Clonal Cytopenia Of Undetermined Significance Research Articles

The impact of cytotoxic therapy on the risk of progression and death in clonal cytopenia(s) of undetermined significance

AbstractClonal cytopenia of undetermined significance (CCUS) is defined by a myeloid driver mutation in the context of otherwise unexplained cytopenia. CCUS has an inherent risk of progressing to myeloid neoplasm. However, it is unknown how exposure to previous cytotoxic therapy may impact the risk of progression and survival. We stratified patients with CCUS by prior exposure to DNA-damaging therapy. Of 151 patients, 46 (30%) had received cytotoxic therapy and were classified as therapy-related CCUS (t-CCUS), whereas 105 (70%) had de novo CCUS. A lower proportion of t-CCUS had hypercellular marrows (17.8% vs 44.8%, P = .002) but had higher median bone marrow blast percentages. After a median follow-up of 2.2 years, t-CCUS had significantly shorter progression-free survival (PFS, 1.8 vs 6.3 years; hazard ratio [HR], 2.1; P = .007) and median overall survival (OS; 3.6 years vs not reached; HR, 2.3; P = .007) compared with CCUS. Univariable and multivariable time-to-event analyses showed that exposure to cytotoxic therapy independently accounted for inferior PFS and OS. Despite the similarities in clinical presentation between CCUS and t-CCUS, we show that exposure to prior cytotoxic therapies was an independent risk factor for inferior outcomes. This suggests that t-CCUS represents a unique clinical entity that needs more stringent monitoring or earlier intervention strategies.

Genetic studies in clonal haematopoiesis, myelodysplastic neoplasms and acute myeloid leukaemia – a practical guide to WHO-HAEM5

Abstract In recent years, technology developments and increase in knowledge have led to profound changes in the diagnostics of haematologic neoplasms, particularly myeloid neoplasms. Therefore an updated, fifth edition of the World Health Organization (WHO) classification of haematolymphoid neoplasms (WHO-HAEM5) will be issued in 2024. In this context, we present a practical guide for analysing the genetic aspects of clonal haematopoiesis of indeterminate potential (CHIP), clonal cytopenia of undetermined significance (CCUS), myelodysplastic neoplasms (MDS), and acute myeloid leukaemia (AML) based on WHO-HAEM5. This guide navigates through the genetic abnormalities underlying myeloid neoplasms which are required to be detected for classification according to WHO-HAEM5 and provides diagnostic algorithms.

Cancer patients with clonal hematopoiesis die from primary malignancy or comorbidities despite higher rates of transformation to myeloid neoplasms.

The occurrence of somatic mutations in patients with no evidence of hematological disorders is called clonal hematopoiesis (CH). CH, whose subtypes include CH of indeterminate potential and clonal cytopenia of undetermined significance, has been associated with both hematologic cancers and systemic comorbidities. However, CH's effect on patients, especially those with concomitant malignancies, is not fully understood. We performed a retrospective evaluation of all patients with CH at a tertiary cancer center. Patient characteristics, mutational data, and outcomes were collected and analyzed. Of 78 individuals included, 59 (76%) had a history of cancer and 60 (77%) had moderate to severe comorbidity burdens. DNMT3A, TET2, TP53, and ASXL1 were the most common mutations. For the entire cohort, the 2-year overall survival rate was 79% (95% CI: 70, 90), while the median survival was not reached. Of 20 observed deaths, most were related to primary malignancies (n = 7, 35%), comorbidities (n = 4, 20%), or myeloid neoplasms (n = 4, 20%). Twelve patients (15%) experienced transformation to a myeloid neoplasm. According to the clonal hematopoiesis risk score, the 3-year transformation rate was 0% in low-risk, 15% in intermediate-risk (p = 0.098), and 28% in high-risk (p = 0.05) patients. By multivariate analysis, transformation was associated with variant allele frequency ≥0.2 and hemoglobin <10 g/dL. In a population including mostly cancer patients, CH was associated with comorbidities and myeloid transformation in patients with higher mutational burdens and anemia. Nevertheless, such patients were less likely to die of their myeloid neoplasm than of primary malignancy or comorbidities.

148 - An odd presentation of abdominal cellulitis in the setting of clonal cytopenia of undetermined significance

148 - An odd presentation of abdominal cellulitis in the setting of clonal cytopenia of undetermined significance

Predicting cytopenias, progression, and survival in patients with clonal cytopenia of undetermined significance: a prospective cohort study

Somatic mutations are frequently reported in individuals with cytopenia but without a confirmed haematological diagnosis (clonal cytopenia of undetermined significance; CCUS). These patients have an increased risk of progression to a myeloid malignancy and worse overall survival than those with no such mutations. To date, studies have been limited by retrospective analysis or small patient numbers. We aimed to establish the natural history of CCUS by prospectively investigating outcome in a large, well defined patient cohort. This prospective cohort study was conducted at the Haematological Malignancy Diagnostic Service, a diagnostic laboratory in Leeds, UK. Patients aged at least 18 years who were referred for investigation of cytopenia were eligible for inclusion; those with a history of myeloid malignancy were not eligible. Targeted sequencing was conducted alongside routine clinical testing. Baseline mutation analysis was then correlated with the main study outcomes: longitudinal blood counts, disease progression to a myeloid malignancy, and overall survival with a median follow-up of 4·54 years (IQR 4·03-5·04). Data were collected manually from hospital records or extracted from laboratory or clinical outcome databases. Bone marrow samples from 2348 patients were received at the Haematological Malignancy Diagnostic Service between July 1, 2014, and July 31, 2016. Of these, 2083 patients (median age 72 years [IQR 63-80, range 18-99]; 854 [41·0%] female and 1229 [59·0%] male) met the inclusion criteria and had samples of sufficient quality for further analysis. 598 (28·7%) patients received a diagnosis on the basis of their biopsy sample, whereas 1485 (71·3%) samples were classified as non-diagnostic; of these, CCUS was confirmed in 400 (26·9%) patients (256 [64·0%] male and 144 [36·0%] female). TET2, SRSF2, and DNMT3A were the most frequently mutated genes in patients with CCUS, with 320 (80%) of 400 patients harbouring a mutation in at least one of these genes. Age (p<0·0001), sex (p=0·0027), and mutations in ASXL1 (p=0·0009), BCOR (p=0·0056), and TP53 (p=0·0055) correlated with a worse overall survival; however, the number of mutations was the strongest predictor for progression to a myeloid malignancy (two mutations, p=0·0024; three or more mutations, p=0·0004). Extended sequencing of samples from a subgroup of patients with sequential samples and no mutations in the initial myeloid gene panel showed recurrent mutations in both DDX41 and UBA1, suggesting that these genes should be included in clinical test panels. Mutation analysis is advised in patients who have undergone bone marrow examination and have an otherwise-unexplained cytopenia. High-risk genetic mutations and increased numbers of mutations are predictive of both survival and progression within 5 years of presentation, warranting clinical surveillance and, when necessary, intervention. MDS Foundation.

Clinical and pathological features of clonal cytopenia of undetermined significance presenting with isolated thrombocytopenia (CCUS-IT).

Clonal cytopenia of undetermined significance (CCUS) is defined as somatic mutations of myeloid malignancy-associated genes in the blood or bone marrow with one or more persistent unexplained cytopenias that do not meet diagnostic criteria for a defined myeloid neoplasm. CCUS with isolated thrombocytopenia (CCUS-IT) is rare. This is a retrospective case series of patients with prolonged isolated thrombocytopenia, a pathogenic mutation on a myeloid molecular panel, and a bone marrow biopsy with morphologic atypia below the WHO-defined diagnostic threshold for dysplasia. Five male patients were identified with a median age at CCUS-IT diagnosis of 61 years (56-74). Median duration of thrombocytopenia prior to CCUS-IT diagnosis was 4 years (3-12), and median platelet count at CCUS-IT diagnosis was 41 × 103 /μL (26-80). All patients had megakaryocytic hyperplasia and megakaryocytes with hyperchromasia and high nuclear-cytoplasmic ratio. Pathogenic SRSF2 mutations were identified in all 5 patients with median variant allele frequency of 36% (28%-50%). Three patients were treated with IVIg and/or steroids with no response; one of three responded to thrombopoietin receptor agonists. Three patients progressed to MDS and one to AML. We describe the clinicopathological features of CCUS-IT which can mimic immune thrombocytopenia.

How to classify risk based on clinical and molecular modeling: integrating molecular markers in the risk assessment of myelodysplastic syndrome.

Myelodysplastic syndrome (MDS), also known as "myelodysplastic neoplasm," is a heterogeneous group of clonal myeloid neoplasms that typically affects older adults. The clinical phenotype, symptoms, and complications relate to the depth of cytopenia and progression to acute myeloid leukemia (AML). The diagnosis of MDS relies on morphologic criteria, such as evidence of dysplasia, disordered maturation, and increasing blast counts, which separate the disease into histologic subtypes with different probabilities for progression to AML. The treatment of MDS is often risk-adapted depending on the prognostic profile of each patient's disease. There has been a coevolution of diagnostic and prognostic systems for MDS developed over the past 40 years, both of which have now incorporated molecular markers. The new International Prognostic Scoring System-Molecular (IPSS-M) improves partitioning of patients compared to prior versions with resultant upgrading of 34% of patients into higher-risk groups due to the presence of mutations. The new IPSS-M also more accurately distinguishes intermediate-risk patients separating them into two tiers. The two new diagnostic classifications include MDS defined by mutations in SF3B1 and TP53, though there are differences in diagnostic criteria. Future efforts to refine MDS prognostication could investigate the interface between MDS and clonal cytopenia of undetermined significance, expand access to genomic testing, obtain results in a less invasive manner, and develop treatment-response predictors and dynamic risk models.

GATA2 Mutation with Bone Marrow Failure. A Review of Ordering Next Generation Sequencing Testing while Triaging Bone Marrows in Patients with Cytopenias – Pathologists Challenge

Abstract Introduction/Objective GATA2 (germline) mutations are a cause of bone marrow (BM) failure in younger patients characterized by pancytopenia and hypoplastic BM with minimal or no dysplasia. These cases may have negative cytogenetic (CG)/FISH (FH) results and are diagnosed by next-generation sequencing (NGS) testing. We present a case where GATA2 testing was performed on a repeat BM resulting in delayed diagnosis. Insurance companies challenge providers and pathologists with frequent claims denials, thus the need to revise pre-authorization (PA) policies for triaging BMs in real time. We also reviewed our data where NGS was performed in patients with cytopenias, negative morphology (MO), flow cytometry (FC) &amp; CG/FH studies. Methods/Case Report We did a retrospective analysis and selected 455 BMs (2018 to 2022) where the clinical indication was cytopenias and had negative MO, FC, CG, and FH. We evaluated MO again with NGS results to ensure diagnostic features were not overlooked. Results (if a Case Study enter NA) The index case was a 22-year-old female failing to show abnormality by MO, FL, CG, or FH. The patient continued to have cytopenias; BM was performed a year later and NGS showed GATA2 mutation. This prompted a retrospective analysis of 455 BMs as described under methods. 101/455 (22%) cases revealed abnormal NGS results with pathogenic mutation resulting in amended reports. 42/455 (9%) cases revealed mutations consistent with clonal hematopoiesis of indeterminate potential (CHIP) or clonal cytopenia of undetermined significance (CCUS). Conclusion 1) PA policy for BM triaging is not practical since a decision for NGS testing is made in real-time; 2) Claim denials lead to underutilization of NGS, thus resulting in delayed patient care; 3) NGS may show pathogenic mutation despite negative MO/FL/CG/FH results; and 4) Insurance companies need to consider reviewing local coverage determination (LCD) policy for hematopoietic disorders as these tests are medically necessary, thus not requiring PA.

Reduced Subclone Diversity in Clonal Cytopenia of Undetermined Significance Compared to Myelodysplastic Syndrome

Introduction: Clonal cytopenias of undetermined significance (CCUS) and myelodysplastic syndromes (MDS) represent a disease continuum that are distinguished by the presence of dysplasia in &amp;gt;10% of blood cells. However, morphologic dysplasia is subject to high inter-observer variability, suggesting that dysplasia may not be ideal to differentiate CCUS from MDS. Defining the clonal architecture of samples from cytopenic patients may provide a more accurate objective measure of disease status than dysplasia. We hypothesize that the number and size of subclones is reduced in patients with CCUS compared to MDS, suggesting that increased subclonal diversity is a hallmark of higher-risk disease. Methods: We performed whole genome sequencing with higher exome coverage (eWGS) on bone marrow (n=58) or peripheral blood (n=4) and paired normal DNA from baseline banked samples from patients with CCUS (n=13), MDS (n=29; IPSS-R very low/low [3], intermediate [5], high/very high [19], no score [2]), and secondary AML (sAML) (n=20), including 32 previously reported patients, to define clonal architecture. Putative somatic variants, including 76 genes that are recurrently mutated in myeloid neoplasms, were validated in hematopoietic and paired normal samples, and available serial samples (n=23), using orthogonal target enrichment sequencing platforms achieving higher coverage (~600-1000x). Clonality of validated somatic mutations was defined using SciClone. Results: The absolute neutrophil count, hemoglobin, and platelet counts trended lower in MDS vs CCUS patients (median, 1.3 vs 2 K/ul [ns]; 9.3 vs 11.35 g/dL [p&amp;lt;0.01]; 63 vs 109.5 K/uL [ns], respectively). The ages and median number of total validated somatic mutations identified by eWGS at baseline was similar for CCUS (n=428), MDS (n=300), and sAML patients (n=420.5). We first defined the founding clone (i.e., the dominant clone with the highest median variant allele frequency [VAF]) and subclones. While the number of total clones per sample was not different between CCUS, MDS, and sAML (median, n=3 for each), the median VAF of all the mutations present in the founding clone (i.e., measure of the maximal molecular disease burden) was significantly lower in CCUS (21.3%) compared to MDS (39.2%, p&amp;lt;0.05) and sAML samples (45.2%, p&amp;lt;0.001), but MDS and sAML were not different (p=0.2) (Figure 1A). In contrast, there was no significant difference in the median VAF of subclones in CCUS and MDS samples (13.4% vs 16.8%), which were both lower than sAML (25.3%, p&amp;lt;= 0.01). However, the proportion of patients with no subclones (i.e., only the founding clone detected) was higher for CCUS (5/13 [38.5%]) compared to MDS and sAML (4/29 [13.8%] and 0/20 [0%], respectively, p 0.0006), suggesting that CCUS samples have reduced subclonal diversity compared to MDS. Consistent with this, genes commonly mutated in subclones occurred less frequently in CCUS vs MDS samples, including activated signaling (0/13 vs 6/29) and transcription factor genes (3/13 vs 9/29, respectively). Nine CCUS patients had serial samples sequenced (median 2 serial samples, range 1-5) at a median follow-up of 539 days (range, 84-4066 days). In CCUS patients with serial samples, there was minimal change in the founding clone (0.16%, range -3.7-23.9%) or the subclone median VAFs (0.2%, range -22.4-22.2%), with only 2 patients having a founding clone or subclone VAF increase of &amp;gt;5%. UPN 529198 had the acquisition of a new SRSF2(P95H)-mutant subclone 4066 days after initial banking but remained with stable cytopenias and no MDS (Figure 1B). One CCUS patient developed MDS 70 days after banking with a blast count that increased from 2% to 15% but had a negligible change in the founding clone VAF (2.8% increase). However, 3 subclones did increase in size (max VAF increase of 6.1%). In summary, while the total number of mutations is similar between CCUS, MDS and sAML samples, the clonal architecture varies across diseases. CCUS has a lower total molecular disease burden and a lower proportion of patients with a subclone compared to MDS patients in our cohort. The data suggest that defining clonal architecture and incorporating subclonal complexity in the evaluation of cytopenic patients could provide an objective measure to characterize and monitor disease burden rather than relying on the presence or absence of dysplasia, especially when considering the diagnosis of CCUS and lower-risk MDS.

Mutant Natural Killer Cell Dysfunction Enables the Immune Escape of Premalignant MDS Cell Clones

Myelodysplastic syndromes (MDS) cannot be cured by standard pharmacological therapies owing to their inability to eradicate aberrant hematopoietic stem cells (HSCs). Given that developing early intervention strategies for MDS patients requires an improved understanding of the mechanisms underlying aberrant HSC expansion, we sought to elucidate how MDS HSCs evade immune surveillance and expand in patients with clonal cytopenias of undetermined significance (CCUS), the pre-malignant stage of MDS. To characterize transcriptomic changes induced by CCUS in the aged immune microenvironment, we used single-cell RNA sequencing (scRNA-seq) of bone marrow (BM) mononuclear cells (MNCs) isolated from 2 young healthy donors (yHDs), 2 elderly healthy donors (eHDs), and 3 CCUS patients harboring mutations in MDS driver genes such as DNMT3A or TET2. CCUS immune cells were enriched in CD8 + T effector and NK cells, which were in activated states, characterized by the significant (P adj&amp;lt;0.05) upregulation of genes involved in protein translation, mitochondrial metabolism, and response to interferon signaling. A computational interactome analysis of ligand-receptor pair expression predicted gained intercellular communications among myeloid cells and CD8 + T and NK cells in CCUS patients compared with yHDs and eHDs, consistent with a tumor recognition process. However, CCUS CD8 + T and NK cells had downregulated NF-kB-mediated inflammatory signaling genes, which suggested a loss of proinflammatory capacity. Because an efficient antitumor CD8 + T-cell response requires functional NK cells, we further dissected their functional state by performing scRNA-seq of CD3 + and/or CD56 + BM cells isolated from 2 yHDs, 2 eHDs, and 3 CCUS patients. A trajectory reconstruction analysis showed that CCUS NK cells were in more advanced differentiation states than HD NK cells were, which was confirmed by the significant downregulation of the transcription factor FOXO1 (P adj=1.17 x 10 -81). Differential gene expression analyses revealed that CCUS NK cells had significantly (P adj&amp;lt;0.05) upregulated MYC and mTOR target genes and genes involved in oxidative metabolism, protein synthesis, and immune signaling (consistent with an NK cell proliferative burst) compared with eHD NK cells, which suggests that CCUS NK cells are hyperactivated. However, cytokine secretion assays with K562 cells revealed that NK cells from 5 CCUS patients secreted significantly (P=0.002) less interferon gamma than those from 6 eHDs did. CCUS NK cells and eHD NK cells produced similar levels of granzyme and perforin, and CCUS NK cells could degranulate (based on CD107a expression); however, CCUS NK cells had significantly lower CD16 expression (P=0.008), which suggests an impaired capacity to form stable immune synapses and degranulate in a polarized manner. Indeed, compared with those from 3 yHDs and 4 eHDs, NK cells from 3 CCUS patients had a significantly (P&amp;lt;0.0001) impaired cytolytic capacity against leukemic cells that could not be rescued by prolonged culture with feeder cells. Moreover, NK cells from 4 CCUS patients failed to kill both heterotypic and isotypic CCUS CD34 + cells ex vivo (Fig. 1). To investigate the molecular mechanisms of NK cell dysfunction, we performed joint targeted single-cell DNA sequencing and immunophenotypic analyses of MNCs from 5 CCUS patients with DNMT3A or TET2 mutations, which revealed that NK cells were enriched in aberrant clones and had mutational burdens similar to those of myelomonocytes (Fig. 2). Deletion of DNMT3A or TET2 by CRISPR/Cas9 in cord blood-derived NK cells and subsequent killing assays showed a significant (P&amp;lt;0.0001) progressive loss of cytolytic capacity with tumor re-challenging in knock-out NK cells, which demonstrated that loss of function mutations in those genes are a direct cause of NK cell dysfunction in the context of sustained immune activation. This study demonstrates that MDS driver mutations in CCUS NK cells induce immune dysfunction, thus enabling the expansion of malignant cells and thereby contributing to MDS onset. Our results suggest that immunotherapy with adoptive NK cell transfer could restore the anti-tumor immune response in patients with CCUS and may be an effective approach to arrest disease progression and prevent MDS onset.

IPSS-M - Use for Predicting Survival and Progression in Patients with Ccus - a Retrospective Multi-Institutional Study

Background: Clonal cytopenia of undetermined significance (CCUS) is characterized by the presence of a clone with somatic mutations in genes associated with myeloid neoplasms (MN) or abnormal cytogenetics, along with unexplained and persistent cytopenias in the absence of significant marrow dysplasia. CCUS is considered a premalignant state with a risk of progression to MN. The clinical outcomes of patients (pts) with high risk CCUS (Weeks et al, NEJM Evidence 2023) may be similar that of some patients with myelodysplastic syndromes (MDS). This study aims to predict the outcomes of CCUS patients using the molecular international prognostic scoring system (IPSS-M) developed for MDS. Methods: A retrospective analysis was conducted in patients diagnosed with CCUS between 2015 and 2023, we included patients harboring pathogenic mutations (MUT) identified through next-generation sequencing (NGS) testing at two institutions: Mayo Clinic and the University of Texas Southwestern Medical Center, Dallas, TX, USA were included. Progression was considered present if patients with CCUS progressed into myeloid neoplasm at follow up. Statistical analysis was performed using JMP® 17.1.0 Software. IPSS-M risk scores were calculated via the IPSS-M Risk Calculator (mds-risk-model.com). Results: A total of 103 patients were included in the study. The median age was 72 years, the majority were male patients (73%), and the median bone marrow blast % at the time of NGS was 1%. Forty-five % had an isolated mutation in a single gene, and 55% had co-mutations in ≥1 gene. The median number of mutations was 2 (range 1 - 5), occurring across 43 different genes. The most common mutations were in TET2 (N=28; 27%), ASXL1 (N=21; 20%), SRSF2 (N=21; 20%), U2AF1 (N=18; 17%), DNMT3A (N=16; 16%), and TP53 (N=12; 12%). Additionally, 25% of patients had an abnormal karyotype. Hematologic and genetic characteristics are summarized in (Table 1A). The median IPSS-M score was -0.9 (-3 to +2.34) and the median IPSS- Revised (R) score was 2 (0 - 6). The majority of patients had low (L) IPSS-M risk category (53%), followed by moderate low (ML) (19%) and very low (VL) (17%). Per IPSS-R, the majority had low-risk category (47%), followed by VL (38%) and intermediate (14%). Overall, 26 (25%) pt died after a median follow-up of 34 months and 21% progressed to MN (MDS 14 &amp; CMML 8), and 1 patient with MDS and 1 with CMML progressed to secondary AML (2%). The median overall survival (mOS) was not reached, with a 2-year estimated (YE) OS and leukemia-free survival (LFS) of 80%. Predictive Power: When utilizing the IPSS-M risk category ( L, M, H) * by combining the risk categories into L *(L+VL), M * (ML+MH), and H *(H+VH) to overcome the low sample size limitation, it significantly predicted OS (p &amp;lt; .0001) ( Figure 1A) and median MN-free survival (FS) (p &amp;lt; .0001) ( Figure 1B). The 2YE-OS rates by IPSS-M risk category were as follows: VL - 93%, L - 87%, ML - 75%, high (H) - 25%, very high (VH) - 0% and the 2YE-OS rates by IPSS-M ( L, M, H) are summarized in Table 1B. IPSS-M hazard ratio (HR) for OS was 1.6 for ( M*) compared to 25 for ( H *) risk category (p &amp;lt; .0001). The ( L *) category, being the largest, was used as the reference level. Conclusion: This study provides the first real-world experience of using the IPSS-M and a modified version of the IPSS-M ( L, M, H) * risk category model to predict survival and progression into MN in CCUS (MUT) pt. The IPSS-M risk category was found to be a significant predictor of OS and MN-free survival. We propose that larger cohorts are needed to validate our findings.

1-Year Data Analysis from a Cancer Center Molecular Tumor Board Dedicated to Clonal Hematopoiesis

Background Nearly 25% of cancer patients harbor clonal hematopoiesis of indeterminate potential (CHIP). Detection of clonal hematopoiesis (CH) in routine clinical practice is increasing due to incidental findings during sequencing analysis of circulating cell-free DNA (cfDNA) or exploration of unexplained cytopenia. To improve clinical management of these patients in our institution, we set up a multidisciplinary molecular tumor board (MTB) dedicated to patient cases with CH, CHIP, and clonal cytopenia of undetermined significance (CCUS) in 2022. Methods Between June 2022 and June 2023, our MTB reviewed a total of 345 cases, of which 212 referred by the solid tumor MTB and 133 referred by hematologists. The former 212 cases with CH were identified through cfDNA sequencing (FoundationOne Liquid CDx) within the Gustave Roussy Cancer Profiling study (NCT04932525), which includes some genes recurrently mutated in hematologic malignancies ( ASXL1, DNMT3A, IDH1, IDH2, JAK2, MPL, MYD88, SF3B1, TET2, U2AF1). A variant allele frequency (VAF) of at least 10% for the CH mutation was required to refer cases to the MTB, except for JAK2, MPL, and MYD88 mutations. The latter 133 cases were screened for CH mutations on peripheral blood leukocytes using a next-generation sequencing (NGS) assay targeting 174 genes recurrently mutated in hematologic malignancies. In addition to molecular data, standard clinical and biological parameters were recorded for each individual case. Results Patients referred by the solid tumor MTB In this cohort of 212 patients, median age was 72 years old (range, 48-91), sex ratio (M/F) was 1.4, median prior anticancer treatment lines was 2 (0-9), and time between MTB and cancer diagnosis was 2.3 years (0.2-34). The most frequent tumor types were lung (23%), colorectal (20%), prostate (19%), gynecological (12%) and breast (9%) cancers. The most frequently mutated genes were DNMT3A (59%), TET2 (30%), ASXL1 (24.5%), JAK2 (23%), SF3B1 (7.5%), and MYD88 (6%), with a median VAF of 4.2%, 3.0%, 8.5%, 1.0%, 5.0%, and 0.20%, respectively. Fifty percent of patients harbored more than 1 mutation. Six patients had a known history of myeloproliferative neoplasm (MPN). The proportion of cases with CH, CHIP, and CCUS was 15%, 59%, and 17%, respectively. The CH risk score of myeloid malignancy (CHRS, Weeks et al.) could be calculated in 126 cases but may underestimate risk due to the limited gene list considered, and revealed 69 (55%) low-risk, 52 (41%) intermediate-risk, and 5 (4%) high-risk patients. Our MTB recommended hematologic consultation for additional investigations in 58 patients, of which 22 were actually referred (main reason for not referring patients was advanced cancer disease). Four patients were diagnosed with hematologic malignancy (1 MPN, 1 chronic myeloid leukemia, 2 myelodysplastic syndromes [MDS]). Patients referred by a hematologist In this cohort of 133 patients, median age was 69 years old (53-89), and sex ratio (M/F) was 0.6. Eighty-six percent of patients had a cancer history, median prior anticancer treatment lines was 2 (0-7), time between MTB and cancer diagnosis was 3.5 years (0.2-34). The most frequent tumor types were lymphoid disorders (39%), breast cancer (15%), and gynecological cancer (15%). The proportion of CH, CHIP, and CCUS was 11%, 33%, and 41%, respectively. The most frequently mutated genes were DNMT3A (48,5%), PPM1D (24%), TET2 (22%), TP53 (17%), ASXL1 (6%), JAK2 (4.5%) and CHEK2 (4.5%), with a VAF of 2.5%, 2,3%, 4.0%, 2.0%, 8.0%, 1.0%, and 2.5%, respectively. Sixty percent of patients harbored more than 1 mutation. The CHRS could be calculated in 98 cases and revealed 34% low-risk, 50% intermediate-risk, and 16% high-risk CH patients. No need for a specific follow-up was recommended by the MTB in 33 patients. Among the 85 patients with hematologic follow-up, 3 (for which the CHRS was intermediate in 2 cases and high in 1 at the time of MTB evaluation) rapidly progressed to a myeloid malignancy ( Figure 1) (2 MDS and 1 MDS/MPN). Conclusions Our study highlights the utility of a MTB dedicated to CH, CHIP and CCUS for the identification of high-risk patients, early detection of hematologic malignancies, and appropriate therapeutic management. Long-term follow-up is needed to validate the CHRS but the design of a specific score for patients with cancer may be helpful due to the specific features of this population (high prevalence of PPM1D mutations, post-treatment cytopenia).

Correlation between Peripheral Blood and Bone Marrow Somatic Mutations Among Patients with Suspected or Established Myelodysplastic Syndromes from the National MDS Study

INTRODUCTION: Myelodysplastic Syndromes (MDS) are caused by progressive clonal dominance of mutated hematopoietic stem cells. While assessment of mutations in peripheral blood (PB) is an established standard for monitoring patients with some diseases such as chronic myeloid leukemia, the sensitivity and precision of PB screening and monitoring for somatic mutations in patients with MDS and related conditions such as clonal cytopenias of undetermined significance (CCUS) is less certain. Multiple published guidelines require bone marrow (BM) evaluations for the above, an invasive procedure not often performed outside of clinical trials. We compared somatic mutations and variant allele frequencies (VAFs) in paired PB and BM samples to assess the utility of PB results as a surrogate for diagnosis and monitoring. METHODS: The National MDS Natural History Study (National MDS Study) is an observational longitudinal cohort study of cytopenic patients suspected of having a diagnosis of MDS. All patients have PB and BM sampled when entering the study, prior to formal diagnosis. For this study, paired PB and BM baseline DNA samples from 36 patients were assessed for somatic mutations. Only subjects with minimum of one variant detected in their BM were included in this study. DNA was extracted from PB using an automated FlexSTAR (AutoGen) and from BM cell pellets using a QIAamp DNA Mini Kit (QIAGEN). Targeted exon sequencing of 96 genes was performed using a NovaSeq 6000 at a mean coverage of &amp;gt;1,200X and a mean breadth (bases covered at ≥100X) of &amp;gt;99.9%. Reads were aligned against a patched version of the build GRCh38 using BWA-MEM. VarScan2 was used to detect single nucleotide variants and short insertions/deletions with a minimum VAF of 2% and 5%, respectively. Resulting variants from 53 genes were manually reviewed to retain likely disease-causing variants. Correlation analysis between PB and BM VAFs was performed using Pearson correlation and linear regression. To confirm paired samples were sourced from the same subject, the Somalier software using a set of highly polymorphic SNPs across different ancestries was utilized to ensure a high level of relatedness. RESULTS: The 36 patients included 10 (28%) with MDS, 2 (6%) with MDS/MPN, 1 (3%) with AML (&amp;lt;30% blasts), and 23 (64%) with CCUS. The median age was 73 years (Table 1). Five of 36 patients had circulating PB blasts. Among the 191 mutations identified, the most common were TET2 (27%), SRSF2 (13%), DNMT3A (9%), SF3B1 (8%), and ASXL1 (8%). Correlation analysis of mutations (n=180) shared between paired PB and BM samples indicated a linear relationship between VAFs detected in PB and BM (Pearson correlation r=0.95, Figure 1), with a slight increase in variance observed with increasing VAFs. The deviation from the perfect (grey line) to the observed (yellow line) linear fit indicated that PB VAFs underestimated VAFs in BM by approximately 23% overall (Figure 1). For example, a BM VAF of 0.20 translated to a mean PB VAF of 0.16 based on the regression fit. The lower sensitivity was confirmed when looking at the number of total missed variants (present in BM, absent in PB): 9 of 101 (9%). Two mutations were detected in PB, but not BM. These mutations and diagnoses were 1) ETNK1 (VAF 0.026) in a patient with MDS-EB-1; and 2) CBL (VAF 0.021) in a patient with MDS with isolated del5q. Next, we assessed the relationship between percent of detected mutations and minimum VAF that was detected using linear regression and found that the higher the minimum VAF, the lower the percent of missed mutations. For example, for a 0.1, 0.2, and 0.3 minimum VAF, 11%, 9%, and 8% of BM mutations were missed, respectively. There was no difference in concordance between MDS and CCUS. SUMMARY &amp; CONCLUSIONS: PB can be used to reliably identify somatic mutations in patients with suspected or established MDS and related conditions. Linear correlation between PB and BM VAFs showed, unsurprisingly, that BM mutations with higher VAFs are more likely to be detected. If PB is positive, this method of variant detection may be used potentially to diagnose and monitor. However, if negative (or if VAF is less than 0.10), bone marrow genomics are still necessary to exclude detectable clonal mutations. For quantitative predictive tools that use VAFs, PB VAFs would need to be corrected to improve predictive results; our estimated linear regression equation could be used to guide this in a larger prospective study.

Comparison of the 2022 ICC and Who Classification Systems of Myelodysplastic Neoplasms

Introduction: Recently, the World Health Organization (WHO) updated the 5th edition classification of myelodysplastic neoplasms (MDS) and the International Consensus Classification (ICC) of myeloid neoplasms and acute leukemia was published. In this study, we aimed to compare several differences between WHO 2022 and ICC classifications. Methods: Our study consisted of 989 newly-diagnosed primary MDS subjects classified using the WHO 2016 criteria from 08/2016 to 07/2022. CD34 and CD117 immunostaining were used in 30 of 38 subjects with low blasts and BM fibrosis to evaluate a proportion of immature myeloid precursors. All subjects were negative for CD117+ cells. CD34+ BM cells ranged from 0% to 5%. Results: According to WHO 2022 classification, 36 MDS subjects with NPM1 mutation were reclassified as AML and 10 MDS-U subjects were reclassified as clonal cytopenia of undetermined significance (CCUS). Applying to the ICC criteria, 20 MDS subjects with NPM1 mutation were reclassified as AML and 8 MDS-U subjects were reclassified as CCUS. We analyzed the remaining patients. Among the 81 subjects classified as MDS-biTP53 according to WHO 2022, 10 subjects did not meet ICC criteria for MDS or MDS/AML with mutated TP53 because the VAF of TP53 mutation(s) was less than 10%. Subjects not qualifying for MDS or MDS/AML with mutated TP53 had lower Revised International Prognostic Scoring System (IPSS-R) scores, better IPSS-R-defined cytogenetics, a higher frequency of SF3B1 mutations and longer survival compared with subjects with MDS or MDS/AML with mutated TP53 according to ICC (All P-values＜ 0.005, Figure 1 Left). Our data suggested that TP53 mutational burden should also be considered in the diagnostic classification and the cut-off value of 10% seems reasonable. An additional difference between these two classifications is that ≥15% ring sideroblasts may be a surrogate for SF3B1 mutation in WHO 2022. But only those with SF3B1 mutation (VAF≥10%), without 5q-, -7 or complex karyotype and RUNX1 mutation can be diagnosed as MDS with mutated SF3B1(MDS- SF3B1) according to ICC. 23 of 76 subjects (30.3%) with MDS- SF3B1 according to the WHO 2022 classification did not meet the ICC criteria for MDS- SF3B1. Subjects not meeting the ICC for MDS- SF3B1 had lower WBCs ( P = 0.003) ,platelet concentrations ( P = 0.001), higher IPSS-M categories ( P = 0.024) and shorter survival compared with those with MDS- SF3B1 according to ICC( P = 0.003, Figure 1 middle). Therefore, our study shown that SF3B1-unmutated MDS-RS cases have different clinical features and outcome in comparison with SF3B1-mutated subjects and ICC criteria defined a more homogeneous disease entity of MDS- SF3B1. Apart from MDS with defining genetic abnormalities, substantial differences in morphologically defined MDS subtypes between WHO 2022 and ICC also need to be addressed. According to the WHO 2022 classification, only MDS-EB patients were furtherly categorized into MDS-EB with or without BM fibrosis. Here, we explore the impact of BM fibrosis in patients with MDS-LB. Among MDS patients without excess blasts and specific genetic abnormalities, 38 patients had fibrosis. Subjects with low blasts and fibrosis (MDS-LBf) had lower platelet concentrations ( P = 0.002), worse IPSS-R-defined cytogenetics and IPSS-R categories ( P ＜0.05) compared with those without excess blasts and myelofibrosis. MDS-LBf had worse survival compared with those with low blasts and without fibrosis (Figure 1 right, P = 0.007). Conclusion: Both the WHO 2022 and ICC criteria allow more accurate diagnoses and risk stratification. However, the presence of two separate classifications leads to the dilemma in clinical application. When it comes to MDS with defining genetic abnormalities, our analyses suggest ICC defines more homogeneous disease entities of MDS-SF3B1, MDS or MDS/AML with mutated TP53 subjects compared with WHO 2022. Although WHO 2022 places an emphasis on morphologically defined MDS and listed hypoplastic MDS (MDS-h) and MDS with fibrosis (MDS-f) as new entities. Our data shown that fibrosis is a poor prognostic factor in MDS subjects without excess blasts. These subjects tend to have more aggressive clinical manifestations than other MDS subjects with low blasts. Collectively, we propose to integrate these two classifications into one pipeline for diagnosis of MDS (Figure 2), avoiding disadvantages for each one. Bing Liand Zhijian Xiao were co-corresponding authors

Ivosidenib for Patients with Clonal Cytopenia of Undetermined Significance and Mutations in IDH1

Background Myeloid neoplasms (MN), including acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), are hematologic malignancies that are highly resistant to therapy and confer a poor prognosis. Recent studies have revealed that hematopoietic stem cells and progenitor cells carrying preleukemic mutations, defined as clonal hematopoiesis (CH), are the cells of origin in MN. CH can occur many years before the diagnosis of MN. Multiple mutations, mutations with a high variant allele frequency (VAF), and mutations in TP53, spliceosome genes, and isocitrate dehydrogenase 1/2 ( IDH1/2) have been identified as high-risk features for CH progression to MN. Individuals with cytopenias who harbor acquired mutations in their blood yet do not meet criteria for hematologic malignancy, an entity called clonal cytopenia of undetermined significance (CCUS), have an even higher risk of developing MN (estimated at 95% over 10 years of follow-up). Thus, despite being almost inevitably destined for progression to malignancy, there are no established preventative therapies for patients with CCUS. The IDH1 inhibitor ivosidenib has been extensively evaluated in clinical studies and has been shown to effectively inhibit the gain-of-function activity of the mutated protein. Clinical data has shown that ivosidenib is safe and well-tolerated with excellent response rates even in patients with relapsed or refractory AML. Individuals with lower co-mutational burden are more likely to have a clinical response and achieve molecular remission with ivosidenib. Since CCUS is characterized by a lower mutation burden compared to AML or MDS, we hypothesize that the use of ivosidenib in IDH1-mutant CCUS will result in a higher and more prolonged clinical response. Study Design and Methods NCT05030441 is a decentralized open label, multicenter pilot study exploring the efficacy of ivosidenib in patients with IDH1-mutant CCUS. The study is offered as a decentralized trial (DCT) where patients across the US can participate with study procedures occurring in the patient's home using telemedicine, mobile phlebotomy services and with local providers. By reducing barriers to trial participation, we expect that the DCT design will improve accessibility for this rare patient population. This represents an important step toward making personalized medicine available to a socio-economically diverse patient population and enables rare mutations to be studied at scale. Patients with CCUS harboring the IDH1 R132 mutation are considered eligible if they do not have any concurrent active malignancy requiring treatment. Patients must have unexplained cytopenia lasting ≥6 months, defined as hemoglobin &amp;lt;10 g/dL, absolute neutrophil count &amp;lt;1.8 × 10 9/L and platelets &amp;lt;100 × 10 9/L, as well as adequate baseline organ function including renal and liver function, as per the National Institutes of Health Common Terminology Criteria for Adverse Events (NCI CTCAE) grading. Recruitment and data collection will be coordinated with local providers for patients that enroll remotely. A total of 15 patients will be accrued to receive ivosidenib 500 mg daily for up to 18 cycles. The primary endpoint is rate of improvement in hematologic parameters using specific cutoffs for erythroid, platelet and neutrophil responses based on the MDS response criteria. The study will be considered positive if at least 6 out of the 15 patients have a hematologic improvement. Secondary endpoints include change in mutant IDH1 VAF, measured at baseline and every 3 cycles on peripheral blood samples, safety of ivosidenib, and AML/MDS-free survival which will be evaluated by descriptive statistics and Kaplan-Meier methodology. Enrollment opened in one US center and by decentralized structure in April 2022, with 3 patients accrued, and is expected to open in other US centers in 2023. If the study endpoints are met, our aim is to expand to a larger population with the goal of determining whether ivosidenib can prevent the development of hematologic malignancy in patients with IDH1-mutant CCUS.

Hypomethylating Agents Are Associated with High Rates of Hematologic Toxicity in Patients with Secondary MDS/AML That Develops after Acquired Aplastic Anemia

Acquired aplastic anemia (AA) is an autoimmune bone marrow failure (BMF) associated with depletion of hematopoietic stem and progenitor cells. Approximately 15-20% of AA patients treated with immunosuppressive therapy (IST) develop late complications of myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). Little is known about managing patients with post-AA myeloid neoplasms (MN). We hypothesized that patients with post-AA MN may be particularly susceptible to hematologic toxicities from cytotoxic therapy because of stem cell deficits. To investigate our hypothesis, we retrospectively analyzed post-AA MN patients treated at our 2 institutions over the past 15 years. Fourteen post-AA MN patients were identified: 11 with MDS, 1 with AML, and 2 with clonal cytopenia of undetermined significance (CCUS). Patients with inherited BMF or allogeneic stem cell transplant (SCT) prior to MN diagnosis were excluded. The median age at MN was 56.5 years (range 5-75) with a median time of 5 years (range 0.25-30) between AA diagnosis and MN. At MN diagnosis, 12 of 14 patients (86%) had a partial or complete response of AA with 5 receiving cyclosporine (CSA) maintenance. Two patients (14%) were on CSA within 6 months of IST without response. After MN diagnosis, CSA was discontinued. Ten adults received hypomethylating agents (HMA) as first-line treatment in preparation for SCT. Three pediatric patients were treated with SCT with no prior HMA. One patient died before receiving treatment. The 10 post-AA patients who received HMA were matched in a 3:1 ratio with a similarly aged, randomly selected non-AA MDS cohort treated with HMA at our center during the same period (Table 1). Compared to patients with non-AA MDS, post-AA MN patients tolerated HMA poorly with frequent, severe complications. Their median per-cycle duration of grade 4 neutropenia was longer (9 v. 1.5 days, p = 0.044), as was median duration of grade 4 thrombocytopenia (13 v. 0 days, p = 0.003). Post-AA patients notably had lower baseline platelets prior to HMA (median 36.5 v. 115 k/mL, p =0.007). Following HMA, the post-AA cohort had higher rates of febrile neutropenia (80% v. 17%, RR 4.8, p &amp;lt; 0.001) and infections ≥ grade 3 (90% v. 13%, RR 6.8, p &amp;lt; 0.001). They also had higher rates of ≥ grade 3 bleeding (40% v. 7%, RR 6.0, p = 0.026) with 2 patients (20%) experiencing intracranial hemorrhage on HMA; no such events occurred in the non-AA cohort. Post-AA patients had more hospital admissions - 18 in 25 total chemotherapy cycles (72%) compared to 12 in 207 cycles (6%) in the matched cohort (RR 12.4, p &amp;lt; 0.001). Post-AA MN patients had more treatment delays &amp;gt;2 weeks (28% v. 8% of planned treatment cycles, RR 3.4, p = 0.01) and dose reductions (40% v. 13%, RR 3.0, p = 0.089). HMA was discontinued due to treatment-emergent adverse events (TEAEs) in 70% of post-AA cases v. 3% of non-AA patients (RR 21.0, p &amp;lt; 0.001). Consequently, post-AA MN patients received fewer cycles of HMA compared to non-AA patients (median 2.5 v. 6, p = 0.021). Death occurred following TEAEs in 20% of post-AA MN patients; no deaths on HMA occurred in the non-AA cohort (RR 14.1, p = 0.058). Among surviving patients, SCT was delayed in 20% of the non-AA cohort due to TEAEs, while no delays occurred in the matched cohort. The median months from final chemotherapy cycle to SCT were 4 (range 1-12) in post-AA v. 1 (1-3) in non-AA, while median months from MN diagnosis to SCT were 8.5 (4-21) in post-AA v. 5 (4-15) in non-AA. For all 14 post-AA MN patients, including those not treated with HMA, overall survival (OS) from MN diagnosis was 71% (95% CI 51-99) at 1 year and 56% (95% CI 34-90) at 3 years. OS of post-AA MN patients differed significantly (p = 0.011) based on treatment with SCT. Among the 5 who did not receive SCT, 4 died within 3 years of MN, while 1 patient is alive 13 months from diagnosis receiving supportive care after intracranial hemorrhage during the first cycle of HMA. In contrast, 7 of 9 (78%) patients who received SCT were alive 3 years after MN diagnosis. Of the 6 patients treated with SCT after HMA, 5 stopped HMA due to toxicity, all had morphologic dysplasia at SCT, and 2 were transplanted with ≥ 5% marrow blasts. Our study shows that patients with MN following antecedent autoimmune AA are at high risk of severe toxicities with standard HMA regimens and have difficulty tolerating repeated cycles. Our results do not support routine use of HMA prior to SCT in this patient population and suggest that early SCT may be the most suitable strategy.

CAR19 Therapy Drives Expansion of Clonal Hematopoiesis and Associated Cytopenias

Background: For patients with relapsed/refractory large B-cell lymphomas (rrLBCL), CD19-directed chimeric antigen receptor T cells (CAR19) improve survival compared to autologous hematopoietic cell transplantation (HCT). However, major toxicities of CAR19 therapy include prolonged cytopenias and associated infections. To better understand the impact of CAR19 on such toxicities, we studied a cohort of LBCL patients achieving durable remissions to assess immune recovery after CAR19 treatment. We (1) compared immune reconstitution in HCT vs CAR19 treated patients, (2) performed molecular analysis of post-CAR19 cytopenic marrow specimens, and (3) profiled emergent mutations in cell free DNA (cfDNA) before and after CAR19. Methods &amp; Results: We first propensity matched rrLBCL patients treated at Stanford with either CAR19 (100% axi-cel) or HCT who achieved durable remissions. Patients were matched based on age, sex, prior systemic lines of therapy, and time from infusion. From 471 eligible cases, propensity score matching was successful in 138 (n=69 per arm). When compared to HCT-treated counterparts, CAR19-treated patients had reduced recovery of absolute lymphocyte counts (ALC) and absolute neutrophil counts (ANC; longitudinal regression day 28-800 ANOVA p&amp;lt;0.005), but similar recovery of hemoglobin and platelets. CAR19-treated patients experienced significantly more Grade ≥3 infections in competing risk analyses (HR 2.61, CI 1.26-5.42), and higher non-relapse mortality (log-rank p=0.027). Next, to characterize mechanisms underlying cytopenias after CAR19, we profiled marrow aspirates from cases requiring biopsy due to prolonged cytopenia or clinical concern for myeloid neoplasms. No patient had evidence of lymphoma relapse at the time of biopsy, and all were &amp;gt;60d from CAR19 infusion (median 377d, range 86-1561d). Among 21 patients profiled by DNA sequencing, 18 (86%) had evidence of ≥1 somatic mutation in genes canonically associated with clonal hematopoiesis (CH) in the marrow ( Fig. 1A), with the most recurrently mutated genes being DNMT3A (38%), TP53 (33%), PPM1D (24%), ASXL1 (14%), and TET2 (14%). Among 6 patients diagnosed with and requiring therapy for a myeloid malignancy, all (100%) had a canonical myeloid karyotypic aberration detected by FISH, as compared with 0 in the 14 other evaluable cases ( Fig. 1A). CAR19 cells were proportionately enriched in the marrow relative to paired peripheral blood by flow cytometry (n = 12, median 2.5-fold enrichment, Wilcoxon p&amp;lt;0.001). Using 10x scRNA-Seq, viable CAR19 was detectable in 7 of 8 marrows (88%) and were predominantly CD4+. We hypothesized that CH clones detectable after CAR19 would also be present in pre-CAR19 blood samples and detectable in cfDNA. To test this, we profiled 786 longitudinal samples from 141 patients using CAPP-seq and serially monitored CH clones in cfDNA. Among 141 eligible cases, 40 (28%) were evaluable for CH, in having both pre- and post-CAR19 infusion specimens, while in durable remission (median follow up 967d). Of 51 CH clones detected in post-infusion cfDNA, 46 (90.1%) were also detectable prior to CAR19, typically expanding post-infusion (median = 1.8-fold, Fig. 1B). We next tested whether expanding CH clones showed evidence for selection after CAR19. Strikingly, among 48 recurrently mutated genes tested, DNMT3A and PPM1D showed significant evidence for clonal selection and expansion after CAR19 (Q-value &amp;lt; 0.05). When compared to patients without emerging CH clones, patients with ≥5-fold clonal expansions of canonical CH genes (23% of cases) had reduced ANC, but not ALC, recovery (median ANC=1.43 vs 2.43 at 6-mo, Wilcoxon p&amp;lt;0.001). This association remained significant in multivariate longitudinal regression that included age, sex, prior lines of therapy, and pre-infusion ANC (ANOVA p = 0.007). Conclusion: CAR19 treated patients experience reduced immune reconstitution and higher infection rates than HCT treated counterparts. Bone marrow findings reveal prolonged CAR19 cytopenia to commonly be associated with clonal cytopenia of undetermined significance (CCUS). Despite durable lymphoma remissions, canonical myeloid clonal expansions are common post-CAR19, and associated with myelosuppression. Non-invasive genotyping could aid in early identification of patients at risk for prolonged cytopenias after CAR19 and inform interventions to decrease associated complications.

Mesenchymal Stromal Cells from Individuals with DNMT3A mut Clonal Hematopoiesis Instruct Young Healthy Hematopoietic Stem/Progenitor Cells Towards a Myeloid-Biased Aging Phenotype Resembling That of Patients with Clonal Cytopenia of Undetermined Significance (CCUS)

Clonal hematopoiesis of indeterminate potential (CHIP) describes the age-related acquisition of somatic mutations in hematopoietic stem/progenitor cells (HSPC) leading to clonal blood cell expansion and variable risk of progression to myeloid malignancy. DNMT3A is the most commonly mutated gene and while single mutations do not raise the likelihood of progression, high variant allele frequencies (VAF) and presence of co-mutations do. In myeloid diseases, the bone marrow (BM) microenvironment exhibits alterations promoting malignant transformation. However, it is unknown whether similar alterations exist in the pre-malignant niche. We set out to analyze whether human mesenchymal stromal cells (MSC) from CHIP individuals with a DNMT3A mutation ( DNMT3A mut) are altered and whether they are able to remodel the HSPC compartment in healthy hematopoiesis. From our published cohort of previously sequenced BM samples from hematologically healthy individuals undergoing hip replacement surgery, we selected samples with either an isolated DNMT3A mut at a low VAF (2.47-6.8%, n=4, median age 73.5y, termed low-risk CHIP), or DNMT3A mut samples with a high VAF (17.5-28.5%) and at least one co-mutation (n=5, median age 73y, termed high-risk CHIP) as well as 12 age-matched samples without any mutation (n=12, median age 72y). HSPC were isolated from 3 younger healthy donors (median age 50y). MSC were expanded by plastic adherence and subjected to multilevel characterization. Compared to age-matched healthy controls, MSC from DNMT3A mut BM samples (CHIP-MSC) exhibited higher proliferation rates, lower colony-forming-unit (CFU) fibroblast capacity, as well as reduced adipogenic and increased osteogenic differentiation potential. To understand how altered CHIP-MSC influence the hematopoietic compartment, younger healthy CD34+ HSPC were co-cultured with the different MSC subgroups for 42 hours in a low cytokine-containing medium, followed by bulk RNAseq on subsequently sorted cell populations (MSC: CD45-/CD90+; HSPC: CD45+/CD34+). We found 31 differentially expressed genes (DEG) (logFC±0.5, FDR&amp;lt;0.05) in CHIP-MSC compared to their age-matched counterparts. Functional analyses suggested an activation of communication towards HSPC via extracellular vesicles. Strikingly, differential gene expression of sorted young healthy HSPC after co-culture revealed 375 DEG (322 up-regulated, 53 down-regulated; logFC±0.5, FDR&amp;lt;0.05) in HSPC cultured with CHIP compared to non-CHIP age-matched MSC (Figure panel A). We then used gene set variation analysis (GSVA) to analyze HSPC compartment composition after co-culture. Based on enrichment scores, unsupervised clustering identified two distinctive profiles that correlated with HSPC cultured with either non-CHIP or high-risk CHIP-MSC, while those cultured with low-risk CHIP-MSC showed an intermediate phenotype (Figure panel B). Co-culture of HSPC with high-risk CHIP-MSC resulted in enrichment of hematopoietic stem cells (HSC) and multipotent progenitors (MPP), as well as myeloid skewing represented by higher scores for common-myeloid (CMP) and granulocyte-monocyte (GMP) progenitors. Conversely, in contrast to the control group, megakaryocyte-erythroid progenitors (MEP) were underrepresented. CFU capacity was increased in healthy HSPC cultured with CHIP-MSC and multiparameter flow cytometry analysis showed a trend towards increased CMP/GMP and decreased MEP numbers, consistent with the RNAseq data. Finally, we evaluated the BM HSPC compartment composition of a cohort of 49 CCUS patients with DNMT3A mut (VAF 1-49%, median age 76y) compared to 56 control BM samples using whole transcriptome sequencing data. Intriguingly, we observed the same profile with a myeloid shift in progenitor populations as in our healthy young HSPC exposed to high-risk CHIP-MSC. Taken together, our results indicate that MSC from individuals harboring a DNMT3Amutation are able to instruct young healthy HSPC and influence their fate, thereby promoting a differentiation bias that shifts the hematopoietic compartment toward that associated with an aged pre-malignant state, even in the absence of DNMT3A mut HSPC. These findings suggest that focusing on the interaction between MSC and HSPC is a promising therapeutic strategy to intercept disease progression. Functional analysis of identified deregulated pathways in DNMT3Amut CHIP is ongoing.

A Randomized Double-Blind Placebo-Controlled Phase II Multi-Center Study of Inflammation Modification of Canakinumab to Prevent Leukemic Progression of Clonal Cytopenias of Unknown Significance (CCUS): Impact Study

Background and Significance: High-risk Clonal Cytopenia of Undetermined Significance (HR-CCUS) is defined by prolonged cytopenias (&amp;gt; 4 months) in 1 or more cell lineages plus myeloid-disorder-associated mutations. CCUS patients with spliceosome mutations, DNMT3A, TET2, or ASXL1 mutations in combination with at least 2 other somatic mutations appear to have an extremely high rate of progression to myeloid neoplasms (MN) with a 95% 5-year cumulative probability of developing a MNsuch asMDS, MPN, or AML (13-fold increased risk compared to patients with cytopenia classified). Several studies implicate the inflammasome in CH progression to MDS/AML. Interleukin (IL)-1β is a key upstream cytokine in the inflammasome that strongly induces IL-6. Mutations in another key protein in the inflammasome, cryopyrin, result in high systemic levels of IL-1β and are associated with auto-inflammatory diseases. We hypothesize that the preclinical and clinical data showing a benefit of IL-1β inhibition in patients with CH, is due to reduced downstream activations of inflammasome proteins. Canakinumab is a high-affinity human monoclonal anti-human IL-1β antibody- FDA approved for the treatment of IL-1β driven inflammatory and oncologic diseases. By binding specifically to human IL-1β, canakinumab blocks the interaction of IL-1β with the IL-1 receptor, leading to inhibition of its downstream targets, thereby preventing IL-1β-induced gene activation and the production of inflammatory mediators. A phase II clinical trial investigating the use of canakinumab in combination with azacitidine is currently studying the impact canakinumab may have on disease progression in relapsed/refractory low or intermediate risk MDS patients (NCT04239157). This has now been extended to newly diagnosed MDS as new emerging data looks promising [unpublished data]. No significant toxicities have been reported. Thus, we hypothesize that the treatment of HR-CCUS patients, for whom there is no current disease modifying therapy, with an inflammasome targeting antibody, would prevent or significantly delay development of a MN, improve cytopenias and decrease the clone size as well as prevent further clonal evolution. Study Design and Methods: This study (NCT05641831) is a Phase II multicenter, randomized, two-arm, double-blind placebo-controlled study in patients with HR-CCUS (Figure 1). Patients with HR-CCUS, no known hematological malignancy, and any mutational combination as deemed appropriate by the inclusion criteria - are randomized to the study Arm or control Arm. Patients assigned to the study arm will be eligible to receive canakinumab, 300 mg subcutaneously every 3 months for 2 years. Patients assigned to the control arm will receive placebo every 3 months for 2 years. Bone marrow biopsies will be done for both arms every 6 months to monitor for disease progression (WHO 2016). PB samples will be collected every 3 months to monitor for disease progression. Patient-reported outcomes will be collected at the time of disease assessment. Statistical plan: The null hypothesis assumes the time to overt MN (MDS/MPN/CMML/AML) is equal in the control and study arms (H 0: HR=1) versus the alternative hypothesis that the risk of an event is lower in the study arm (H 1: HR&amp;lt;1). Assuming exponential survival, 71 events (overt MN) are required for the final analysis to detect a hazard ratio of 0.55 (median 2 years for the control arm versus 3.636 years for the study arm) using a log-rank test with 80% power and one-sided significance level of 5%. This includes one interim futility analysis when 50% of the targeted number of events (36) have been observed. At the time of the interim analysis, futility will be declared if the hazard ratio is greater than 1 and in favor of the control arm. The futility boundary is statistically non-binding in that there is not a final significance level adjustment. If the futility boundary is crossed, then the study will terminate early; patients randomized to the control arm will continue standard of care off study and patients randomized to the study arm will discontinue treatment with Canakinumab. Accounting for 5% drop-out, this calculation assumes accrual of 89 patients over 3 years and a minimum follow-up of 5 years (or until withdrawal, death, or study closure; earliest event). To date, 5 patients have been randomized and enrolled on study (Table 1).

Clonal Hematopoiesis Is Associated with Severe Cytokine Release Syndrome in Patients Treated with Chimeric Antigen Receptor T-Cell (CAR-T) Therapy

Background: Among patients receiving CD19 or B-cell maturation antigen (BCMA) CAR-T therapy, inflammation pre- and post-CAR-T infusion is attributed in the development of toxicities such as cytokine release syndrome (CRS), immune effector cell-associated neurotoxicity syndrome (ICANS), and prolonged cytopenias. Clonal hematopoiesis (CH), the clonal expansion of hematopoietic stem cells with somatic mutations, has been associated with inflammatory disorders such as rheumatoid arthritis and graft-versus-host disease, as well as clonal cytopenias of undetermined significance. In the setting of CAR-T, others have reported an association between CH and both ICANS and treatment-associated myeloid neoplasms. Herein, we examined the prevalence of pre-CAR-T CH in a predominantly transplant-naïve cohort of recipients with non-Hodgkin lymphoma (NHL) or multiple myeloma (MM), and assessed the relationship between CH and CAR-T related outcomes including CRS, ICANS, prolonged cytopenia, progression-free survival (PFS), and overall survival (OS). Methods: This study included 62 patients with NHL or MM who underwent CD19 or BCMA CAR-T therapy from 2017 to 2022 at City of Hope and had available pre-CAR-T cryopreserved peripheral blood mononuclear cells (PBMCs). DNA was isolated with QIAamp DNA Mini Kit (Qiagen) from PBMC samples (94% collected &amp;lt;30d of CAR-T infusion), on which we performed targeted exome sequencing (108 pre-defined gene panel with 1000x sequencing depth) to determine the presence of CH (variant allele frequency [VAF] ≥2%). Multivariable logistic regression was used to examine the association between CH (Yes/No) and absolute neutrophil count (ANC) recovery at day +60 (Y/N), maximum grade CRS and ICANS, grade &amp;lt;2 vs 2+, and OS and PFS at 1y. Covariables considered were age at CAR-T, baseline ANC, sex, race, CAR-HEMATOTOX (Rejeski et al. 2021), bridging therapy (Y/N), and number of prior lines of therapy. ANC recovery was defined as grade 2 or better for 3 measurements without growth factor support &amp;gt;2 weeks. Those without ANC recovery and who started new treatment before day +60 were excluded from that analysis. Results: Overall, the median age was 64y (range 21y-85y); 37 (60%) had de novo diffuse large B-cell lymphoma, 17 (27%) had transformed follicular lymphoma, 2 (3%) had MM, 2 (3%) had mantle cell lymphoma, and the remaining patients had other transformed indolent lymphomas. Median prior lines of therapy was 3 (1-12), and only 6% had previously undergone autologous hematopoietic cell transplantation. Systemic bridging therapy prior to CAR-T was required in 27 (44%), and 8 (13%) received radiation as bridging. All received fludarabine and cyclophosphamide for lymphodepleting chemotherapy. Axicabtagene ciloleucel was the most common (76%) CAR-T product, followed by tisagenlecleucel in 16% of patients. Overall, 51 (82%) and 29 (47%) patients experienced CRS and ICANS, respectively. had delayed ANC recovery. One-year PFS was 50% and 1y OS was 73%. Clonal hematopoiesis: 15 (24%) patients had at least one pathogenic CH mutation; 4 (6.5%) had ≥2 CH mutations. Of the 28 CH mutations identified, the most common were DNMT3A (18%), CHEK2 (11%), PMS2 (7%) and ASXL1 (7%); 29% of mutations had VAFs &amp;gt;10%. Outcomes after CAR-T: Patients with CH were significantly more likely to develop grade ≥2 CRS (60% vs. 28%, p=0.03) compared to those without CH (odds ratio [OR] 3.9, 95% CI 1.2-13.2; p=0.027). Accounting for baseline ANC (which was unexpectedly higher among the CH cohort and associated with delayed ANC recovery, p=0.02) patients with CH did not have a significantly different rate of delayed ANC recovery compared to those without CH (adjusted OR 0.37, 95% CI 0.09-1.5; p=0.17). There was no association between CH and ICANS, nor with 1y PFS and OS. Conclusion: CH was frequent (24%) in this cohort of CAR-T recipients and was associated with a higher risk of ≥2 CRS after CAR-T. Additional validation studies are currently underway, which may set the stage for consideration of pre-CAR-T CH as a biomarker for risk stratification towards more proactive CRS prophylaxis Acknowledgements: Funding through the CoH Hematological Malignancies Program Pilot Project Award. The authors acknowledge the work provided by CoH Center for Informatics, notably Research Informatics, and the utilization of the POSEIDON platform and the Honest Broker process.