to HC, possibly in an attempt to compensate TET2 dysfunction (Fig1C). In addition, TET3 expression did not correlate with TET2 mutational burden, confuting a compensatory feedback mechanism in TET2 mutant cases. Further uni- and multivariate analyses showed that elevated TET3 levels compensated TET2 deficiency in terms of clinical outcomes (Fig1D) and linear regression analyses confirmed that indeed lack of compensation by TET3 (low TET3 expression) was associated with high risk features. To explore whether other factors might be associated with low TET2 levels, we studied TET2 expression in WT cases as to the presence of other mutations. We found that TET2 expression was significantly lower in patients harboring DNMT3A (P< 0.0001), SF3B1 (P< 0.0001) and SRSF2 (P= 0.04) compared to HC. However, lack of correlation between levels of TET2 and mutational burden failed to prove a direct relationship of these mutations (Fig1E). Decreased hydroxylation of 5-mC may also be caused by endogenous L-2-hydroxyglutarate (L2HG) produced via malate shunt. Accordingly, L2HG dehydrogenase (L2HGDH) levels catabolizing L2HG and malate dehydrogenases (MDH1/2) supplying L2HG, would influence TET2 activity in a reciprocal fashion. Consistently we found that MDH1/2 levels were increased in MDS and that L2HGDH showed also a likely compensatory increase to handle elevated L2HG loads. Further, linear regression analyses revealed that L2HGDH levels were correlated inversely with TET2 and positively with TET3 expression in WT cases (Fig1F). In sum, MDS can be considered a wide-ranging 5-hmC deficiency disorder driven by direct or indirect loss of TET2functions by mutations or down-modulation due to a variety of mechanisms. Disease phenotypes and outcomes are both influenced by counteracting factors such as expression of TET3. Application of precision therapeutic approaches should be informed by the analyses of all these factors. Figure 1 Figure 1. Disclosures Carraway: Astex: Other: Independent review committee; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Stemline: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Agios: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AbbVie: Other: Independent review committee; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Takeda: Other: Independent review committee; Celgene, a Bristol Myers Squibb company: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Kim: Paladin: Consultancy, Honoraria, Research Funding; Bristol-Meier Squibb: Research Funding; Pfizer: Honoraria; Novartis: Consultancy, Honoraria, Research Funding. Minden: Astellas: Consultancy. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Maciejewski: Bristol Myers Squibb/Celgene: Consultancy; Novartis: Consultancy; Regeneron: Consultancy; Alexion: Consultancy.

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Immunogenetic Drivers in Post-Transplant Acute Myeloid Leukemia Recurrence: Genomic Dysfunction of Human Leukocyte Antigen Diversity

Blood ◽

10.1182/blood-2021-153577 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 3921-3921

Author(s):

Simona Pagliuca ◽

Carmelo Gurnari ◽

Laila Terkawi ◽

Ishani Pandit ◽

Tariq Kewan ◽

...

Keyword(s):

T Cell ◽

Human Leukocyte Antigen ◽

Board Of Directors ◽

Research Funding ◽

Human Leukocyte ◽

Review Committee ◽

Advisory Committees ◽

Leukocyte Antigen ◽

Mutational Burden ◽

Independent Review

Abstract Structural and functional variability of human leukocyte antigen (HLA) is the foundation for competent anti-tumor and infectious adaptive immune responses. HLA genomic heterogeneity enables the presentation of a broad immune-peptidome, sustaining an efficient diversification of T cell receptor repertoires (TCR). 1,2,3 Any perturbation impacting this diversity may be at the basis of pathological processes, hampering antigen presentation capabilities and T-cell reactivity. In allogeneic hematopoietic cell transplantation (allo-HCT) setting, the graft versus leukemia (GvL) effect should ensure disease control allowing the recognition of recipient neoantigen burden by donor T-cell effectors. However, the molecular dissection of graft versus host responses (GvH) remains elusive. Herein, by means of a broad immunogenetic study of a cohort of patients with myeloid malignancies who received a donor matched allo-HCT, we investigated how dysfunction of HLA variability could have an impact on alloreactive responses, ultimately hindering disease control. To that end, we combined NGS-based HLA genotyping and TCR-beta sequencing to molecularly characterize the HLA region in terms of locus-specific divergence and somatic mutational profile, and dissect features and clonotypic spectra of TCR repertoires. We first hypothesized that more diverse HLA genotypes could better present leukemic neoantigen burden than less diverse complexes, enhancing the GvL effect. Hence, we performed a matched-pair analysis between allo-HCT recipients relapsing after 3mo (median 6.2 mo. [IQR=4.6-12]), N=75) compared to patients without recurrence (N=193, matched for ethnicity, age, disease, graft source and conditioning regimens) and characterized the patterns of HLA evolutionary divergence (HED), 1 a metric recently conceived to quantitate the pair-wise distance (based on physiochemical composition) between the amino acids located within the peptide-binding groove of two homologous HLA alleles. Overall, the relapsed group was characterized by a lower global (class I/II) mean HED (p=.0029) compared to non-relapsed patients, with major differences seen for C (p=.0041), DQB1 (p=.0291), and DPB1 (p=.0396) loci. When studying the landscape of post-transplant TCR reconstitution (+3 months) in a subset of 25 patients, we observed an inverse correlation between TCR clonal expansion and global HED (AdjR 2=0.04, p=<2e-16), contributing to decrease the diversity of TCR repertoires in patients with lower HED. Although not different in number, the expansion of clonotypes with known anti-cancer specificity was higher in non-relapsing group (p=6.3e-08), possibly underlying a better tumor-surveillance. Next, we sought to investigate the patterns of somatic HLA dysfunction in relapsing patients (intended as allelic loss or mutations). Indeed, through a recently implemented HLA mutational calling algorithm, we observed somatic events encompassing both class I and II alleles in 23% (N=8/34 profiled patients). Interestingly, when analyzing patients with relapse who received a donor lymphocyte infusion-based treatment (DLI), none of the cases harboring mutational events (N=4/4) responded to this salvage strategy. It is noteworthy that in this last group, one patient relapsed with an extramedullary localization along with the acquisition of HLA mutations. HLA mutated group had a higher (although not significant) leukemia mutational burden compared to non-mutated group (mean number of leukemia-associated mutations: 3.6 vs 1.9/patient), underscoring the need for further driver mutational events compensating the possible lower immunogenic potential of HLA mutant clones. Despite a mild increase in mutational burden, driver hits (such as IDH1/2, FLT3, TP53, NPM1) were never present in patients carrying HLA aberrations, who instead harbored in a few cases mainly lesions in epigenetic regulators and chromatin modifiers (TET2, EP300, DNMT3A, EZH2). Altogether these findings pinpoint the role of the dysfunction of the structural variability of HLA complexes within both germline (HED) and somatic (HLA loss/mutations) scenarios as mechanisms hampering a successful neoantigen presentation and TCR recovery processes, possibly conveying a higher risk of disease relapse or treatment-resistance. Disclosures Balasubramanian: Servier Pharmaceuticals: Research Funding. Carraway: Takeda: Other: Independent review committee; AbbVie: Other: Independent review committee; Stemline: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Agios: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Celgene, a Bristol Myers Squibb company: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Astex: Other: Independent review committee. Hamilton: Syndax: Membership on an entity's Board of Directors or advisory committees; Equilium: Membership on an entity's Board of Directors or advisory committees. Majhail: Anthem, Inc: Consultancy; Incyte Corporation: Consultancy. Maciejewski: Bristol Myers Squibb/Celgene: Consultancy; Regeneron: Consultancy; Alexion: Consultancy; Novartis: Consultancy.

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Phase I Study of Ixazomib with Conventional Chemotherapy in the Treatment of Acute Myeloid Leukemia in Older Adults

Blood ◽

10.1182/blood-2020-140584 ◽

2020 ◽

Vol 136 (Supplement 1) ◽

pp. 7-8

Author(s):

Philip C. Amrein ◽

Eyal C. Attar ◽

Geoffrey Fell ◽

Traci M. Blonquist ◽

Andrew M. Brunner ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Board Of Directors ◽

Myeloid Leukemia ◽

Research Funding ◽

Remission Rate ◽

Conventional Chemotherapy ◽

Advisory Committees ◽

Secondary Aml ◽

Grade 3 ◽

Acute Myeloid

Introduction: Outcomes for acute myeloid leukemia (AML) among older patients has remained largely unchanged for decades. Long-term survival for patients aged >60 years is poor (median survival 10.5 months). Targeting the proteasome in AML is attractive, since leukemia stem cells have demonstrated sensitivity to proteasome inhibition in preclinical models, perhaps through down regulation of nuclear NF-KB (Guzman, Blood 2001). AML cell lines are susceptible to synergistic cytotoxicity when bortezomib, a proteasome inhibitor, is combined with daunorubicin and cytarabine. We have shown that adding bortezomib to standard treatment in AML results in a high remission rate, although grade 2 sensory neurotoxicity was noted in approximately 12% of treated patients. A newer generation proteasome inhibitor, ixazomib, is less frequently associated with neurotoxicity, and, therefore, was selected for combination with conventional chemotherapy in this phase I trial. The primary objective of this study was to determine the maximum tolerated dose (MTD) of ixazomib in combination with conventional induction and consolidation chemotherapy for AML. Herein are the initial results of this trial. Methods: Adults >60 years of age with newly diagnosed AML were screened for eligibility. Patients with secondary AML were eligible, including those with prior hypomethylating agent therapy for myelodysplastic syndromes (MDS). We excluded those with promyelocytic leukemia. There were 2 phases in this study. In the first phase (A), the induction treatment consisted of the following: cytarabine 100 mg/m2/day by continuous IV infusion, Days 1-7; daunorubicin 60 mg/m2/day IV, Days 1, 2, 3, and ixazomib was provided orally at the cohort dose, Days 2, 5, 9, and 12. Consolidaton or transplant was at the discretion of the treating physician in phase A. In the second phase (B), induction was the same as that with the determined MTD of ixazomib. All patients were to be treated with the following consolidation: cytarabine at 2 g/m2/day, days 1-5 with ixazomib on days 2, 5, 9, and 12 at the cohort dose for consolidation. A standard 3 + 3 patient cohort dose escalation design was used to determine whether the dose of ixazomib could be safely escalated in 3 cohorts (1.5 mg/day, 2.3 mg/day, 3.0 mg/day), initially in induction (phase A) and subsequently in consolidation (phase B). The determined MTD of ixazomib in the first portion (A) of the trial was used during induction in the second portion (B), which sought to determine the MTD for ixazomib during consolidation. Secondary objectives included rate of complete remission, disease-free survival, and overall survival (OS). Results: Thirty-six patients have been enrolled on study, and 28 have completed dose levels A-1 through A-3 and B1 through B-2. Full information on cohort B-3 has not yet been obtained, hence, this report covers the experience with the initial 28 patients, cohorts A-1 through B-2. There were 12 (43%) patients among the 28 with secondary AML, either with prior hematologic malignancy or therapy-related AML. Nineteen patients (68%) were male, and the median age was 68 years (range 61-80 years). There have been no grade 5 toxicities due to study drug. Three patients died early due to leukemia, 2 of which were replaced for assessment of the MTD. Nearly all the grade 3 and 4 toxicities were hematologic (Table). There was 1 DLT (grade 4 platelet count decrease extending beyond Day 42). There has been no grade 3 or 4 neurotoxicity with ixazomib to date. Among the 28 patients in the first 5 cohorts, 22 achieved complete remissions (CR) and 2 achieved CRi, for a composite remission rate (CCR) of 86%. Among the 12 patients with secondary AML 8 achieved CR and 2 achieved CRi, for a CCR of 83%. The median OS for the 28 patients has not been reached (graph). The 18-month OS estimate was 65% [90% CI, 50-85%]. Conclusions: The highest dose level (3 mg) of ixazomib planned for induction in this trial has been reached safely. For consolidation there have been no serious safety issues in the first 2 cohorts with a dose up to 2.3 mg, apart from 1 DLT in the form of delayed platelet count recovery. The recommended phase 2 dose of ixazomib for induction is 3 mg. Accrual to cohort B-3 is ongoing. Notably, to date, no grade 3 or 4 neurotoxicity has been encountered. The remission rate in this older adult population with the addition of ixazomib to standard chemotherapy appears favorable. Figure Disclosures Amrein: Amgen: Research Funding; AstraZeneca: Consultancy, Research Funding; Takeda: Research Funding. Attar:Aprea Therapeutics: Current Employment. Brunner:Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Forty-Seven Inc: Membership on an entity's Board of Directors or advisory committees; AstraZeneca: Research Funding; Takeda: Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Research Funding. Hobbs:Constellation: Honoraria, Research Funding; Novartis: Honoraria; Incyte: Research Funding; Merck: Research Funding; Bayer: Research Funding; Jazz: Honoraria; Celgene/BMS: Honoraria. Neuberg:Celgene: Research Funding; Madrigak Pharmaceuticals: Current equity holder in publicly-traded company; Pharmacyclics: Research Funding. Fathi:Blueprint: Consultancy; Boston Biomedical: Consultancy; BMS/Celgene: Consultancy, Research Funding; Novartis: Consultancy; Kura Oncology: Consultancy; Trillium: Consultancy; Amgen: Consultancy; Seattle Genetics: Consultancy, Research Funding; Abbvie: Consultancy; Pfizer: Consultancy; Newlink Genetics: Consultancy; Forty Seven: Consultancy; Trovagene: Consultancy; Kite: Consultancy; Daiichi Sankyo: Consultancy; Astellas: Consultancy; Amphivena: Consultancy; PTC Therapeutics: Consultancy; Agios: Consultancy, Research Funding; Takeda: Consultancy, Research Funding; Jazz: Consultancy. OffLabel Disclosure: Ixazomib is FDA approved for multiple myeloma. We are using it in this trial for acute myeloid leukemia.

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Efficacy of Single-Agent Decitabine in Relapsed and Primary Refractory (rel/ref) Acute Myeloid Leukemia (AML)

Blood ◽

10.1182/blood.v126.23.2518.2518 ◽

2015 ◽

Vol 126 (23) ◽

pp. 2518-2518

Author(s):

Andrew Hantel ◽

Niloufer Khan ◽

Richard A. Larson ◽

Lucy A. Godley ◽

Michael J. Thirman ◽

...

Keyword(s):

Board Of Directors ◽

Genetic Risk ◽

Research Funding ◽

De Novo ◽

Median Number ◽

Advisory Committees ◽

Secondary Aml ◽

Induction Regimen ◽

De Novo Aml ◽

Wbc Count

Abstract Introduction Improving therapy for rel/ref AML remains a challenge. Decitabine, a DNA methyl-transferase inhibitor, initially showed promise in AML as a 5-day, first-line induction regimen and more recently as a 10-day regimen in older and unfit patients (1). However, little is known about the activity of decitabine in the rel/ref patient population despite increased use. Therefore, we sought to analyze the outcomes of these pts treated at our institution. Methods To obtain data regarding decitabine efficacy in rel/ref AML, we performed a retrospective analysis of outcomes following decitabine treatment in 34 adult pts treated at The University of Chicago from January 2009 to June 2014. Permission to access patient charts was granted by the medical centerÕs Institutional Review Board. AML was defined by WHO criteria, genetic risk grouping and complete remission (CR) was according to ELN classification; PR was defined as >50% decrease in bone marrow blasts and normalization of blood counts. Rel/ref AML was defined as either having had a prior CR with recurrence of disease or having received a prior induction regimen (1-2 cycles) without CR. Results Median pt age was 62 yrs (range, 18-81) and 60% were male. Median Charlson comorbidity index (CCI) was 5 (range, 0-8); 29% had ECOG performance status 0-1 and 71% had >2. 21 pts (62%) had de novo AML (7 with myelodysplasia-related changes), 3 (9%) had therapy-related myeloid neoplasm (t-MN), and 10 (29%) had secondary AML after myelodysplastic syndrome. 6% were in the ELN favorable genetic group, 3% intermediate-I, 18% intermediate-II, and 67% adverse; 2 cases were unevaluable. The median number of prior treatment regimens was three. 9% had received prior azacitidine, 85% had received prior HiDAC, and 38% had a prior allogeneic stem cell transplant (SCT). 34 pts received a total of 71 cycles of decitabine, 20 mg/m2 daily, in 5 or 10-day cycles every 28 days. All patients received 10-day courses, 91% had an initial 10-day course, and 74% had only 10-day courses. The median number of cycles per pt was 2; 59% received >1 cycle. 7 (21%) achieved CR and 4 (12%) had a partial response (PR), for an overall response rate (OR) of 33%. Responses occurred in 24% of pts with de novo AML, 66% with t-MN, and 50% with secondary AML. Intermediate and adverse group pts had OR of 14% and 39%, respectively. All pts achieving CR did so after 1 cycle; PR required a median of 3 cycles. Pts who achieved CR or PR had a significantly lower pretreatment WBC count (median, 9.5 vs 49.5 x 103/µL in non-responders; p=0.015) and blast percentage (44 vs 59.4; p=0.035) than those who did not. Pts with secondary AML or t-MN had a higher probability of OR compared to those with de novo AML (54 vs 23%; p=0.042). Median overall survival (OS) of all pts was 256 days; prior SCT was associated with reduced OS (p=0.017). When comparing de novo to secondary AML & t-MN, 1-year OS was not significantly different (Figure 1). Responders had a significantly longer OS (median, 622 days vs 278 days for non-responders; p=0.012). Age, race, CCI, ECOG PS, genetic risk group, prior HiDAC, dysplasia, azacitidine, and number of prior treatments did not impact OR or OS. 16 (47%) pts proceeded to SCT. During treatment, 70% had a grade 3-4 non-hematologic toxicity (based on NCI CTACE v4.0); the most common was fatigue. The median number of hospitalizations for complications per patient was 2 (range, 0-7). Causes of hospitalization were febrile neutropenia (40%), infection (22%), cytopenias (18%), rash (6%), acute kidney injury (6%), and 8% were for other causes. Conclusion Decitabine treatment of 34 adults with rel/ref AML resulted in an OR of 33% (21% CR) and allowed nearly one-half of these pts to proceed to SCT. All pts achieving CR did so after 1 cycle. Responding pts had improved OS over those without response (p=0.012). Interestingly, secondary AML or t-MN were 7.8 times more likely to achieve a response compared to de novo AML (p=0.046); lower WBC count and marrow blast percentage also correlated with higher OR. Further delineation of molecular subsets associated with response to decitabine should be evaluated in a larger prospective trial in this high-risk AML population. Citation 1. Blum KA, et al. Phase I trial of low dose decitabine targeting DNA hypermethylation in patients with chronic lymphocytic leukaemia and non-Hodgkin lymphoma: dose-limiting myelosuppression without evidence of DNA hypomethylation. Br J of Haem. Jul 2010;150(2):189-195. Figure 1. Figure 1. Disclosures Off Label Use: Decitabine is indicated for treatment of MDS but is often used to treat newly diagnosed or relapsed/refractory AML. In this study we analyzed results of patients with AML who were treated with decitabine in the relapsed/refractory setting.. Thirman:AbbVie: Research Funding; Pharmacyclics LLC, an AbbVie Company: Research Funding; Gilead: Research Funding; Merck: Research Funding; AbbVie: Research Funding; Gilead: Research Funding; Merck: Research Funding. Odenike:Sunesis: Membership on an entity's Board of Directors or advisory committees, Research Funding. Liu:Astra Zeneca/Medimmune: Consultancy; Pfizer: Consultancy; Astra Zeneca/Medimmune: Consultancy; Pfizer: Consultancy. Stock:Gilead: Membership on an entity's Board of Directors or advisory committees.

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Mutations Highly Specific for Secondary AML Are Associated with Poor Outcomes in Patients with NPM1-Mutated ELN Favorable Risk AML

Blood ◽

10.1182/blood-2021-150759 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 686-686

Author(s):

Onyee Chan ◽

Najla Al Ali ◽

Hammad Tashkandi ◽

Austin Ellis ◽

Somedeb Ball ◽

...

Keyword(s):

Board Of Directors ◽

Research Funding ◽

Univariate Analysis ◽

Prognostic Significance ◽

Cancer Center ◽

Cell Transplant ◽

Intermediate Risk ◽

Advisory Committees ◽

Secondary Aml ◽

The Impact

Abstract Background: NPM1 is commonly mutated in acute myeloid leukemia (AML) and represents a distinct entity under the WHO 2016 classification. It is one of the few mutations that can potentially support favorable risk by European LeukemiaNet (ELN) 2017 criteria. Mutations that are highly specific for secondary AML including SRSF2, SF3B1, U2AF1, ZRSR2, ASXL1, EZH2, BCOR, and STAG2 (sMut) (Lindsley et al.) have been shown to confer poor prognosis. The impact of these mutations on NPM1-mutated AML warrants further investigation. Objective: In this study, we explore the outcomes in patients with NPM1-mutated AML. Methods: This was a retrospective study of NPM1-mutated AML patients who were diagnosed and treated at the Moffitt Cancer Center from 2013 to March 2021. Inclusion was restricted to NPM1-mutated patients with mutation analysis (NGS) performed at diagnosis (n=159). Kaplan-Meier, univariate, and multivariate analyses were performed. Results: Among 159 patients (78M/81F, median age 63 years at diagnosis), 80.5% had de novo AML. By ELN 2017 criteria, 63.5% (101/159) had favorable risk, 27.7% (44/159) had intermediate risk, and 8.2% (13/159) had adverse risk disease. Almost 90% had intermediate risk cytogenetics at the time of diagnosis. Common co-mutations included DNMT3A (47.2%), FLT3-ITD (35.8%), TET2 (26.4%), IDH1 (17.6%), FLT3-TKD (15.1%), and IDH2 (13.8%). sMut comprised 19.5% (31/159) of patients and 20.8% (21/101) of those with ELN favorable risk. In patients with treatment response data, those with sMut never achieved CR/CRi in 35.7% (10/28) compared to 17.2% (22/128) of patients without sMut (p=0.038). The overall survival (OS) was 43.7 months with a median follow up of 35.5 months. Patients with sMut had worse OS compared to those without sMut (14.7 months vs 57.6 months, p=0.011). Among patients with favorable risk disease, OS was 11.6 months compared to not reached for those with sMut and without sMut, respectively (p<0.0001). Univariate analysis showed sMut and allogeneic hematopoietic cell transplant (HCT) significantly impacted OS (sMut: HR 3.48, 95% CI: 1.80-6.72, p<0.001; HCT: HR 0.17, 95% CI: 0.07-0.44, p<0.001). Multivariate regression using covariates including age, AML type, sMut, and HCT confirmed their prognostic significance on survival (sMut: HR 2.40, 95% CI: 1.17-4.93, p=0.017; HCT: HR 0.26, 95% CI: 0.08-0.56, p=0.002). Conclusions: Our findings suggest NPM1-mutated AML patients with sMut have significantly worse prognosis despite being classified primarily as favorable risk by ELN 2017 at diagnosis. This may have treatment implications altering the need for and/or timing of HCT. These findings should be assessed prospectively and validated in independent datasets. Figure 1 Figure 1. Disclosures Hussaini: Adaptive: Consultancy, Honoraria, Speakers Bureau; Stemline: Consultancy; Amgen: Consultancy; Seattle Genetics: Consultancy; Celegene: Consultancy; Decibio: Consultancy; Guidepoint: Consultancy; Bluprint Medicine: Consultancy. Talati: AbbVie: Honoraria; Pfizer: Honoraria; Astellas: Speakers Bureau; BMS: Honoraria; Jazz: Speakers Bureau. Kuykendall: Incyte: Consultancy; Novartis: Honoraria, Speakers Bureau; Protagonist: Consultancy, Research Funding; Celgene/BMS: Honoraria; Abbvie: Honoraria; Blueprint: Honoraria; Pharmaessentia: Honoraria. Padron: Blueprint: Honoraria; Incyte: Research Funding; Kura: Research Funding; Stemline: Honoraria; Taiho: Honoraria; BMS: Research Funding. Sallman: Shattuck Labs: Membership on an entity's Board of Directors or advisory committees; Syndax: Membership on an entity's Board of Directors or advisory committees; Magenta: Consultancy; Takeda: Consultancy; Kite: Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Incyte: Speakers Bureau; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees; Intellia: Membership on an entity's Board of Directors or advisory committees; AbbVie: Membership on an entity's Board of Directors or advisory committees; Agios: Membership on an entity's Board of Directors or advisory committees; Aprea: Membership on an entity's Board of Directors or advisory committees, Research Funding. Sweet: Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Astellas: Consultancy, Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees; Bristol Meyers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees; AROG: Membership on an entity's Board of Directors or advisory committees. Komrokji: Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Geron: Consultancy; BMSCelgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Acceleron: Consultancy; AbbVie: Consultancy; Jazz: Consultancy, Speakers Bureau; Taiho Oncology: Membership on an entity's Board of Directors or advisory committees; PharmaEssentia: Membership on an entity's Board of Directors or advisory committees. Lancet: AbbVie: Consultancy; Celgene/BMS: Consultancy; Daiichi Sankyo: Consultancy; ElevateBio Management: Consultancy; Millenium Pharma/Takeda: Consultancy; BerGenBio: Consultancy; Jazz: Consultancy; Agios: Consultancy; Astellas: Consultancy.

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