Secondary myelodysplastic syndromes identified via next-generation sequencing in a non-small cell lung cancer patient

Background Myelodysplastic syndrome (MDS) is a group of clonal disorders characterized by ineffective and dysplastic hematopoiesis in the bone marrow with a high risk of progression to leukemia. Many studies have demonstrated that chemo-radiotherapy for cancer patients and exposure to certain chemicals may increase the risk of secondary MDS, which is characterized by specific chromosomal abnormalities and genomic alterations. Since next-generation sequencing (NGS) has been widely used for the diagnosis of cancer patients, advanced analysis of the sequencing data may provide supplementary information for secondary MDS. Case presentation A male patient with non-small cell lung cancer (NSCLC) and bone metastases has presented distal obstructive inflammation, the enlargement of the left hilar, mediastinal lymph node metastases, and multiple bone metastases. This patient has undergone long-term exposures to certain chemicals. Moreover, the deletion of chromosome 7 and 5q is detected in his peripheral blood sequencing, indicating secondary MDS, subsequently confirmed by bone marrow examination. Conclusion In this case, an NSCLC patient was diagnosed with secondary MDS via NGS analysis, indicating that the NGS analysis may serve as supplementary for diagnosis of secondary MDS and provide useful information of therapeutic regimens for subsequent-line treatment of EGFR-mutated lung cancer. To the best of our knowledge, this is the first report of acquired MDS in a lung adenocarcinoma patient.

Clonal Hematopoiesis Driven By MDM4 Amplification Defines a Canonical Route Towards Secondary MDS/AML in Fanconi Anemia Patients

Introduction Fanconi anemia (FA) is the most frequent inherited DNA-repair disease in human, driving hematopoietic stem cell (HSC) failure in children and a major predisposition to poor-prognosis myelodysplastic syndrome (MDS) and acute leukemia (AML) in children or young adults. MDS/AML secondary to FA have a dismal prognosis in this frail population with a high chemotherapy-related toxicity. How bone marrow (BM) cells progress to myeloid malignancies in a background of cell intrinsic genomic instability and stem cell exhaustion is still poorly understood. Here we aimed to identify the molecular and functional determinants of BM progression to MDS/AML in FA patients. Methods We studied a cohort of 335 FA patients, representing virtually all FA patients seen in France from 2002 to 2020. We performed longitudinal clinical studies (cytopenia, BM morphology and staging, HSCT, survival), somatic genomics (karyotype, myeloid cancer gene panel, aCGH, WES, WGS), expression analysis by RNAseq on clonal cells, and functional studies (gene modulation in HSPCs, transgenic MDM4 mice, CFU and competitive engraftment experiments). Paired clonal BM and skin fibroblasts samples were available for 62 MDS/AML FA patients; WES and WGS files from age-matched non FA MDS/AML were used as controls. Results 98 out of 335 patients (29%) experienced clonal evolution, first seen at a median age of 13y, including 51 (15%) with blastic evolution (>5% BM blasts, median age 16y). Unbalanced chromosomal translocations rather than point mutations underlaid clonal evolution in comparison to age-matched, sporadic (non-FA) AML cases. The most prominent driver lesion was chromosome 1q duplication (1q+), found in 52% of the clonal FA patients, while other recurrent lesions were gain of 3q (3q+/EVI1; 40%), translocations/del/mut involving the RUNX1 gene (35%), monosomy 7/7q- (31%), and signaling gene mutations (18%). Based on longitudinal studies and ranking models, we evidenced that 1q+ occurred early, yielding preleukemic clonal hematopoiesis, whereas 3q+, -7/del7q, RUNX1 and signaling mutations occurred later along with BM transformation. Regarding genomic instability, WGS analysis of FA AML cells revealed a unique mutational signature that shares features with BRCA-related solid cancers [homologous recombination deficient (HRD)-type substitution signature, accumulation of small/intermediate-size deletions and large structural variants (SV)]. SV breakpoint analysis identified microhomology-mediated end joining (MM-EJ, also known as Alt-EJ) as the preferential DNA repair mechanism in the FA context. Specifically, a fragile site in the 1q pericentromeric repeated region underlaid 1q+ translocations. Next, we found that the MDM4 oncogene, a negative modulator of p53 response located in the minimal 1q duplicated region, was overexpressed in 1q+ but not in clonal non-1q FA cells. We hypothesized that 1q+ may attenuate the FA-associated p53 pathway hyperactivation through increased gene dosage of MDM4. Consistently, RNA-seq of patient cells before and after clonal progression showed p53 pathway activation before clonal evolution and subsequent p53 downregulation along with 1q+. When evaluated in vitro by CFU assay, lentiviral overexpression of MDM4 rescued clonogenicity defect of HSCPs from both FA patients and Fanc-/- mice, at the same level as TP53 knockdown. We produced a transgenic mouse bearing a duplicated Mdm4 locus and showed that MdM4 overexpression conferred an advantage to FA-like HSPCs in competitive transplant experiments, modeling clonal hematopoiesis. Exposure of 1q+ FA cells to Mdm4 inhibitors raised therapeutic potential. Conclusions The somatic genomic landscape of FA MDS/AML reveals a unique FA mutational signature, characterized by structural rearrangements and copy number abnormalities rather than point mutations. Our results define a canonical oncogenic route towards secondary MDS/AML in FA patients, in which the early modulation of the p53 pathway through 1q+/MDM4 oncogene overexpression plays a pivotal role, raising novel monitoring and therapeutic prospects for the FA patients. Disclosures Sebert: BMS: Consultancy; Abbvie: Consultancy. Dalle: Jazz Pharmaceuticals: Honoraria. Socie: Alexion: Research Funding. Peffault De Latour: Pfizer: Membership on an entity's Board of Directors or advisory committees, Other: Travel support, Research Funding; Amgen: Consultancy, Other, Research Funding; Jazz Pharmaceuticals: Honoraria; Alexion, AstraZeneca Rare Disease: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel support, Research Funding.

Updated Efficacy of Eltanexor Monotherapy in Patients with Higher Risk Hypomethylating Myelodysplastic Syndrome Primary Refractory to Hypomethylating Agents

Background: Patients with higher-risk myelodysplastic syndrome (MDS) refractory to hypomethylating agents (HMAs) have limited therapeutic options and poor prognosis with a median overall survival (mOS) of 4-6 months. Lack of response to HMA therapy, advanced age at relapse, male sex, bone marrow blasts >5% and high risk disease classification by International Prognostic Scoring System (IPSS) confer worse outcomes. Eltanexor is a second-generation, oral, selective inhibitor of nuclear export (SINE) compound with markedly reduced brain penetration relative to selinexor in preclinical models. This is believed to result in attenuation of centrally mediated anorexia, weight loss, and nausea, allowing for more frequent dosing. Early results from a phase 1/2 study of eltanexor in patients with higher-risk HMA-refractory MDS demonstrated marrow complete responses (mCRs), hematologic improvement (HI) and stable disease (SD); side effects were primarily low-grade, dose-dependent, and reversible (Lee EHA 2021). Here we provide an update on baseline characteristics, blast reduction in mCR patients, extent of transfusion independence and additional subgroup analyses. Methods: This phase 1/2 study (NCT02649790) evaluated oral eltanexor monotherapy in patients with high-risk or intermediate-2 by IPSS and 5%-19% myeloblasts. Of 20 patients enrolled, 15 patients were evaluable for efficacy and constitute the population studied in this analysis; 5 patients were non evaluable for efficacy due to trial discontinuation prior to response assessment. Two doses of eltanexor were evaluated: 10 mg (n=5) or 20 mg (n=10) each given qd 5 days per week. Results: Amongst the 15 efficacy evaluable patients, there were 8 males, median age 76 years (range 62-89), 10.0% (range 7-18%) median bone marrow blasts at enrollment, and with a median of two prior regimens (range 1-4). All patients primary HMA-refractory MDS; 9 patients (60%) with high risk and 5 (33%) with intermediate-2 per IPSS, 1 with intermediate-1 per IPSS. Similarly, using the global MD Anderson Cancer Center risk prognosis model, 14 patients (93%) had intermediate-2 or high-risk MDS. The overall response rate (mCR+HI) was 53% including 47% mCRs. Additionally, 5 patients (33%) had SD. Median blast reduction in the 7 patients with mCR was 78.6% (range 55.6%, 85.7%). Four patients had hematologic improvement (HI) including 2 patients with tri-lineage HI. Of the 7 patients who achieved mCR, 4 had significant reduction in transfusion requirements with 3 of these patients achieving complete transfusion independence for 5-10 cycles. In the 10-mg cohort (n=5), all patients derived clinical benefit with 3 patients reaching mCR and 2 patients with SD. In the 20-mg cohort (n=10), 4 patients had mCR and 3 had SD. Median overall survival for all efficacy evaluable patients was 9.86 months. OS for patients who reached mCR (n=7) was significantly longer than for patients who did not reach mCR (n=8): median 11.86 vs 8.67 months (hazard ratio [HR]=0.27, p=0.05), and significantly longer than OS for patients with PD (n=3, mOS=3.15 months, HR=0.23, p=0.04). Notably, mCR was seen in the 3 patients treated with >2 prior therapies and/or with secondary MDS: 1 patient with secondary MDS and 4 prior therapies; 1 with secondary MDS and one prior therapy; and 1 with de novo MDS and 3 prior therapies). Conclusions: Single-agent oral eltanexor was active in patients with higher-risk, primary HMA-refractory MDS including those with secondary MDS or with >2 lines of prior therapy. Patients with mCR had significantly longer mOS than patients without mCR and had median blast reduction of 78.6%. Further evaluation of eltanexor in MDS as a single agent and in combination with other agents is ongoing. Disclosures Lee: Innate: Consultancy, Membership on an entity's Board of Directors or advisory committees; AstraZeneca: Consultancy, Membership on an entity's Board of Directors or advisory committees; BMS: Consultancy, Membership on an entity's Board of Directors or advisory committees; Pin Therapeutics: Consultancy, Membership on an entity's Board of Directors or advisory committees. Mohan: Astex: Research Funding; Incyte: Research Funding. Knupp: Karyopharm Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Chamoun: Karyopharm Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Karasik: Karyopharm Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Bai: Abbvie: Current equity holder in publicly-traded company; Takeda: Current Employment, Current equity holder in publicly-traded company; Karyopharm Therapeutics Inc.: Current equity holder in publicly-traded company, Ended employment in the past 24 months. Ingalls: Karyopharm Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Yang: Karyopharm Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Shah: Karyopharm Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Kauffman: Karyopharm Therapeutics Inc.: Current Employment, Current equity holder in publicly-traded company. Shacham: Karyopharm: Current Employment, Current equity holder in publicly-traded company, Patents & Royalties: (8999996, 9079865, 9714226, PCT/US12/048319, and I574957) on hydrazide containing nuclear transport modulators and uses, and pending patents PCT/US12/048319, 499/2012, PI20102724, and 2012000928) . Bhatnagar: Astellas: Honoraria; Cell Therapeutics: Honoraria, Research Funding; Celgene: Honoraria; Pfizer: Honoraria; Kite: Honoraria; Karyopharm Therapeutics Inc.: Honoraria, Research Funding; Novartis: Honoraria; Sumitomo Dainippon Pharma: Research Funding.

The association between myelodysplastic syndromes (MDS) and inflammatory bowel diseases (IBD): Analysis of Nationwide Inpatient Sample (NIS) database.

e19033 Background: The co-occurrence of MDS and IBD has been gradually recognized in the literature. Yet, large-scale national studies are required to investigate this observed association further. We aimed to delineate the clinical features, outcomes between the concurrent of MDS with IBD and MDS or IBD alone in a nationally representative database. Methods: Data were obtained from the NIS 2010-2014, using appropriate ICD-9 codes to identify patients who were admitted with a principal diagnosis of MDS with IBD as secondary (MDS-1/IBD) and MDS without IBD and patients who were admitted with a principal diagnosis of IBD with MDS (IBD-1/MDS) and without MDS. We assessed the mortality rate as the primary outcome, mean length of stay (LOS), and rate of blood transfusion as secondary outcomes by Pearson χ2 -test and univariate regression (logistic regression). Results: We identified 190 hospitalizations for MDS-1/IBD and 4895 hospitalizations for IBD-1/MDS. The mean LOS was higher for MDS-1/IBD group than for IBD or MDS only (11.7 vs. 6.1 and 7 days). However, the mortality rate in the MDS-1/IBD group was lower than in patients with IBD or MDS only (2.6% vs. 3.8% and 4.4%). While the rate of blood transfusion was higher among males in the MDS group, it was significantly higher among females when there is a concurrent MDS-1/IBD. However, the differences were not significant when MDS is not the primary diagnosis i.e IBD-1/MDS. In univariate analysis, age and Charlson comorbidity index were significantly associated with an increased mortality rate when there are IBD and MDS than MDS or IBD alone. Conclusions: While unable to assess appropriateness, NIS data indicate that there are significant differences in outcomes such as mean LOS, rate of blood transfusion and mortality rate when there is a concurrence of MDS and IBD than MDS or IBD alone. The underlying pathogenicity remains unclear and warrants additional study.[Table: see text]

Prognostic Markers of Myelodysplastic Syndromes

Myelodysplastic syndrome (MDS) is a clonal disease characterized by multilineage dysplasia, peripheral blood cytopenias, and a high risk of transformation to acute myeloid leukemia. In theory, from clonal hematopoiesis of indeterminate potential to hematologic malignancies, there is a complex interplay between genetic and epigenetic factors, including miRNA. In practice, karyotype analysis assigns patients to different prognostic groups, and mutations are often associated with a particular disease phenotype. Among myeloproliferative disorders, secondary MDS is a group of special entities with a typical spectrum of genetic mutations and cytogenetic rearrangements resembling those in de novo MDS. This overview analyzes the present prognostic systems of MDS and the most recent efforts in the search for genetic and epigenetic markers for the diagnosis and prognosis of MDS.

Secondary myelodysplastic syndrome and leukemia in acquired aplastic anemia and paroxysmal nocturnal hemoglobinuria

Acquired aplastic anemia (AA) and paroxysmal nocturnal hemoglobinuria (PNH) are pathogenically related nonmalignant bone marrow failure disorders linked to T-cell–mediated autoimmunity; they are associated with an increased risk of secondary myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Approximately 15% to 20% of AA patients and 2% to 6% of PNH patients go on to develop secondary MDS/AML by 10 years of follow-up. Factors determining an individual patient’s risk of malignant transformation remain poorly defined. Recent studies identified nearly ubiquitous clonal hematopoiesis (CH) in AA patients. Similarly, CH with additional, non-PIGA, somatic alterations occurs in the majority of patients with PNH. Factors associated with progression to secondary MDS/AML include longer duration of disease, increased telomere attrition, presence of adverse prognostic mutations, and multiple mutations, particularly when occurring early in the disease course and at a high allelic burden. Here, we will review the prevalence and characteristics of somatic alterations in AA and PNH and will explore their prognostic significance and mechanisms of clonal selection. We will then discuss the available data on post-AA and post-PNH progression to secondary MDS/AML and provide practical guidance for approaching patients with PNH and AA who have CH.

Methylation profiling of hypomethylating agent response and treatment failure in pediatric and young adult MDS/AML.

e22502 Background: Hypomethylating agents (HMAs) have favorable toxicity profiles and anti-leukemia activity in adult AML/MDS. We previously reported similar activity in eight pediatric patients (Phillips et al., British Journal of Hematology 2013), however, it remains unclear which factors influence outcome and sustainability of response. We sought to update our clinical experience and determine molecular correlates of HMA response and relapse with the goal of identifying potential biomarkers and physiologic insights. Methods: Clinical data was retrospectively collected through chart review from 2012 to 2017. Cryopreserved patient bone marrow was obtained from our institution’s biorepository under an IRB-approved protocol. Leukemic blasts were enriched by FACS, and genomic DNA was extracted and subjected to reduced representation bisulfite sequencing (RRBS). Differentially methylated regions (DMRs) were calculated using MethylKit. Results: Fourteen patients were treated with hypomethylating agents. Median age was 9.5 years (range 2-34). Two patients (14%) had germline TP53 mutations, secondary MDS/AML, and achieved complete response (CR). Four patients (29%) had monosomy 7, with 2 CR (50%) and 2 partial responses (PR). Contrarily, in the non-monosomy 7 patients, only 1 patient achieved a CR, 2 PR, and one had stable disease. DMRs were identified by comparing diagnostic and relapse samples, as well as responsive and refractory specimens. As expected, there was global DNA hypomethylation following treatment with HMAs. Pathway analysis of DMRs identified in relapse vs diagnostic samples revealed promoter hypomethylation in processes related to DNA binding, transcription factor activity, and RNA biosynthesis, as well as promoter hypomethylation of polycomb repressive complex 2 targets and gene sets classically associated with histone H3 K27 trimethylation. Gene set enrichment analysis (GSEA) of relapse versus remission marrow samples demonstrated reduced methylation of promoter regions regulating DNA repair, responses to DNA damage, and adaptive immune signaling. Conclusions: Our data suggests that HMA response and relapses after treatment may exhibit unique biological signatures reflected in methylation changes. These findings can inform further hypothesis generation and potentially combination therapies.

Secondary myelodysplastic syndrome identified via next-generation sequencing in non-small cell lung cancer patients.

e19531 Background: Chemotherapy and radiotherapy used in cancer treatment are associated with increased risk of secondary myelodysplastic syndrome (MDS). MDS is characterized with specific chromosomal abnormalities and genomic alterations in JAK2, KRAS, CBL, DNMT3A, TET2, IDH1/2, EVI1, RUNX1, GATA2, EZH2, ASXL1, SF3B1, U2AF1, SRSF2 and ZRSR2. Since next generation sequencing (NGS) techniques have been widely used for the detection of actionable genomic variation in solid tumor patients, analysis of NGS data for chromosomal abnormalities and gene mutations may be supplementary for diagnosis of secondary MDS. Methods: We retrospectively analyzed targeted NGS data of paired tumor and blood samples from patients with non-small cell lung cancer (NSCLC) for chromosomal abnormalities and gene mutations. Sequence panel covered whole exons of 381 genes associated with cancers. Sequence data were processed using a customized analysis pipeline designed to accurately detect multiple classes of genomic alterations in routine clinical specimens. All testing was done in a CLIA-certified, CAP-accredited laboratory. Clinical information of cases with chromosomal abnormalities was reviewed, including treatment for previous cancer, blood and bone marrow tests. Results: We found 4 cases carrying MDS associated chromosome abnormalities among 3523 NSCLC patients with the prevalence of0.1%. They were old (from 66 to 71 years old), and were more likely to be male (3 males and 1 females). All of 4 cases included common abnormalities associated with MDS like 5q-, 7q-, -7, +21. 3 cases had complex (≥3) abnormalities and 1 case had double abnormalities. Point mutations were identified in blood samples of 3 cases. Mutations in TP53 occurred in 3 cases, mutations in ASXL1, DNMT3A, FLT3 and CBL occurred in one case respectively. Among the 4 cases, 2 cases were confirmed as MDS by blood and bone marrow tests. Conclusions: We identified 4 MDS associated chromosomal abnormalities from 3523 NSCLC patients through analyzing NGS data. NGS techniques could serve as supplementary for diagnosis of secondary MDS. [Table: see text]

Idiopathic aplastic anemia vs hypocellular myelodysplastic syndrome

Proper diagnostic distinction of bone marrow failure syndromes can often be challenging. In particular, for older patients with idiopathic aplastic anemia (AA), differential diagnosis includes myelodysplastic syndrome (MDS), which can atypically present in a hypocellular form. In addition to blasts and overt dysplasia, the presence of chromosomal abnormalities and a spectrum of somatic mutations may be revealing. Both clonal cytogenetic aberrations and somatic mutations most typically correspond to a clonal myelodysplasia, but clonal somatic mutations have also recently been found in AA. True driver myeloid mutations are uncommon in AA. Marrow hypocellularity in AA and occasionally in MDS patients points toward a similar immune mechanism responsible for deficient blood cell production and indicates that cytopenias in early hypocellular MDS might be treated with immunosuppressive modalities. Primary hypocellular MDS has to be distinguished from post-AA secondary MDS, most commonly associated with del7/7q. Post-AA MDS evolves at the rate of about 10% in 10 years, but recent observations suggest that widespread use of eltrombopag may influence the risk of progression to MDS. This complication likely represents a clonal escape, with founder hits occurring early on in the course of AA. A similar mechanism operates in the evolution of paroxysmal nocturnal hemoglobinuria (PNH) in AA patients, but PNH clones are rarely encountered in primary MDS.

Stem cell mutations can be detected in myeloma patients years before onset of secondary leukemias

Key Points Leukemia-associated mutations can be detected many years before the onset of secondary leukemias in myeloma patients. Stem and progenitor cells can act as reservoirs of mutations before the onset of secondary MDS and AML after treatment of myeloma.