scholarly journals Der(1;7)(q10;p10) Presents with a Unique Genetic Profile and Frequent ETNK1 Mutations in Myeloid Neoplasms

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1513-1513
Author(s):  
Rurika Okuda ◽  
Yasuhito Nannya ◽  
Yotaro Ochi ◽  
Maria Creignou ◽  
Hideki Makishima ◽  
...  
Keyword(s):  
Research Funding ◽  
Genetic Profile ◽  
Unbalanced Translocation ◽  
Monosomy 7 ◽  
Male Predominance ◽  
Myeloid Neoplasm ◽  
Myeloid Neoplasms ◽  
Otsuka Pharmaceutical ◽  
Targeted Capture ◽  
Capture Sequencing

Abstract Background Der(1;7)(q10;p10) (der(1;7) is an unbalanced translocation recurrently found in myeloid neoplasms, particularly in myelodysplastic syndromes (MDS) and related disorders. Caused by a recombination between two homologous alphoid sequencing D1Z7 and D7Z1 on chromosomes 1 and 7, respectively, it results in monosomy 7q and trisomy 1q, which is implicated in the pathogenesis of der(1;7)-positive myeloid neoplasms. Previous studies reported frequent co-occurrence of +8 and del(20q), as well as RUNX1 mutations, the genetic and clinical characteristics of this abnormality has not fully been elucidated. Methods In this study, we enrolled a total of 153 cases myeloid neoplasms positive for der(1;7) from Japanese and German cohorts, in which co-occurring genetic lesions were analyzed using whole exome and/or targeted-capture sequencing. An additional 3,223 MDS and related neoplasm cases were also analyzed using targeted-capture sequencing to identify der(1;7)-specific genomic features. Results Ethnicity was evaluated comparing the frequency of der(1;7) in 944 German MDS cases and 763 Japanese MDS cases. Der(1;7) cases were observed at a higher frequency in Japanese MDS cohort compared to German MDS cohort (73/763 cases versus 4/944 cases, p < 0.00001). Der(1;7) cases showed a strong male predominance (86.3%) (p<0.001). Of 153 myeloid neoplasm patients harboring der(1;7), 114 were diagnosed with MDS, 28 with AML, 5 with MDS-MPN and 1 with MPN. Targeted-capture sequencing revealed mutations in common myeloid drivers (n=61) in 96% of der(1;7) cases. The most frequently mutated gene was RUNX1 with 46%, followed by ETNK1 (24.5%) and EZH2 (24.5%). Of interest, ETNK1 mutation was identified as the most unique to der(1;7) when compared to myeloid neoplasm cases without der(1;7) (n=3,066) [odds ratio (OR)=15.06], followed by ETV6 (OR=9.35) and EZH2 (OR=6.52). To further examine the uniqueness of this mutation profile, the mutational profile of der(1;7) was compared to those myeloid neoplasm cases harboring amp(1q) (n=52) and monosomy 7 (n=105). Highly frequent ETV6 and ETNK1 mutations were highly unique to der(1;7) cases when compared to amp(1q) cases (OR=3.72, OR=2.57, respectively). BCOR and ETNK1 mutations were highly unique to der(1;7) cases when compared to monosomy 7 cases (OR=35.88, OR=4.29, respectively). Both amp(1q) and monosomy 7 cases showed a higher mutation rate in TP53 compared to der(1;7) cases (49.1% and 51%, respectively, vs 3.5 %) . From these mutational characteristics, ETNK1 was identified as being the most unique to der(1;7) when compared to amp(1q), monosomy 7 and other myeloid neoplasm cases. ETNK1-mutated der(1;7) cases were featured with eosinophilia (p < 0.0005), a lack of RAS pathway mutations and trisomy 8 when compared to ETNK1-wild type der(1;7) cases. Survival analysis was conducted to elucidate the difference in survival in der(1;7) cases (n=65) versus myeloid neoplasm cases (n=2066). Der(1;7)-harboring myeloid neoplasm cases had a median overall survival of 6.8 months (95% CI, 3.5 to 11.9) and non-der(1;7) harboring myeloid neoplasm cases were 11.8 months (95% CI, 10.5 to 12.6). Thus, der(1;7)-harboring myeloid neoplasm cases had poorer prognosis (p<0.001). Conclusion In conclusion, der(1;7) is an unbalanced translocation that occurs predominantly in males and is seen more frequently in Japanese than Caucasian populations. Der(1;7) cases present with a mutational profile that is distinct from other myeloid neoplasm cases such as those with amp(1q) and monosomy7/del(7q), showing frequency of ETNK1 mutations. Disclosures Nannya: Otsuka Pharmaceutical Co., Ltd.: Consultancy, Speakers Bureau; Astellas: Speakers Bureau. Kern: MLL Munich Leukemia Laboratory: Other: Part ownership. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Atsuta: Astellas Pharma Inc.: Speakers Bureau; Mochida Pharmaceutical Co., Ltd.: Speakers Bureau; AbbVie GK: Speakers Bureau; Kyowa Kirin Co., Ltd: Honoraria; Meiji Seika Pharma Co, Ltd.: Honoraria. Handa: Ono: Honoraria; BMS: Honoraria; Janssen: Honoraria; Daiichi Sankyo: Research Funding; Celgene: Honoraria, Research Funding; Chugai: Research Funding; Kyowa Kirin: Research Funding; Takeda: Honoraria, Research Funding; Sanofi: Honoraria, Research Funding; Abbvie: Honoraria; MSD: Research Funding; Shionogi: Research Funding. Ohyashiki: Novartis Pharma: Other: chief clinical trial; Bristol Myers Squibb: Membership on an entity's Board of Directors or advisory committees. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Ogawa: Otsuka Pharmaceutical Co., Ltd.: Research Funding; Eisai Co., Ltd.: Research Funding; Kan Research Laboratory, Inc.: Consultancy, Research Funding; Dainippon-Sumitomo Pharmaceutical, Inc.: Research Funding; ChordiaTherapeutics, Inc.: Consultancy, Research Funding; Ashahi Genomics: Current holder of individual stocks in a privately-held company.

scholarly journals Therapy-Related Myeloid Neoplasm Has a Distinct Pro-Inflammatory Bone Marrow Microenvironment and Delayed DNA Damage Repair

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 37-38
Author(s):  
Monika M Kutyna ◽  
Li Yan A Wee ◽  
Sharon Paton ◽  
Dimitrios Cakouros ◽  
Agnieszka Arthur ◽  
...  
Keyword(s):  
Dna Damage ◽  
Board Of Directors ◽  
Research Funding ◽  
High Dose ◽  
Cytotoxic Therapy ◽  
Advisory Committees ◽  
Myeloid Neoplasm ◽  
Myeloid Neoplasms ◽  
Damage Repair

Introduction: Therapy-related myeloid neoplasms (t-MN) are associated with extremely poor clinical outcomes in otherwise long-term cancer survivors. t-MN accounts for ~20% of cases of myeloid neoplasms and is expected to rise due to the increased use of chemotherapy/radiotherapy (CT/RT) and improved cancer survivorship. Historically, t-MN was considered a direct consequence of DNA damage induced in normal hematopoietic stem cells (HSC) by DNA damaging cytotoxics. However, these studies have largely ignored the bone marrow (BM) microenvironment and the effects of age and concurrent/previous cancers. Aim: We performed an exhaustive functional study of mesenchymal stromal cells (MSC) obtained from a comparatively large cohort of t-MN patients and carefully selected control populations to evaluate the long-term damage induced by cytotoxic therapy to BM microenvironment and its impact on malignant and normal haematopoiesis. Methods: Four different cohorts were used: (1) t-MN, in which myeloid malignancy occurred after CT/RT for a previous cancer (n=18); (2) patients with multiple cancer and in which a myeloid neoplasm developed following an independent cancer which was not treated with CT/RT (MC-MN; n=10); (3) primary MN (p-MN; n=7) untreated and without any prior cancer or CT/RT; (4) age-matched controls (HC; n=17). Morphology, proliferation, cellular senescence, differentiation potential and γH2AX DNA damage response was performed. Stem/progenitor supportive capacity was assessed by co-culturing haematopoietic stem cells on MSC feeder-layer in long-term culture initiating assay (LTC-IC). Cytokine measurements were performed using 38-plex magnetic bead panel (Millipore) and RNA sequencing libraries were prepared with Illumina TruSeq Total RNA protocol for 150bp paired-end sequencing on a NextSeq500 instrument. Functional enrichment analysis was performed using EnrichR software. Results: MSC cultured from t-MN patients were significantly different from HC, p-MN and MC-MN MSC according to multiple parameters. They exhibited aberrant morphology consisting of large, rounded and less adhesive cells compared to typical spindle-shaped morphology observed with controls. MSC from myeloid neoplasm also showed impaired proliferation, senescence, osteo- and adipogenic differentiation with t-MN MSC showing the greatest differences. DNA repair was dramatically impaired compared to p-MN and HC (Fig.1A). Importantly, these aberrant t-MN MSC were not able to support normal or autologous in vitro long-term haematopoiesis (Fig.1B). The biological characteristic and poor haematopoietic supportive capacity of MSC could be "cell-intrinsic" or driven by an altered paracrine inflammatory microenvironment. Interestingly, several inflammatory cytokines were higher in t-MN compared with marrow interstitial fluid obtained from p-MN patients (Fig.1Ci) and many of these including Fractalkine, IFNα2, IL-7 and G-CSF were also significantly higher in t-MN MSC conditional media (Fig.1Cii). Together, this data suggest that t-MN microenvironment is distinct from p-MN with paracrine production of pro-inflammatory milieu that may contribute to poor HSC supportive capacity. Preliminary whole transcriptome analysis revealed differential gene expression between t-MN and HC (Fig.1Di) and p-MN MSC. Importantly, the deregulated genes play critical role in cell cycle, DNA damage repair, and cellular senescence pathways explaining phenotypical characteristic of t-MN MSC (Fig.1Dii). Moreover CXCL12 expression, a key regulator of haematopoiesis, was significantly lower in t-MN compared to HC (p=0.002) and p-MN MSC (p=0.009), thus explaining poor HSC supportive capacity. The key difference between the p-MN, MC-MN and t-MN is prior exposure to CT/RT. To study this we obtained MSC from two t-MN patients for whom we had samples at the time of their primary cancer, post high-dose chemotherapy and at the time of t-MN. MSC displayed aberrant proliferation and differentiation capacity after high-dose cytotoxic therapy (2 to 4 years prior to developing t-MN) and remained aberrant at t-MN diagnosis (Fig.1E). Conclusions: BM-MSC from t-MN patients are significantly abnormal compared with age-matched controls and typical myeloid neoplasm. Importantly, prior CT/RT leads to long-term irreversible damage to the BM microenvironment which potentially contributes to t-MN pathogenesis. Disclosures Hughes: Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Hiwase:Novartis Australia: Research Funding.

Genetic Landscape and Clonal Evolution Following 5-Aza Therapy in Patients with High-Risk Myelodysplastic Syndromes

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4304-4304
Author(s):  
June Takeda ◽  
Yusuke Shiozawa ◽  
Yuichi Shiraishi ◽  
Yusuke Okuno ◽  
Keisuke Kataoka ◽  
...  
Keyword(s):  
High Risk ◽  
Myelodysplastic Syndromes ◽  
Research Funding ◽  
Clonal Evolution ◽  
Clone Size ◽  
Chugai Pharmaceutical ◽  
Before And After ◽  
Targeted Capture ◽  
Post Therapy ◽  
Capture Sequencing

Abstract Background: DNA hypomethylating agents, such as 5-azacitidine (5-aza) and decitabine, comprise the current standard in therapy for patients with high-risk myelodysplastic syndromes (MDS), with dramatic responses in some patients. However, the responses are poorly predictable and their impact on clonal dynamics has not been fully elucidated. Patients and Methods: We enrolled a total of 119 patients with high-risk MDS who were treated with 5-aza . Bone marrow samples were collected before (n = 71) and both before and after (n = 48) treatment and analyzed by targeted-capture sequencing using RNA baits designed for 67 known or putative driver genes in myeloid neoplasms and 1,674 single nucleotide polymorphisms, which enabled detection of both mutations and copy number alterations on the same platform. In 9 of the 48 patients, pre- and post-therapy samples were further analyzed by whole exome sequencing (WES). Results: Average number of driver mutations before 5-aza was 2.8 per patient and 107 (90%) patients had multiple mutations. Most frequently mutated were TP53 (27%), followed by RUNX1, TET2, DNMT3A, and ASXL1. Reflecting high-risk disease subtypes of the subjects, splicing factor mutations were relatively rare (29 %) in the current cohort. Chromosomal abnormalities were identified in 65 (55%) patients, where 7q- and /or 5q- were the most frequent. Among 48 patients with serially collected samples, 46 had one or more mutations, enabling an evaluation of clone dynamics. In total 163 and 146 mutations were detected before and after treatment, respectively. About two thirds (110/163) of the mutations before 5-aza remained detectable after treatment. By contrast, the remaining one third showed a dynamic clonal behavior; 36 mutations in 22 cases were newly acquired, whereas 53 in 28 cases disappeared. Among those newly acquired, most frequently observed were mutations in STAG2 and EP300 (n = 3), of which STAG2 (7 cases) also represented the most frequent targets of disappeared mutations after treatment. In WES in 9 patients, a total of 112 mutations were identified either before or after 5-aza treatment with a mean of 10.4 or 8.9 mutations per sample, respectively. Among these, 63 were found at both pre- and post-therapy samples, whereas 17 and 32 mutations were newly acquired or disappeared during treatment, Given that only 4 newly acquired and 8 lost mutations had been detected by targeted-capture sequencing, respectively, WES enabled more sensitive detection of alternation of clones during 5-aza treatment, which were demonstrated in 8 (89%) subjects, rather than 5 (56%) in targeted-capture sequencing. Clinical outcomes have been reported for 22 patients as of the time of abstract submission; 5 achieved complete remission (CR), 9 stable disease (SD), and 5 progressive disease (PD). Alteration in clone size was frequently associated with clinical response. The size of dominant clones significantly decreased in 4 of 5 cases with CR, whereas stable or increased in 12 of 14 patients with SD or PD. In patients with SD or PD, acquisition of new mutations was common (10/14) during 5-aza treatment and potentially implicated in the resistance to 5-aza-treatment. Of interest, newly acquired mutations were also found in 2 CR samples, albeit at low allele frequency, even though the clone size of dominant clones was substantially reduced, suggesting the evolution of alternative MDS subclones or expansion of preexisting non-leukemic hematopoietic clone. Although CR was achieved in 3 of 6 patients with TP53 mutations, the TP53-mutationsdid not totally disappeared but were still detectable in CR samples in 2 cases, suggesting that TP53 mutated clones have not been completely eradicated by 5-aza treatment. Conclusion: Our study successfully depicted the structure of clones and their dynamics in high-risk MDS on 5-aza treatment. Alteration in the size of the dominant clones was frequently associated with a clinical response. Clonal evolution was common even in patients who achieved CR. Tracking the mutations in MDS patients during 5-aza treatment provides the opportunity to detect clones resistant to 5-aza and might be used to guide 5-aza therapy. Disclosures Kataoka: Kyowa Hakko Kirin: Honoraria; Boehringer Ingelheim: Honoraria; Yakult: Honoraria. Kiyoi:Celgene Corporation: Consultancy; Nippon Boehringer Ingelheim Co., Ltd.: Research Funding; JCR Pharmaceutlcals Co.,Ltd.: Research Funding; AlexionpharmaLLC.: Research Funding; Sumitomo Dainippon Pharma Co., Ltd.: Research Funding; Toyama Chemikal Co.,Ltd.: Research Funding; Mochida Pharmaceutical Co., Ltd.: Research Funding; Novartis Pharma K.K.: Research Funding; Alexion Pharmaceuticals: Research Funding; MSD K.K.: Research Funding; Takeda Pharmaceutical Co., Ltd.: Research Funding; Phizer Japan Inc.: Research Funding; Yakult Honsha Co.,Ltd.: Research Funding; Eisai Co., Ltd.: Research Funding; Astellas Pharma Inc.: Consultancy, Research Funding; Nippon Shinyaku Co., Ltd.: Research Funding; Fujifilm Corporation: Patents & Royalties, Research Funding; Zenyaku Kogyo Co.LTD.: Research Funding; Kyowa-Hakko Kirin Co.LTD.: Research Funding; Chugai Pharmaceutical Co. LTD.: Research Funding. Naoe:Sumitomo Dainippon Pharma Co.,Ltd.: Honoraria, Research Funding; Chugai Pharmaceutical Co.,LTD.: Honoraria, Patents & Royalties; Astellas Pharma Inc.: Research Funding; Kyowa-Hakko Kirin Co.,Ltd.: Honoraria, Patents & Royalties, Research Funding; TOYAMA CHEMICAL CO.,LTD.: Research Funding; Amgen Astellas BioPharma K.K.: Honoraria; Bristol-Myers Squibb: Honoraria; Celgene K.K.: Honoraria, Research Funding; CMIC Co., Ltd.: Research Funding; Fujifilm Corporation: Honoraria, Patents & Royalties, Research Funding; Nippon Boehringer Ingelheim Co., Ltd.: Honoraria, Research Funding; Otsuka Pharmaceutical Co.,Ltd.: Honoraria, Research Funding; Pfizer Inc.: Research Funding. Makishima:The Yasuda Medical Foundation: Research Funding. Ogawa:Sumitomo Dainippon Pharma: Research Funding; Kan research institute: Consultancy, Research Funding; Takeda Pharmaceuticals: Consultancy, Research Funding.

Whole Exome Sequencing Detecting Kinesin Family Gene Defects In Myeloid Neoplasm

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2762-2762
Author(s):  
Chantana Polprasert ◽  
Hideki Makishima ◽  
Bartlomiej P Przychodzen ◽  
Naoko Hosono ◽  
Wenyi Shen ◽  
...  
Keyword(s):  
Research Funding ◽  
Somatic Mutations ◽  
Snp Array ◽  
Chromosome 17 ◽  
Therapeutic Window ◽  
Myeloid Malignancies ◽  
Myeloid Neoplasm ◽  
Myeloid Neoplasms ◽  
Whole Exome ◽  
Kinesin Family

Abstract Clinical and pathomorphologic diversity in MDS is a reflection of heterogeneity of molecular lesions. Somatic mutations and chromosomal deletions/amplifications affect various pathways in a convergent and divergent fashion, generate phenocopy and can occur in a variety of combinations. Recent technological advances, including high density arrays and the new generation sequencing (NGS) led to the discovery of novel pathway mutations or gene families affected by somatic defects, e.g., cohesin or spliceosomal mutations. We have performed whole exome NGS of paired (tumor/germ line) samples in 222 patients with myeloid neoplasms from the Cleveland Clinic and University of Tokyo. Clinical parameters were studied including age, gender, overall survival (OS), bone marrow blast count, and metaphase cytogenetics. Additionally, we also used in our analysis data sets from 197 AML included in the Cancer Genome Atlas (TCGA). We found 1.4% (6/419) of non-canonical somatic mutations of KIF2Bwhich is a member of kinesin13 family located on the long arm of chromosome 17; 3 cases from our cohort (p.V32M (c.G94A), p.T113M (c.C338T), p.R163C (c.C487T)) and 3 cases from TCGA database (p.T47M (c.C140T), p.T310M (c.C929T), p.H551N (c.C1651A)). By analyzing clonal architecture and intra-tumor heterogeneity in 2 cases (RCMD and RAEB) by targeted deep sequencing, allelic frequencies of KIF2B mutations were more than 45% and larger than for any other concomitant mutations, suggesting that KIF2B mutations might consequently constitute ancestral events followed by subclonal acquisitions of the other mutations. Of note is that 6 non-sense mutations were also reported in lung cancer. Based on SNP-array mapping of chromosomal abnormalities, deletions of 17q involving the KIF2B locus (17q22) was present about 3% (6/215) of myeloid neoplasm. KIF2B defects were frequently detected in higher-risk MDS and AML phenotypes (9%). KIF2B performed an important role in regulation of kinetochore-microtubule attachment. Previous studies showed that the velocity of chromosomes’ movement in KIF2B-deficient cells is reduced 80% comparing to control and fail to perform cytokinesis. In our series, 56% of myeloid neoplasms with KI2B defects had complex cytogenetics and 67% cases of them were also UPD, suggesting that KIF2B defects might lead to inducing abnormal chromosomal movements and segregations. We then, expanded our study to the whole kinesin gene family: 17 somatic mutations and 57 deletions were identified in KIF1A (n=6), KIF23 (n=1), KIF26A (n=1), KIF27 (n=7), KIF1C (n=9), KIF21B (n=2), KIF13A (n=10), KIF14 (n=2), KIF17 (n=15), KIF25 (n=1), KIF3C (n=8), KIF6 (n=2) and CENPE (n=10). All mutations were heterozygous and mutually exclusive. By survival analysis of such mutated cases, a tendency towards worse prognosis was observed (HR; 1.72, 95%CI 0.86-3.37). Analysis of concomitant mutations associated with whole kinesin family mutations or deletions showed that most frequently affected genes are TET2 (n=14), DNMT3A (n=8), IDH1/2 (n=8) and MLL (n=5), all involved in epigenetic regulation. In conclusion, somatic mutations in kinesin family genes are found in myeloid malignancies and might be responsible for another pathogenesis of the disease. KIF2B is most frequently found in myeloid malignancies and associated with aggressive type of MDS. Since knockout mice of multiple kinesin family genes (KIF5A, KIF16B and EG5) were lethal in embryo and all the mutations occur in a heterozygous configuration, it is likely synthetic lethal approach might create therapeutic window between defective malignant cells and healthy controls. Kinesin family of motor proteins may be an emerging novel therapeutic target. In fact some kinesins have been already successfully targeted in solid tumors. Disclosures: Polprasert: MDS foundation: Research Funding. Makishima:AA & MDS international foundation: Research Funding; Scott Hamilton CARES grant: Research Funding. Maciejewski:NIH: Research Funding; Aplastic anemia&MDS International Foundation: Research Funding.

Clonal Hematopoiesis Increases Risk of Therapy-Related Myeloid Neoplasms

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 38-38
Author(s):  
Koichi Takahashi ◽  
Feng Wang ◽  
Hagop M. Kantarjian ◽  
Doss Denaha ◽  
Kanhav Khann ◽  
...  
Keyword(s):  
Cancer Diagnosis ◽  
Research Funding ◽  
Driver Mutations ◽  
Control Cohort ◽  
Clonal Hematopoiesis ◽  
Myeloid Neoplasms ◽  
Targeted Capture ◽  
Molecular Barcode ◽  
Pre Treatment ◽  
Barcode Sequencing

Abstract Introduction Therapy-related myeloid neoplasms (t-MNs) are often fatal secondary malignancies. There is no predictive biomarker for t-MNs. Recent studies suggested that individuals with clonal hematopoiesis have higher risk of developing leukemia. We hypothesized that cancer patients with clonal hematopoiesis have increased risk of developing t-MNs. Methods We studied 14 patients with t-MNs who had paired samples of t-MN bone marrow (BM) and peripheral blood (PB) that were previously obtained at the time of primary cancer diagnosis and before therapy. We performed targeted capture sequencing (median depth 245x) on t-MN BM and detected driver mutations. Then we performed molecular barcode deep sequencing (median 1,606x) on the prior PB samples to detect pre-leukemic driver mutations. Using the same method, we detected clonal hematopoiesis in the pre-treatment PB samples from 54 patients with lymphoma who did not develop t-MNs (control cohort). We further validated association between clonal hematopoiesis and t-MNs in a separate cohort of 74 patients with lymphoma. Results Targeted capture sequencing of the 14 t-MN BM samples revealed 29 driver mutations in 16 genes. TP53 mutations were detected in 5 patients (36%). The median variant allele frequency (VAF) of the mutations was 26.2% (range: 8.8% - 97.2%). Among the 29 driver mutations detected in t-MN BM samples, 21 mutations (72%) were detectable as pre-leukemic clonal hematopoiesis in 10 patients' prior PB samples (71%). The median VAF of the clonal hematopoiesis was 8.5% (range: 0.7-36.9%). There were also 12 mutations in prior PB samples that did not become drivers in t-MN BM. The VAF was significantly higher in the mutations that became drivers than in the mutations that did not become drivers (8.5% [range: 0.7-36.9%] vs. 1.2% [range: 0.1-7.6%], P < 0.001). The control cohort included 54 patients with lymphoma who did not develop t-MNs after therapy. Using the same molecular barcode sequencing, we detected 22 mutations in 17 (31%) patients' pre-treatment PB samples. Compared to the 14 t-MN cases, patients who developed t-MNs had significantly higher incidence of clonal hematopoiesis at the time of cancer diagnosis (71% vs. 31%, P = 0.008). The rate of t-MN development at 5 years was significantly higher in patients with clonal hematopoiesis than in patients without (30% [95% CI: 16-51%] vs. 7% [95% CI: 2-21%], P = 0.015). The median VAF of the mutations detected as clonal hematopoiesis was significantly higher in the t-MN cases than in the control (2.4% [range: 0.1-37%] vs. 0.8% [range: 0.3-1.8%], P = 0.001). The validation cohort included 74 patients with lymphoma who received frontline CHOP-based regimen. Median age was 56 years (range: 17-83 years) and 35 (47%) and 16 (22%) patients received radiation therapy and autologous stem cell transplant (auto-SCT), respectively. During the median follow up duration of 14.8 years (95% CI: 14.5-15.1 years), 5 patients (7%) developed t-MNs with the median 5.4 years latency (range: 1.5-12.8 years). Molecular barcode sequencing of pre-treatment PB samples detected total 17 mutations as clonal hematopoiesis in 15 patients (23%). Clonal hematopoiesis was detected in 4 of 5 patients (80%) who developed t-MNs, while it was detected in 11 of 69 patients (16%) who did not develop t-MNs (P = 0.005). The positive predictive value and negative predictive value of clonal hematopoiesis were 26.7% (95% CI: 7.8-55.1%) and 98.3% (95% CI: 90.9-99.9%), respectively. The rate of t-MN development at 10 years was significantly higher in patients with clonal hematopoiesis than in patients without (29% [95% CI: 12-59%] vs. 0% [95% CI: 0-0%], P = 0.001). Multivariate Cox model revealed that clonal hematopoiesis and auto-SCT significantly increased the risk of t-MNs (clonal hematopoiesis: HR 12.0 [95% CI: 1.3-108.7], P = 0.027 and auto-SCT: HR 10.5 [95% CI: 1.2-95.1], P = 0.037). Conclusion Pre-leukemic clonal hematopoiesis was frequently detected in patients with t-MNs at the time of primary cancer diagnosis and before exposure to therapy. Detection of clonal hematopoiesis significantly increased the risk of t-MN development in both case-control and validation study. These data suggest potential approaches of screening clonal hematopoiesis in cancer patients to identify patients at risk of t-MN development and warrants a validation in prospective trial investigating a role of clonal hematopoiesis as a predictive marker for t-MNs. Disclosures DiNardo: Abbvie: Research Funding; Daiichi Sankyo: Research Funding; Agios: Research Funding; Celgene: Research Funding; Novartis: Research Funding. Samaniego:Karus Therapuetics: Research Funding.

scholarly journals Prognostic Impact of a Composite Genetic Profile Defined By Cytogenetics and Next Generation Sequencing at Diagnosis on Treatment Outcomes Following Allogeneic Hematopoietic Stem Cell Transplantation in Acute Myeloid Leukemia

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3317-3317
Author(s):  
Georgina S. Daher-Reyes ◽  
TaeHyung Kim ◽  
Kyoung Ha Kim ◽  
Jae-Sook Ahn ◽  
Tracy L. Stockley ◽  
...  
Keyword(s):  
Board Of Directors ◽  
Research Funding ◽  
Tp53 Mutation ◽  
Gene Mutations ◽  
Genetic Profile ◽  
Advisory Committees ◽  
Hematopoietic Stem ◽  
Monosomy 7 ◽  
Genetic Profiles ◽  
Generation Sequencing

Introduction: The introduction of next-generation sequencing (NGS) has expedited the discovery of novel genetic lesions in acute myeloid leukemia (AML), thereby allowing better risk stratification with respect to overall survival (OS). We have previously reported that AML patients with PTPN11 and NPM1 mutations had longer OS following chemotherapy, while those carrying mutations in ASXL1, JAK2, RUNX1, TP53 and SRSF2 had a shorter OS (Daher-Reyes,ASH 2018). Little is known, however, regarding the impact of genetic profiles (somatic mutations and cytogenetic abnormalities) at initial AML diagnosis on the treatment outcomes following allogeneic hematopoietic stem cell transplantation (HCT). Methods & Patients: We enrolled AML patients who had available NGS data at time of initial diagnosis as part of the AGILE project between February 2015 and December 2018, and who subsequently underwent allogeneic HCT. NGS was performed on DNA samples isolated from peripheral blood or bone marrow samples at diagnosis. Analysis was performed using the TruSight Myeloid Sequencing Panel on the MiSeq sequencer (Illumina; San Diego, CA). Transplant outcomes (overall survival (OS), relapse-free survival (RFS), relapse incidence (RI), and non-relapse mortality (NRM)) after HCT were compared according to genetic profiles defined at diagnosis. Survival analysis for OS and RFS was performed using Cox's proportional hazard model, while the Fine-Gray model was used for RI and NRM analyses. Variables considered in the model included CR status prior to HCT (CR1 vs. beyond CR1), de novo AML (vs. secondary/therapy-related AML), induction chemotherapy used (3+7 vs. others), conditioning regimen (myeloablative vs. reduced intensity), WBC, age, donor type, mutation status of commonly mutated genes, and the composite adverse genetic profile (defined as having at least one of monosomal karyotype (MK), TP53 mutation, del(5), complex karyotype (CK), and monosomy 7), given that these 5 features were highly co-occurring, adverse prognostic factors (Figure 1A). Results: We identified 435 patients in whom frontline NGS was performed, of whom a total of 178 patients (40.9%) received HCT and were included in the final analysis. A total of 598 (median 4, IQR 2-5) mutations were identified in 165 patients (n=165/178, 92.7%). Among 54 genes in the panel, 12 genes were mutated in more than 10% of the cohort, with the most commonly mutated genes being DNMT3A (30.3%), TET2 (25.3%), NPM1 (22.5%), RUNX1 (18.5%), IDH2 (16.9%), FLT3 (15.7%), ASXL1 (12.4%), BCOR (12.4%), CEBPA (11.2%), NRAS (11.2%), IDH1 (10.1%), and SRSF2 (10.1%). In univariate analysis, the groups with a composite adverse genetic profile (n=30/178, 16.9%) showed decreased OS (HR 2.19 [1.30-3.67]; p=0.003), while patients harbouring spliceosome gene (SF3B1, SRSF2, U2AF1, and ZRSR2) mutations (n=37/178, 20.8%) had longer OS (HR 0.39 [0.18-0.85]; p=0.018), with 2-year OS rates of 24.9% and 57.9%, respectively (p=0.002)) (Figure 1B). The composite adverse genetic profile was also associated with shorter RFS (HR 2.23 [1.34-3.69]; p=0.002), while spliceosome gene mutations were associated with longer RFS (HR 0.42 [0.20-0.88]; p=0.022), with 2-year RFS rates of 23.7% vs. 57.9%, respectively (p=0.001)). The composite adverse genetic profile was also associated with higher RI (HR 2.94 [1.52-5.66]; p=0.001), with 2-year RI rates of 47.2% vs. 17.2%, respectively, for patients with and without adverse genetic features (p=0.002) (Figure 1C). Neither the composite adverse genetic profile, nor spliceosome gene mutations, were associated with NRM, with HR of 1.21 [0.55-2.65], p=0.64) and 0.45 [0.16-1.31], p=0.15, respectively (Figure 1D). Multivariate analyses confirmed that the composite adverse genetic profile and spliceosome gene mutations were independent prognostic factors for OS, RFS, and RI (p=0.004, p=0.002, and p=0.001, respectively) and for OS and RFS (p=0.020 and p=0.022, respectively). Conclusion: In our cohort, the composite adverse genetic profile (i.e. having at least one of MK, TP53 mutation, del(5), CK and monosomy 7 remained as a poor prognostic factor even after allogeneic HCT. To clarify the role of genetic risk stratification in HCT, further analysis using a larger cohort is warranted. In addition, a comparative analysis between HCT vs no-HCT groups according to the genetic profile, is ongoing in a in a larger patient cohort. Figure 1 Disclosures Michelis: CSL Behring: Other: Financial Support. Mattsson:Gilead: Honoraria; Celgene: Honoraria; Therakos: Honoraria. Schimmer:Novartis Pharmaceuticals: Consultancy; Otsuka Pharmaceuticals: Consultancy; Jazz Pharmaceuticals: Consultancy; Medivir Pharmaceuticals: Research Funding. McNamara:Novartis Pharmaceutical Canada Inc.: Consultancy. Maze:Pfizer Inc: Consultancy; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees. Gupta:Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees; Sierra Oncology: Honoraria, Membership on an entity's Board of Directors or advisory committees; Incyte: Honoraria, Research Funding; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Yee:Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Astex: Research Funding; Hoffman La Roche: Research Funding; MedImmune: Research Funding; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees; Merck: Research Funding; Millennium: Research Funding; Astellas: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees. Minden:Trillium Therapetuics: Other: licensing agreement. Schuh:Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees; AbbVie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Agios: Honoraria; Teva Canada Innovation: Honoraria, Membership on an entity's Board of Directors or advisory committees; Astellas: Honoraria, Membership on an entity's Board of Directors or advisory committees; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees.

Clinicopathological Features and Outcome of Der(1;7)(q10;p10) In Myelodysplastic Syndrome and Acute Myeloid Leukemia: A Single-Center Analysis of Japanese Patients

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 1878-1878
Author(s):  
Hiroki Yokoyama ◽  
Noriko Usui ◽  
Nobuaki Dobashi ◽  
Shingo Yano ◽  
Yuichi Yahagi ◽  
...  
Keyword(s):  
Myeloid Leukemia ◽  
De Novo ◽  
Risk Group ◽  
Hemoglobin Level ◽  
Clinicopathological Features ◽  
Unbalanced Translocation ◽  
Male Predominance ◽  
Myeloid Neoplasms ◽  
Acute Myeloid ◽  
Better Than

Abstract Abstract 1878 Introduction: The unbalanced translocation of der(1;7)(q10;p10) is relatively rare in myeloid neoplasms, which was reported at frequencies of 2% in de novo myelodysplastic syndrome (MDS), 0.5% in de novo acute myeloid leukemia (AML) and 3–7% in therapy-related myeloid neoplasms. Although chromosome 7 abnormality is generally considered as a poor prognostic factor in MDS and AML, it is still unclear whether or not this unbalanced translocation has a negative impact on prognosis. In addition, there appears to be some unique clinicopathological features such as male predominance, low blast counts, high hemoglobin level, presence of eosinophilia and a high rate of sole chromosomal abnormality. Methods: We retrospectively analyzed 122 der(1;7)(q10;p10) and -7/del(7q) adult patients with MDS or AML who were diagnosed at our institute between February 1995 and March 2010. According to the French-American-British (FAB) classification, 29 patients had AML (M0, n=5; M1, n=6; M2, n=10; M4, n=3; M5, n=1; M6, n=4) and 93 patients had MDS (RA, n=50; RARS, n=2; RAEB, n=35; RAEB-t, n=3; CMML, n=3). We compared the clinicopathological features and outcome of 33 der(1;7) patients with those of 89 -7/del(7q) patients. Results: The median age was 71 years for the der(1;7) patients and 67 years for -7/del(7q) patients (p=0.29). Male predominance was observed in both patients in the der(1;7) and the -7/del(7q) (p=0.52). The proportion of the sole abnormality in the der(1;7) was significantly higher than that in the -7/del(7q) (58% vs 13%, p<0.001). Among the MDS patients, the hemoglobin level, platelet counts and rates of eosinophil between the der(1;7) and -7/del(7q) patients were significantly different (9.1g/dl vs 7.4g/dl, p=0.006; 16.1×109/L vs 7.0×109/L, p<0.001; 6.5% vs 1.0%, p<0.001, respectively). The median survival time (MST) of the der(1;7) patients was significantly better than that of the -7/del(7q) patients (22.1 months vs 10.2 months, respectively, P=0.002). A subgroup analysis of the MDS patients revealed that the MST of the der(1;7) patients was significantly better than that of the -7/del(7q) patients (22.1 months vs 12.1 months, respectively, P=0.004). According to the international prognostic scoring system (IPSS) for MDS patients, the MST was 39.4 months for intermediate-1 risk group, 12.7 months for intermediate-2 risk group and 7.2 months for high risk group (p=0.005). A multivariate analysis revealed that the der(1;7) was associated with a significantly better MST, even after adjusting IPSS and other prognostic factors including age, additional chromosome abnormality, and prior exposure to chemotherapy and/or radiation therapy. Conclusions: Our study suggested that the der(1;7) might be a subgroup characterized by distinct clinicopathologic features and outcome among patients with MDS and AML. Disclosures: No relevant conflicts of interest to declare.

Integrated Molecular Analysis of Myelodysplastic Syndromes Using Whole Genome Sequencing

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5512-5512
Author(s):  
Yasuito Nannya ◽  
Yoshida Kenichi ◽  
Keisuke Kataoka ◽  
Yasunobu Nagata ◽  
Tetsuichi Yoshizato ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Research Funding ◽  
Genetic Alterations ◽  
Whole Genome ◽  
Structural Variations ◽  
Coding Regions ◽  
Molecular Events ◽  
Targeted Capture ◽  
Capture Sequencing

Abstract Background Myelodysplastic syndromes (MDS) are a heterogeneous group of myeloid malignancies characterized by refractory cytopenias with marrow dysplasia, which frequently progress to acute myeloid leukemia (AML). Although poorly understood in the previous era, the molecular events that underlie the pathogenesis of MDS have been intensively studied using advanced genomics in the past decade and are now fully catalogued into an array of well-defined functional pathways. However, mostly obtained through exome/targeted-capture sequencing, our knowledge about these molecular events is largely confined to those of single nucleotide variations (SNVs) and short indels, as well as arm-level copy number lesions, mostly within the coding sequences. Alterations in the non-coding regions, particularly a diversity of structural variations, in MDS genomes remain to be investigated in most part, even though the relevance of such lesions has recently been unequivocally demonstrated for other cancer types through large-scale whole genome sequencing (WGS) studies. Unfortunately, however, only a small number of MDS samples have been fully analyzes and inspected for genetic alterations using WGS. Patients and Methods In the present study, we performed an integrated, unbiased molecular study of 60 MDS cases, using whole genome sequencing (WGS) in combination with exome and transcriptome sequencing as well as methylome analysis. Paired tumor/germline DNA were obtained from patients' bone marrow and buccal smear samples. Sequencing data were analyzed using novel in-house pipelines, which were tuned to optimize detection of complex structural variations (SVs) and abnormalities in non-coding sequences. For some patients, multiple longitudinal materials were obtained along with their clinical course. Results WGS identified SNVs across the entire genome with a mean of 5.7/Mb/genome with a clear predominance of age-related C to T transitions, followed by other signatures. The spectrum of major targets of somatic mutations successfully recapitulated the previously reported one in MDS, including those involving splicing factors (SRSF2, SF3B1, U2AF1, and ZRSR2), epigenetic regulators (DNMT3A, ASXL1, TET2, BCOR, and EZH2), transcription factors (RUNX1, ETV6, and CUX1), signal transducing molecules (NRAS, KRAS, FLT3, PTPN11, CBL), and other critical molecules (TP53, NPM1, and STAG2). Moreover, other somatic variants within the coding regions were also identified that had already been reported in other human cancers but not in MDS, such as NCOR2X, MUC6, and TIAM2. The analysis of SVs unexpectedly revealed the complexity of MDS genomes. Most of the MDS genomes analyzed had a heavy burden of SVs including tandem duplications, deletions, translocations, and inversions, with a mean of 7.2/genome, which was far more than expected from conventional cytogenetics and array-based karyotyping. Complex rearrangements were common, frequently converging into particular chromosomes, suggesting multiple genetic events at a single genetic insult. Known targets of SNVs and indels were often affected by SVs, which largely escaped from conventional exome and targeted-capture sequencing, including RUNX1, TET2, FHITand other genes, suggesting that conventional platforms may substantially underestimate the frequency of alterations for some genes. Concomitant transcriptome analysis allowed to correlated abnormal splicing with somatic intronic events otherwise undetectable. Furthermore, comprehensive analysis of genomic aberrations in longitudinal samples enabled us to delineate the clonal architecture of the cellular population in MDS and their dynamics during the AML progression or clonal changes caused by AZA treatment. Conclusions Integrated molecular analysis using WGS and other platforms revealed the complexity of MDS genomes previously unexpected and reveal novel genetic alterations. Our results should help to extend our knowledge about the genomic landscape of MDS and provide novel insights into the molecular pathogenesis and clonal dynamics of MDS. Disclosures Kataoka: Kyowa Hakko Kirin: Honoraria; Boehringer Ingelheim: Honoraria; Yakult: Honoraria. Naoe:Pfizer Inc.: Research Funding; CMIC Co., Ltd.: Research Funding; Kyowa-Hakko Kirin Co.,Ltd.: Honoraria, Patents & Royalties, Research Funding; Otsuka Pharmaceutical Co.,Ltd.: Honoraria, Research Funding; Nippon Boehringer Ingelheim Co., Ltd.: Honoraria, Research Funding; Amgen Astellas BioPharma K.K.: Honoraria; TOYAMA CHEMICAL CO.,LTD.: Research Funding; Chugai Pharmaceutical Co.,LTD.: Honoraria, Patents & Royalties; Celgene K.K.: Honoraria, Research Funding; Sumitomo Dainippon Pharma Co.,Ltd.: Honoraria, Research Funding; Fujifilm Corporation: Honoraria, Patents & Royalties, Research Funding; Bristol-Myers Squibb: Honoraria; Astellas Pharma Inc.: Research Funding. Kiyoi:Celgene Corporation: Consultancy; MSD K.K.: Research Funding; Mochida Pharmaceutical Co., Ltd.: Research Funding; Nippon Boehringer Ingelheim Co., Ltd.: Research Funding; Kyowa-Hakko Kirin Co.LTD.: Research Funding; Fujifilm Corporation: Patents & Royalties, Research Funding; JCR Pharmaceutlcals Co.,Ltd.: Research Funding; Alexion Pharmaceuticals: Research Funding; Yakult Honsha Co.,Ltd.: Research Funding; Eisai Co., Ltd.: Research Funding; Chugai Pharmaceutical Co. LTD.: Research Funding; Toyama Chemikal Co.,Ltd.: Research Funding; Astellas Pharma Inc.: Consultancy, Research Funding; Phizer Japan Inc.: Research Funding; Novartis Pharma K.K.: Research Funding; Nippon Shinyaku Co., Ltd.: Research Funding; Takeda Pharmaceutical Co., Ltd.: Research Funding; Sumitomo Dainippon Pharma Co., Ltd.: Research Funding; Zenyaku Kogyo Co.LTD.: Research Funding; AlexionpharmaLLC.: Research Funding. Ogawa:Kan research institute: Consultancy, Research Funding; Takeda Pharmaceuticals: Consultancy, Research Funding; Sumitomo Dainippon Pharma: Research Funding.

scholarly journals Functional Roles of DDX41 Mutations in the Development of Myeloid Malignancies

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 150-150
Author(s):  
Ayana Kon ◽  
Masahiro Marshall Nakagawa ◽  
Keisuke Kataoka ◽  
Hideki Makishima ◽  
Manabu Nakayama ◽  
...  
Keyword(s):  
Stem Cells ◽  
Innate Immunity ◽  
Research Funding ◽  
Pharmaceutical Research ◽  
Mutant Mice ◽  
Loss Of Function ◽  
Chugai Pharmaceutical ◽  
Myeloid Malignancies ◽  
Myeloid Neoplasms ◽  
Otsuka Pharmaceutical

Abstract DDX41 is a newly identified leukemia predisposition gene encoding an RNA helicase, whose germline mutations are tightly associated with late-onset myeloid malignancies. Importantly, germline DDX41 mutations were also found in as many as ~7 % of sporadic cases of high-risk MDS, conferring the largest germline risk for myeloid malignancies. In typical cases, a germline loss-of-function allele (most commonly p.A500fs or p.D140fs, depending on the ethnicity) is compounded by a somatic missense mutation affecting the helicase domain in the remaining allele (p.R525H). However, little is known about the molecular mechanism by which DDX41 mutations lead to myeloid neoplasms. To clarify the role of these distinct DDX41 alleles, we generated mice models carrying either or both of conditional/constitutive Ddx41 knock-out (KO) and conditional R525H knock-in (KI) alleles. BM-specific biallelic Ddx41 deletion using Vav1-Cre resulted in embryonic lethality, suggesting that Ddx41 is indispensable for normal hematopoietic development. Next, by crossing these mice and further breeding with Rosa26-CreERT2 transgenic mice, we engineered mice that were wild-type for Ddx41 (Ddx41+/+), heterozygous Ddx41 KO (Ddx41+/-), homozygous Ddx41 KO (Ddx41-/-), heterozygous for the Ddx41 R525H mutation (Ddx41R525H/+), or hemizygous for the Ddx41 R525H mutation (Ddx41R525H/-), in which expression of the mutant allele was induced by tamoxifen administration. First, we assessed cell intrinsic effects of these Ddx41 alleles, using noncompetitive transplantation experiments. Shortly after tamoxifen administration, most of the recipient mice that were reconstituted with BM from Ddx41-/- or Ddx41R525H/- mice died within a month after CreERT2 induction due to severe BM failure (BMF). None of the mice transplanted with BM from Ddx41+/+, Ddx41+/- or Ddx41R525H/+ mice developed myeloid neoplasms. We also assessed the reconstitution capacity of whole BM cells from different Ddx41 mutant mice in competitive transplantation experiments. The donor chimerism of Ddx41-/- or Ddx41R525H/- mice-derived cells in PB was markedly reduced compared to that of cells derived from Ddx41+/+ mice. In contrast, Ddx41+/- or Ddx41R525H/+ mice-derived cells showed no significant changes in competitive bone marrow reconstitution compared to Ddx41+/+ mice-derived cells. Notably, about half of the recipient mice died due to BMF when Ddx41R525H/--derived BM cells were co-transplanted with Ddx41+/--derived BM cells but not with wild-type BM cells, suggesting some non-cell autonomous effect of Ddx41R525H/- cells on Ddx41+/- cells. Transcriptome analysis of stem cells (Kit +Sca-1 -Lin low cells) from different Ddx41 mutant mice revealed significant changes in gene expression and splicing patterns in many genes in stem cells from all the mutant mice, with larger changes for Ddx41R525H/- than Ddx41+/- or Ddx41 R525H/+ cells. Notably, Ddx41R525H/- -derived stem cells exhibited a significant upregulation of genes involved in innate immunity, including an upregulation of cGAS-STING innate immunity pathways, as well as an enhanced Trp53 pathway, whereas there was a downregulation of genes related to RNA metabolism and ribosome biogenesis. Proteomics analysis confirmed the significant downregulation of ribosomal proteins in hematopoietic cells derived from Ddx41R525H/- mice. In summary, our results revealed an essential role of Ddx41 in normal hematopoiesis. While both heterozygous Ddx41 KO and heterozygous R525H knock-in did not develop myeloid neoplasm, compound biallelic loss-of function and R525 alleles led to a compromised function of hematopoietic stem cells, which was evident from reduced competitive repopulation capacity and impaired hematopoietic differentiation, where activated innate immunity and impaired ribosome functions may play important roles. Their roles in myeloid neoplasms need further evaluation. Disclosures Nakagawa: Sumitomo Dainippon Pharma Oncology, Inc.: Research Funding. Kataoka: Celgene: Honoraria; Eisai: Honoraria; Astellas Pharma: Honoraria; Novartis: Honoraria; Chugai Pharmaceutical: Honoraria; AstraZeneca: Honoraria; Sumitomo Dainippon Pharma: Honoraria; Kyowa Kirin: Honoraria; Janssen Pharmaceutical: Honoraria; MSD: Honoraria; Takeda Pharmaceutical: Honoraria; Otsuka Pharmaceutical: Honoraria; Asahi Genomics: Current equity holder in publicly-traded company; Otsuka Pharmaceutical: Research Funding; Chordia Therapeutics: Research Funding; Chugai Pharmaceutical: Research Funding; Takeda Pharmaceutical: Research Funding; Bristol-Myers Squibb: Research Funding; Eisai: Other: Scholarship; Otsuka Pharmaceutical: Other: Scholarship; Ono Pharmaceutical: Other: Scholarship; Kyowa Kirin: Other: Scholarship; Shionogi: Other: Scholarship; Takeda Pharmaceutical: Other: Scholarship; Summitomo Dainippon Pharma: Other: Scholarship; Chugai Pharmaceutical: Other: Scholarship; Teijn Pharma: Other: Scholarship; Japan Blood Products Organization: Other: Scholarship; Mochida Pharmaceutical: Other: Scholarship; JCR Pharmaceuticals: Other: Scholarship; Genetic Alterations: Patents & Royalties: PD-L1 abnormalties . Ogawa: Ashahi Genomics: Current holder of individual stocks in a privately-held company; Otsuka Pharmaceutical Co., Ltd.: Research Funding; Eisai Co., Ltd.: Research Funding; Kan Research Laboratory, Inc.: Consultancy, Research Funding; Dainippon-Sumitomo Pharmaceutical, Inc.: Research Funding; ChordiaTherapeutics, Inc.: Consultancy, Research Funding.

scholarly journals CTX-712, a Novel Clk Inhibitor Targeting Myeloid Neoplasms with SRSF2 Mutation

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 205-205
Author(s):  
Akinori Yoda ◽  
Daisuke Morishita ◽  
Yotaro Ochi ◽  
Akio Mizutani ◽  
June Takeda ◽  
...  
Keyword(s):  
Research Funding ◽  
Nuclear Translocation ◽  
Synthetic Lethality ◽  
Sr Proteins ◽  
High Dose ◽  
Dependent Manner ◽  
Publicly Traded ◽  
Myeloid Neoplasms ◽  
Otsuka Pharmaceutical

Abstract Splicing factors (SFs) are among the most frequent mutational targets in myeloid neoplasms, particularly in myelodysplastic syndromes (MDS) and a subset of acute myeloid leukemia (AML), designated as chromatin/spliceosome-mutated AML, where major SFs mutated include SF3B1, SRSF2, U2AF1, and ZRSR2. SF mutations are largely mutually exclusive and except for ZRSR2 mutations, heterozygous, suggesting synthetic lethality of homozygous or multiple mutations. Thus, SF functions might be a plausible target of therapy for MDS/AML. Of potential interest in this regard is serine/arginine-rich (SR) domains ubiquitously shared by many SFs, including U2AF1, SRSF2, and ZRSR2, which need to be phosphorylated for their nuclear translocation by evolutionally conserved kinases, known as CLK family of proteins. CLK family kinases regulate mRNA splicing by phosphorylating various SR proteins, and inhibition of CLK family kinases resulted in reduction of phosphorylation levels of SR proteins, induction of splicing alterations and protein depletion for multiple genes. In addition, a recent report showed that CLK inhibition can induce skipped exons, cell death, and cell growth suppression. Thus, CLK inhibitors might have a role in the therapeutics of SF-mutated MDS/AML, by further compromising RNA splicing. We have recently developed an orally available and highly potent CLK inhibitor, CTX-712, and evaluated its anti-leukemic activities both in vitro and in vivo. When tested in human myeloid cell lines (K562 and MV-4-11), CTX-712 showed a strong inhibitory effect on cell proliferation (IC 50=0.15 and 0.036 μM, respectively). The anti-leukemic effect was also confirmed by survival assay using a total of 79 primary AML cells (the average of IC 50 was 0.078 μM). In addition, CTX-712 suppressed phosphorylation of multiple SR proteins including SRSF3/4/6, all of which bind to SRSF2. RNA-seq analysis revealed that CTX-712 induced global splicing changes, which typically resulted in skipped exon. Notably, the degree of splicing (percent spliced-in value) in skipped exon events induced by the drug was positively correlated with the sensitivity to the drug (IC 50) in primary AML cells (n=32, R=0.61, P=0.00018). To further investigate the effect of CTX-712 on tumor growth in vivo, we established 13 MDS/AML-derived xenografts (PDXs), which were treated with varying doses of CTX-712. Among the 13 PDX models, SRSF2 mutation was found in 2 cases, which had the SRSF2 P95H or P95L mutation. The SRSF2 P95H PDX showed a significant response to CTX-712 in a dose-dependent manner. Of note, 4 out of 5 mice treated using a high dose protocol (12.5 mg/kg) achieved complete remission (the tumor shrank completely to unmeasurable size). Two weeks after treatment, tumor volumes (mm 3) were 762 ± 147 (vehicle), 331 ± 64 (low dose of CTX-712: 6.25mg/kg, P=0.0395), and 39 ± 39 (high dose, P=0.0064) (N=5 each, mean ± SEM). Interestingly CLK inhibition induced aberrant splicing events including skipped exons in vivo, which were more strongly affected in the SRSF2-mutated model. In addition, CTX-712 efficacy was also confirmed in the model with the SRSF2 P95L mutation. The SRSF2 P95L model showed a significant reduction in tumor volumes (mm 3) 2 weeks after CTX-712 treatment; 406 ± 94 (vehicle) and 75 ± 17 (high dose, P=0.0162) (N=6 each, mean ± SEM). CTX-712 also significantly improved the survival of the SRSF2 P95L-mutated model (high dose, P=0.0030) (N=6 each). Overall, 10 out of 13 PDX AML/MDS models, including 2 SRSF2-mutated models, showed anti-tumor effect of CTX-712. Complete disappearances of tumors were obtained in the SRSF2 P95H mutation model. These results provide mechanistic insights of CLK inhibition and a rationale for further investigation of the novel CLK inhibitor in MDS/AML. Disclosures Yoda: Chordia Therapeutics Inc.: Research Funding. Morishita: Chordia Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Mizutani: Chordia Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Tozaki: Chordia Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Satoh: Chordia Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Nannya: Otsuka Pharmaceutical Co., Ltd.: Consultancy, Speakers Bureau; Astellas: Speakers Bureau. Miyake: Chordia Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Ogawa: Kan Research Laboratory, Inc.: Consultancy, Research Funding; Dainippon-Sumitomo Pharmaceutical, Inc.: Research Funding; Eisai Co., Ltd.: Research Funding; Otsuka Pharmaceutical Co., Ltd.: Research Funding; ChordiaTherapeutics, Inc.: Consultancy, Research Funding; Ashahi Genomics: Current holder of individual stocks in a privately-held company.

scholarly journals Distinct, Ethnic, Clinical, and Genetic Characteristics of Myelodysplastic Syndromes with Der(1;7)

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 5392-5392 ◽  
Author(s):  
Rurika Okuda ◽  
Hideki Makishima ◽  
Yasuhito Nannya ◽  
Yotaro Ochi ◽  
Tetsuichi Yoshizato ◽  
...  
Keyword(s):  
Myelodysplastic Syndromes ◽  
High Frequency ◽  
Copy Number ◽  
Research Funding ◽  
Trisomy 8 ◽  
Employment Equity ◽  
Monosomy 7 ◽  
Asian Populations ◽  
Myeloid Neoplasms ◽  
Equity Ownership

der(1;7)(q10;p10) is a recurrent chromosomal abnormality found in a wide variety of myeloid neoplasms observed in as high as 6% of myelodysplastic syndromes (MDS) in Asian populations, while rarely observed in Caucasian populations. It is thought to be generated by a recombination between two highly homologous centromere alphoid sequences which lead to an unbalanced abnormality of monosomy of 7q and trisomy of 1q. However, despite the presence of -7q, der(1;7) has been associated with a better prognosis compared to monosomy 7 or other del(7q) (-7/del(7q)). In addition to its association with +8 and del(20q), frequent RUNX1 mutations and a paucity of mutated TP53 have been reported in der(1;7) tumors, but otherwise, the molecular features of this abnormality have been poorly characterized in the literature. This is most likely because it is very rare in Caucasians, even though it represents one of the most prevalent lesions among Asian populations. The purpose of our study is to clarify the frequency and mutational landscape of der(1;7) in myeloid neoplasms on the basis of targeted-capture sequencing. A total of 1,707 MDS cases, including 944 German and 763 Japanese cases, were enrolled, from which we identified 73 (4.0%) cases with der(1;7). The prevalence was >20 times higher in Japanese (9.0%) than German (0.43%) cohorts (p<0.0001). We also identified a strong male predominance in der(1;7)-positive cases (90.4%) compared to negative cases. Also including an additional 22 cases, somatic mutations and copy number abnormalities in der(1;7) were interrogated in a total of 95 cases, which included 84 (88.4%) with MDS, 9 (9.5%) with AML, and 2 (2.1%) with MPN. Among MDS patients, 29 were low-risk, 47 were high-risk, and the rest were not specified. In mutation analysis, at least one mutation was detected in 98% of der(1;7) cases, most frequently affecting RUNX1 (42%), followed by EZH2 (26%), and ETNK1 (25%). Copy number analysis showed a high frequency of del(20q) and trisomy 8 in der(1;7) cases: 27.4% and 18.9% respectively. On the basis of mutant cell fractions, most of these mutations were present in subclones acquired within the major population harboring der(1;7). In particular, most of the EZH2 (7q35-q36) mutations were thought to be secondary events in der(1;7)-positive cases, while representing initial events acquired before UPD(7q) or -7/del(7q) in der(1;7)-negative cases. Of interest, der(1;7) was associated with a low frequency of TP53 mutations, which were seen only in 3% of cases with der(1;7), whereas highly prevalent in non-der(1;7) cases with -7/del(7q) (52%), which is concordant with a better clinical outcome was observed in der(1;7) cases compared with non-der(1;7) cases with monosomy 7 or other del(7q). Another unique feature of der(1;7) positive MDS was an extremely high frequency of RUNX1 mutations. However, the most prominent finding with secondary mutations in der(1;7) cases is the frequent hot spot mutation in ETNK1, which were originally reported in 8.8% of myeloid neoplasms with MPN features, like SETBP1 mutations. ENTK1 mutations were found in as many as 25% (23/95) of der(1;7) cases, while rarely seen in -7/del(7q) (1/89) (p<0.0001) or amp(1q) (2/68) (p=0.0001). Despite the high frequency of trisomy 8 observed in der(1;7) cases, none were associated with ETNK1 mutations. In addition, all of the RAS pathway mutations (positive in 16 cases) were observed in der(1;7) cases with wild-type ETNK1, while none were in ETNK1-mutant cases. Morphologically, these ETNK1-mutated der(1;7) cases presented with an increased eosinophil count in peripheral blood (760.9/ul vs. 78.1/ul) (p<0.001), compared to those without EKNK1 mutations, suggesting that ENTK1-mutated der(1;7) cases represent a novel disease entity within der(1;7), characterized by unique genetic features and increased eosinophils. In conclusion, der(1;7) is a genetically and clinically distinct subset of myeloid neoplasms, which showed unique features that are distinct from MDS cases in -7 and other del(7q). Especially, ETNK1 mutations subdivided cases with der(1;7) into two groups of genetically distinct subsets as shown in Figure 1. In the future, inhibition of the kinase activity in ETNK1 could be a novel therapeutic strategy in such a previously unrecognized subset as characterized by der(1;7) and eosinophilia. Figure 1 Disclosures Kern: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Baer:MLL Munich Leukemia Laboratory: Employment. Nadarajah:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Atsuta:Janssen Paharmaceutical K.K.: Honoraria; Mochida Pharmaceutical Co. Ltd: Honoraria; Kyowa Kirin Co., Ltd: Honoraria; Chugai Pharmaceutical Co., Ltd.: Honoraria. Handa:Ono: Research Funding. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Ogawa:Qiagen Corporation: Patents & Royalties; Kan Research Laboratory, Inc.: Consultancy; ChordiaTherapeutics, Inc.: Consultancy, Equity Ownership; Dainippon-Sumitomo Pharmaceutical, Inc.: Research Funding; Asahi Genomics: Equity Ownership; RegCell Corporation: Equity Ownership.

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