Kusne, Yael

Abstract Introduction: The DEAD-box helicase 41 (DDX41) gene, located on chromosome 5q35, is a tumor suppressor gene involved in RNA processing. Germline mutations in this gene can predispose patients to myeloid malignancies. Studies have suggested a more favorable prognosis in those with germline mutations in DDX41, with progression of disease being a frequently encountered cause of death. In this retrospective study, we explored the causes of death in a cohort of patients with pathogenic DDX41 mutations. Methods: This was a retrospective study of patients diagnosed with myeloid neoplasms between 2009-2024 and found to have DDX41 mutation (DDX41m) via next generation sequencing (NGS) at our institution. Myeloid NGS was obtained at or after the diagnosis of myeloid disease. Germline testing (when available) was performed through buccal/skin samples. Carriers of DDX41m without a myeloid neoplasm diagnosis and patients with only DDX41m VUS were excluded. Baseline characteristics at the time of myeloid neoplasm diagnosis included age at diagnosis, DDX41m variant allele frequency (VAF), blood counts (hemoglobin, white blood cell count, platelets), cytogenetics, bone marrow blast percentage, number of co-mutations, and treatment received. Unadjusted comparisons were made using continuous or categorical variables. Median overall survival (OS) was calculated from the time of diagnosis with myeloid neoplasm to the time of death, using BlueSky Statistics V.10.3.4. Results: Of the 112 patients identified to have pathogenic DDX41m, 29 (26%) patients were deceased at the time of data analysis. In this cohort of 29 patients (median age at diagnosis 72 years, 17 (59%) males), disease groups at initial diagnosis included 17 (59%) patients with MDS, 9 (31%) AML, and 3 (10%) MPN. Fourteen of the 17 (82%) of the patients with MDS were classified as MDS-EB1 or MDS-EB2. Seven of the 17 (41%) patients with MDS progressed to AML at the time of death, with 57% of the patients having more than 30% bone marrow blasts at time of progression. Blood counts at diagnosis in the cohort included a median hemoglobin of 9.8 g/dL, platelets of 83 x 109/L, and white blood cell count of 2.1 x 109/L. Twenty-one (72%) of patients had normal cytogenetics. Nine (31%) patients had both a pathogenic mutation and a variant of uncertain significance (VUS) in DDX41, with the remaining 20 patients harboring only a pathogenic DDX41 mutation. Eight (27%) patients underwent germline testing, with 7 confirmed to harbor a germline DDX41m. In the deceased cohort, 9 (31%) patients underwent HSCT. Three of the patients with AML and 1 patient with MDS were observed and did not undergo treatment. Median overall survival of the deceased cohort was 29 months. The median time to AML progression in the group with MDS was 14 months. Causes of death included infection in 11 (38%) patients, 9 (31%) with disease progression/relapse, 3 (10%) with acute gastrointestinal graft versus host disease (GVHD), and 1 (3%) from cerebral bleed. The cause of death was unknown in the remaining 5 (17.2%) patients. Infections included pneumonia, bacteremia, neutropenic enterocolitis, fungal, and unknown etiology. Of the 4 patients who were observed, 2 died from unknown cause and 2 died from disease progression. Of the 16 patients with AML at time of death, 9 (56%) died from disease progression or relapse, 3 (19%) from infection, 2 (13%) from GVHD, and 2 (13%) from unknown causes. Of the 10 deaths in the MDS group, 7 (70%) were from infection, 1 (10%) from GVHD, 1 (10%) from cerebral bleed, and 1 (10%) from an unknown cause. Three cases of infection in the MDS group occurred during remission. Infection was a more common cause of death in the MDS group compared to the AML group, where disease progression prevailed as a cause of death (70% vs 19%, p=0.01). Eight (80%) of the patients with MDS who died from infection were neutropenic prior to death, and 4 (50%) of those patients were on neutropenic antimicrobial prophylaxis. Conclusions: In this cohort of 29 deceased patients with a DDX41-mutated myeloid neoplasm, we characterized causes of death. Disease progression/relapse was a significantly more common cause of death in those with AML, compared to infection in patients with MDS. Our work underscores the need for additional studies looking into non-leukemic causes of death in patients with DDX41m myeloid diseases and potential strategies to mitigate infection-related mortality in this population.

Abstract Background: Clonal cytopenia of undetermined significance (CCUS) is defined as clonal hematopoiesis in the absence of a hematologic neoplasm, along with unexplained cytopenia. While several studies have identified risk factors and developed scores to predict progression to overt myeloid neoplasms, the clinical and molecular features during the progression process remain poorly understood. Aim: Evaluate the clinical and clonal characteristics of patients with CCUS, with a focus on the longitudinal evolution of clonal and clinical parameters over time. Methods: After IRB approval, we retrospectively reviewed charts of patients with unexplained cytopenia (2015-2024), recording data at the time of CCUS diagnosis (WHO 2022 diagnostic criteria) and at time of follow-up bone marrow biopsy after diagnosis. Follow-up CBC and karyotype data were recorded for patients who had repeat bone marrow biopsies (n= 111), while follow-up clonal parameters and risk scores were calculated for those who underwent repeat NGS (n= 74). A reduction or expansion in clone size was defined as a change exceeding 5% (CE5%), or change exceeding 10% (CE10%) from the baseline value. Overall survival (OS) was calculated from diagnosis to last follow-up. For statistical analysis, we used BlueSky Statistics V10.3.1. Results: 214 CCUS patients (median age 73, 68% males) were included. At baseline, 30% of patients had abnormal cytogenetics, with del (20q) being the most common one (8%; n= 18), followed by trisomy 8 (6%; n= 13), and loss of chromosome Y (5%; n= 10). The median number of mutations was 2 (range, 1-5), with the most common mutations TET2 (38%), SRSF2 (21.5%), ASXL1 (21%), ZRSR2 (18.5%), DNMT3A (9.5%), and U2AF1 (9%). Most patients had high risk CHRS (60%), followed by intermediate (30%), and low risk (10%). On the other hand, 41% had high risk CCRS, 29% had intermediate risk, and 30% had low risk. After a median follow-up of 46 months, 62 patients died (median OS not reached). A decrease in the white blood cell (WBC) count from the time of diagnosis to follow-up was more frequently seen among CCUS patients who progressed to MN (70% vs 50%, p= 0.04), however, changes in hemoglobin and platelets did not differ between those who progressed and those who did not (p> 0.05). Although the frequency of abnormal karyotypes at diagnosis was similar between patients who eventually progressed (28%) and those who did not (31%) (p= 0.6), 4 (2%) patients with initially normal karyotypes acquired chromosomal abnormalities during follow-up, and all progressed to MDS. Among the 74 patients who had follow-up NGS, 31% acquired new mutations, clonal expansion of pre-existing mutations were seen in 54% using CE5% and 19% per CE10%, and 16% developed new variants of uncertain significance (VUS). Acquiring new pathogenic mutations was similar in patients who progressed to MN compared to those who did not progress (34% vs 28%, p= 0.6). On the other hand, clonal expansion was significantly more observed in patients who progressed compared to those who did not, using both CE5% (73% vs 31%, p = <0.001) and CE10% (27% vs 9%, p= 0.03). At follow-up, ASXL1 was the most commonly acquired mutation among patients who did not progress (4 cases), followed by TET2 (2 cases), and U2AF1, GATA2, DNMT3A, SF3B1, ZRSR2, TP53, and CBL (1 case each). On the other hand, SRSF2, SETBP1, CBL, JAK2, TET2, and RUNX1 were more frequently acquired among those who progressed to myeloid neoplasms (each appeared in 2 patients). When recalculating CCRS, CHRS, IPSS-M, and IPSS-R at follow-up for patients who had repeat NGS, there was no significant difference in score changes - either upward or downward - between those who progressed and those who did not (p> 0.05). Conclusion: In CCUS patients who progressed to myeloid neoplasms, WBC decline, clonal expansion (more frequent), and evolving chromosomal aberrations (less frequent) were observed, supporting the value of longitudinal genomic and clinical monitoring in CCUS.

Abstract Germline mutations in the RNA-helicase gene DDX41 cause predisposition to myeloid malignancies (MDS/AML) with a penetrance of 50% by age 90. DDX41 germline mutations are heterozygous and predominantly truncating variants, indicative of loss-of-function. More than half of DDX41-mutated carriers that develop MDS/AML will acquire a second-hit mutation in the other allele of DDX41, frequently causing the amino acid substitution p.R525H. Single-cell analysis from a biallelic DDX41-mutated MDS patient showed that the p.R525H mutation was highly enriched in dendritic cells (DCs) but less frequent in other cell types. We hypothesized that p.R525H causes the hematopoietic stem and progenitor cells (HSPCs) to differentiate preferentially into DC. To precisely model the germline of DDX41-mut patients, we generated human induced pluripotent stem cells (iPSC) with a frameshift mutation in exon 6 of one allele of DDX41, modeling the most common germline mutation. We attempted to modify the other allele of DDX41 to express the p.R525H mutation but could not derive viable cells. To circumvent potential lethality of the acquired mutation, we inserted a Doxycycline (DOX)-inducible wild-type DDX41 expression cassette in the AAVS1 safe harbor locus. Then we modified the endogenous allele to cause the p.R525H mutation in trans to the existing frameshift mutation. In this manner, we derived iPSCs that would model the most common configuration of DDX41 mutations (DDX41R525H/-) upon the withdrawal of DOX from the culture. In undifferentiated iPSC cultures, we observed profound defects in cell proliferation and survival upon DOX withdrawal. To determine the effect of the p.R525H mutation on hematopoietic cells, we differentiated the iPSCs into CD34+ HSPCs in the presence of DOX, and then withdrew DOX and studied the effect of the DDX41R525H/- genotype on HSPC function. In colony formation assays, DDX41R525H/- cells produced fewer and smaller myeloid and erythroid colonies after DOX withdrawal. In liquid culture, DDX41R525H/- cells showed cell cycle arrest by EdU incorporation assay and protein synthesis deficit by HPG assay. Thus, we conclude that DDX41 is required for proliferation and survival in iPSC and hematopoietic progenitor cells and that p.R525H lacks the essential function. Next, we tracked HSPC differentiation in liquid culture containing Flt3 ligand, stem cell factor and thrombopoietin with or without GM-CSF. Identification of DC subsets by flow cytometry was based on the literature (Sontag S, et al. Stem Cells 2017;35(4)). We observed reduced overall differentiation in DDX41R525H/- cultures, evidenced by maintenance of CD34 positivity. However, among the CD45+CD34- cells, DDX41R525H/- cells were 3-4 fold more likely to be identified as plasmacytoid DC (pDC) compared to control conditions (+DOX or DDX41+/- cells). Notably, in DDX41R525H/- CD45+CD34- cells, overall CD123 and CD304 expression were profoundly upregulated and CD11c was downregulated, indicative of increased pDC character. We used a similar DOX-inducible approach to generate Molm13 human AML cell line with DDX41R525H/- and homozygous knockout (DDX41-/-) genotype and found that these cells had profound survival defects. Both genotypes exhibited DC-like morphological change with extended multiple projections upon DOX withdrawal. In flow cytometry analysis, both genotypes exhibited upregulated Clec9a (conventional DC1 (cDC1) marker) and Clec10a and CD1c (cDC2 marker) upon DOX withdrawal. DDX41R525H/- cells specifically exhibited pDC features shown by upregulated CD123 by flow cytometry and increased IRF7 by western blotting, while DDX41-/- had decreased IRF7. Furthermore, we found that DDX41R525H/- cells specifically showed increased IRF9 and phosphorylated STAT1 and STAT2, which are downstream of interferon receptor activation, indicating that type-I interferon produced by DDX41R525H/- pDC activates interferon signaling in autocrine/paracrine manner. These results indicate that p.R525H promotes differentiation into pDC, which is not observed in DDX41-/- cells. In conclusion, DDX41 p.R525H mutation has bimodal functions in HSPC: loss-of-function for proliferation/survival and gain-of-function for skewed differentiation into pDC. Dysregulated DCs may contribute to the pathogenesis of DDX41-mutated MDS/AML, particularly in light of recent descriptions of AML with pDC differentiation and the broader role of DC dysregulation in MDS/AML.

Abstract Somatic mutations in hematopoietic stem and progenitor cells (clonal hematopoiesis) are known to alter the immune milieu and can result in autoimmune disorders including VEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) syndrome. There are currently no curative strategies for CH-linked autoimmune disorders besides allogenic hematopoietic stem cell transplantation. Recent work has shown a high prevalence of autoimmune syndromes among patients with IDH1/2 mutant myeloid neoplasms (MN). We thus hypothesized that IDH1/2-mutant CH might drive a subset of autoimmune disorders. To further characterize a possible association between IDH-mutant CH and autoimmune disease, we used data from two observational cohort studies, the UK Biobank (N=454,218) and All of Us (N=414,830). We observed 264 individuals with IDH1/2-mutant CH. IDH1/2 CH was associated with autoimmune disease (OR=1.8, p=4e-3), and, when compared to other CH genes with at least 100 carriers, showed the strongest effect size. When comparing autoimmune subtypes, we observed significant associations with polymyalgia rheumatica (OR=4.0, p=1e-3) and giant cell arteritis (OR=8.1, p=1e-6). IDH1/2 CH carriers had elevated CRP levels compared to other CH-carriers (p=1e-2) and non-carriers (p=8e-3). IDH1/2 CH was associated with lower neutrophil counts and higher monocyte counts. While most (68%) had blood counts outside the normal range, only a minority (11%) had severe cytopenias that met criteria for CCUS. Since IDH1/2 CH is associated with both autoimmune disease and blood count abnormalities, we sought to define the frequency, clinical presentation, and outcomes of IDH1/2-associated autoimmune disease among individuals with bone marrow biopsy confirmed CCUS. We used data from three CCUS cohorts: first, a multi-institutional cohort of CCUS patients with systemic autoinflammatory disease (SAID) who were UBA1-negative, second, a hospital-based cohort at Mayo Clinic, and third, a cohort of IDH1 carriers enrolled on a phase II clinical trial of ivosidenib (NCT05030441). Within 193 SAID patients who were free of myeloid neoplasm at the time of recruitment, IDH1/2 pathogenic variants were the most observed CH driver, occurring in 2% of individuals. These individuals (N=4) all had recurrent fevers and dermatologic manifestations, requiring chronic glucocorticoid treatment with 75% having inflammatory arthritis requiring multiple Disease-Modifying Antirheumatic Drugs (range 1-7, median=5). Within the Mayo Clinic cohort, 275 patients with CCUS were serially ascertained. Among those 8 (2.9%) were IDH1-mutant of whom 50% had autoimmune disease (three with seronegative rheumatoid arthritis and one with Sweet syndrome). At last follow up (median 16 months), 2 (25%) of 8 patients had progressed to MN. Within our open-label decentralized trial of ivosidenib (IDH1 inhibitor) in CCUS, we enrolled 20 patients, of whom 5 (25%) had a diverse array of pre-existing autoimmune disorders, including two cases of seronegative rheumatoid arthritis and one case each of Sweet syndrome, polymyalgia rheumatica, and Sjögren's syndrome. Underlying the clinical presentation of all five cases was episodic joint pain, with half also experiencing episodic dermatologic manifestations. The majority (58%, 11/19) of the IDH1mt-CCUS patients had an elevated hsCRP (>=5; range 6.91–46.2) including all four with co-occurring autoimmune disorders (range 7.97–46.2). Out of the 20 enrolled patients, 17 received at least 8 weeks of therapy, of which 9 had elevated hsCRP at baseline. Most of these (7/9) had normalization of hsCRP (falling below 5 mg/L) while on treatment (median time to hsCRP normalization of 58 days). Among the four patients with autoimmune disease, all had subjective improvement in their autoimmune symptoms following treatment with ivosidenib. In conclusion, we show that IDH1/2 CH is associated with autoimmune disorders and is particularly enriched among IDH1/2 CH carriers with co-occurring cytopenias. IDH1/2-associated autoimmune disease can range from classic rheumatic conditions such as rheumatoid arthritis to more severe VEXAS like presentations. IDH inhibition demonstrates efficacy for improving inflammatory manifestations within an ongoing clinical trial. Together these results nominate IDH mutant CH as a driver of autoimmune diseases with therapeutic implications.

Abstract Background: TP53-mutated (TP53mut) myeloid neoplasms (MN) are a biologically and clinically distinct subgroup of blood cancers associated with extremely poor outcomes and limited response to conventional therapies. In some patients, MN are preceded by clonal cytopenia of undetermined significance (CCUS). Prior cytotoxic exposure (treatment related, TR) is an independent predictor for survival in CCUS (Li et al, Blood Adv. 2024). As TP53mut CCUS and MN are enriched in TR cases, the interaction between cytotoxic exposure and TP53mut status on the risk of progression and survival remains unclear. Methods: Adult patients with CCUS who were evaluated at the Mayo Clinic or South Australian myelodysplastic syndrome (MDS) Registry (Adelaide, Australia) were included. CCUS and MDS were defined according to the 5th edition of the WHO classification for MN (Khoury et al, 2022), except for the exclusion of cases harboring MDS-defining cytogenetics. Next-generation sequencing was performed using a targeted panel covering genes commonly mutated in MN. In cases with >1 TP53mut, VAFs were summed. Survival outcomes were assessed by Kaplan-Meier with log-rank testing. Univariate and multivariate analyses were estimated using Cox proportional hazards regression. Results: Of 320 CCUS cases, 50 (15.6%) harbored TP53mut (TP53mut CCUS), whereas 270 (84.4%) were wild-type (TP53wt CCUS). Median age at diagnosis was 71 years (range 16-99). TP53mut CCUS had a greater proportion of females (60% vs 33.7%, p<0.001) and TR (66% vs 23%, p<0.001) compared to TP53wt. Hematologic parameters including hemoglobin, red cell distribution width, mean corpuscular volume, white blood count, absolute neutrophil count, platelets, and bone marrow blasts were comparable between the two groups. Almost all TP53mut (n=48, 96%) were located in the DNA-binding domain and the median variant allele frequency (VAF) was 9% (range 2-46%). Five (10%) cases harbored 2 TP53mut. The distribution of TP53mut VAF among patients was as follows: ≤2.5% (n=2), 2.5-5% (n=10), 5-10% (n=19), 10-20% (n=11), and ≥20% (n=7). The proportion of cases with cytogenetic abnormalities was smaller in TP53mut compared to TP53wt CCUS(12% vs 25.9%, p=0.035). Both cohorts had a comparable median number of mutations: 2 (range 0-7) in TP53mut and 2 (range 0-5) in TP53wt. The most common co-mutations in TP53mut CCUS were TET2 (n=8, 17.8%), PPMD1 (n=7, 15.6%), DNMT3A (n=6, 13.3%), ASXL1 (n=6, 13.3%), and SRSF2 (n=4, 8.9%). At last follow up, the rate of progression was comparable between TP53mut and TP53wt CCUS (12% vs 22%, p=0.13). Median time to MN progression was not reached in TP53mut and 6.25 months in TP53wt CCUS (p=0.5197). A significantly higher proportion of TP53mut cases acquired complex cytogenetics compared to TP53wt cases (33% vs 2%, p=0.024) at MN progression. Of 20 deaths observed in the TP53mut cohort, non-myeloid hematologic malignancies (n=6, 30%), infections (n=5, 25%), and TP53mut MN (n=4, 20%) were the 3 most common causes. With a median follow-up of 4 years (IQR 1.2-4.8), median OS was longer in de novo (dn) cases (8.7 years for dn TP53wt; not reached for dn TP53mut) and shorter in TR cases (3.3 years for TR TP53wt; 4.8 years for TR TP53mut). Notably, TP53mut showed no independent prognostic impact in the entire cohort, or when stratified by TR vs dn CCUS. On multivariate analysis that included TP53mut status, factors independently associated with inferior OS included prior therapy (HR 2.21, 95% CI 1.41-3.45, p<0.001), anemia (HR 4.1, 95% CI 1.88-8.99, p<0.001), and thrombocytopenia (HR 2.38, 95% CI 1.43-3.95, p<0.001). Similarly, TR CCUS (HR 1.6, 95% CI 1.06-2.4, p=0.03) and anemia (HR 2.15, 95% CI 1.25-3.7, p=0.006) were independently associated with inferior progression free survival. Conclusion: TP53 mut in CCUS did not independently predict inferior survival or increase leukemic transformation. While TP53mut CCUS were less likely to harbor cytogenetic abnormalities at diagnosis, significantly more cases harbored genomic instability at leukemic transformation. The poor outcomes attributed to TP53mut CCUS were driven by prior cytotoxic exposure, cytopenia – particularly anemia, and non-leukemic causes of death. These findings suggest risk stratification in CCUS should prioritize clinical context over TP53mut status alone.

Abstract Background: Germline predisposition states (GPS), including inherited bone marrow failure syndromes (IBMFS) are seen in 5-10% of individuals with myeloid neoplasms (MN). Given overlap with somatic driver genes, blood, saliva, and buccal swabs are suboptimal specimens for GPS testing in MN; the latter two due to contamination with blood cells(Jerez, 2024). Skin biopsy with fibroblast culture-derived DNA remains the gold standard, but the process is expensive, takes 6-8 weeks to complete, and fibroblast culture failure can occur in some patients with telomere biology disorders. Given the need to rapidly screen donors for HSCT and adjust therapy/conditioning in certain IBMFS, we developed a rapid hematologic germline testing algorithm using hair follicle-derived DNA. Methods The study was conducted after IRB approval through the Mayo Clinic GPS/IBMFS clinic. To perform PCR-based hair follicle testing, we obtained 15-25 hair follicles (bulbs) per patient. The bulbs were placed in a microcentrifuge tube and subjected to a 24-hour digestion and extraction protocol using a modified version of the QIAGEN DNA Purification from Dried Blood Spots protocol. DNA quality was assessed by Nanodrop and Qubit.Testing included either validation of known or suspected germline variants (e.g., RUNX1, DDX41, ETV6), or panel testing (e.g., GPS or IBMFS). Pathogenic variants were validated by repeat testing in a CAP/CLIA certified lab prior to medical decision making. 23 patients underwent whole exome sequencing (WES) in a CAP/CLIA lab, and 13 patients had concurrent germline testing using alternate DNA sources (8 skin biopsies, 1 saliva, 4 buccal swabs). Results Ninety-three patients (49 male, 53%) underwent hair follicle-derived germline DNA testing (median age 63 years). Indications for germline testing included the presence of a suspected variant on somatic testing with variant allele frequency (VAF) between 35%-60% ( n= 66, 71%), patient age <50 years (n=26, 28%), antecedent thrombocytopenia (n=15, 16%), presence of syndromic features (n=4, 4%), patient history of multiple malignancies (n=4, 4%), and positive family history (n=15, 16%). Time to reporting variants after receipt of hair follicle-derived DNA was <14 days. There were zero complications associated with the procedure. DNA quality as assessed by Nanodrop revealed a median nucleic acid concentration of 25.64 ng/μL. The median A260/A280 ratio was 1.86 (range 0.701-2.133) and the median A260/A230 ratio was 1.27 (range -8.193-9.223). DNA quality was insufficient for chromosomal microarray (CMA) assessments. Of 93 patients evaluated, 67 (72%) had ≥1 germline variant, with 3 having >1 germline variant for a total of 72 variants. Pathogenic/likely pathogenic variants identified included: DDX41 (30, 41.7%), TP53 (4, 5.6%), ANKRD26 (4, 5.6%), RUNX1 (4, 5.6%), GATA2 (3, 4.2%), TERT (3, 4.2%), JAK3 (2, 2.8%), SAMD9/SAMD9L (2, 2.8%), ATM (2, 2.8%), and 1 each (1.4%) in BCL2, BCOR, BPGM, CDKN2A, CEBPA, CHEK2, CSF3R, CXCR4, DNMT3A, ETV6, GATA1, MPL, MPO, POT1, PTPN11, RPL5, and SH2B3. In the 13 patients that had concurrent germline testing, results were identical in all cases, except for 1 false negative in a buccal specimen (PTPN11) and 1 case of germline mosaicism, where the TP53 variant was identified in the blood and hair follicle DNA but not in skin fibroblast DNA. After testing, 30 (44.7%) patients had a change in their management plan: 8 (27%) with DDX41-GPS were observed due to known latency of DDX41-mutant MN, 6 (20%) were referred for HSCT based on the germline variant (CEBPA, DDX41, GATA1, GATA2, RPL5, TP53), 6 (20%) were placed on an enhanced surveillance plan for cancer screening (1 ANKRD26, 3 TERT, 2 TP53), 4 (13%) patients undergoing HSCT had related donors removed from consideration as they were carriers (2 DDX41, 1 ANKRD26, and 1 SAMD9), 2 (7%) patients with neutropenia and underlying germline variants (1 ATM, 1 DDX41) had G-CSF therapy discontinued due to concerns for clonal stimulation, and 1 (3%) patient with a germline CDKN2A mutation (hematological diagnosis- CMML) was recommended to avoid radiation therapy for prostate cancer. Conclusion In summary, we validate a rapid and simple hair follicle-derived DNA based germline assessment for patients with hematological disorders and demonstrate a positive impact on clinical care in 44% of patients. We are currently optimizing DNA quality so that germline copy number alterations can be better detected using CMA.

Abstract Heterozygous germline variants of DDX41 occur in 2-4% of adult Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML) cases, making them the most prevalent cause of inherited predisposition to these diseases. Homozygous deleterious variants are never observed in the germline, and loss of both DDX41 alleles causes apoptosis of proliferative cells, consistent with essentiality. Most disease-associated germline variants cause loss of full-length protein expression (truncating). However, 30-40% are missense (non-truncating) and their role in disease risk compared to truncating variants remains in question. Previous reports have shown that both truncating and non-truncating Pathogenic/Likely Pathogenic (P/LP) variants (defined by ACMG scoring) are associated with DDX41-specific disease features, including co-mutation of the contralateral allele of DDX41. In contrast, variants of unknown significance (VUS) are less associated with these features. Acquired co-mutations of DDX41, of which p.R525H accounts for 50-70%, are restricted to DDX41-mutated patients and are always missense. Our previous studies indicated that p.R525H lacks the essential DDX41 function and cannot support hematopoietic progenitor proliferation. However, the frequency with which this mutation occurs and the absence of acquired truncating mutations suggest that p.R525H has a specific effect on DDX41 function that is distinct from complete loss and promotes pathogenesis specifically in the context of existing P/LP DDX41 mutation. To understand how germline non-truncating variants predispose to disease, we characterized the effect of six recurrent non-truncating P/LP variants (p.G173R, p.R219H, p.P258L, p.Y259C, p.K331del, and p.I396T) and three VUS (p.K9E, p.Y33H, and p.M155H) on DDX41 function. We utilized a genetic complementation approach in murine lineage-negative (Linneg) bone marrow cells with inducible deletion of DDX41. We found that all non-truncating P/LP and VUS forms of DDX41 could fully rescue the colony forming potential of Ddx41-deficient cells to a similar level as wild-type protein, whereas the p.R525H variant completely failed to rescue. To determine the effect of the non-truncating variants on DDX41 function at endogenous expression levels, we utilized CRISPR to modify the DDX41 alleles in MOLM13 human AML cells. We produced viable, proliferating cell lines with homozygous mutations for all 3 VUS and 4/6 P/LP variants. For p.P258L and p.K331del, like p.R525H, we could not produce homozygous mutant cell lines despite screening hundreds of clones and finding several with heterozygosity. To further study the P/LP variants that were functional in the cell line, we generated C57Bl/6 mouse lines harboring p.G173R, p.Y259C, and p.I396T mutations in the endogenous Ddx41 alleles. Heterozygous mutant mice were phenotypically normal in all three strains. However, we could not obtain homozygous mutant mice for p.G173R or p.Y259C, indicating these cannot support embryonic/fetal development. In contrast, p.I396T-homozygous mutant mice were born at Mendelian ratios and were phenotypically normal until at least 15 months of age. Since p.R525H mutation is common in patients with non-truncating P/LP variants, we sought to model the combined effect of these mutations. We utilized the Linneg cells with inducible knockout of Ddx41, co-expressed each non-truncating variant with p.R525H by viral transduction, and monitored the colony formation potential. Remarkably, cultures expressing P/LP variants or M155I combined with p.R525H had dramatically reduced colony formation, while wild-type DDX41 and the other 2 VUS supported normal colony formation when co-expressed with p.R525H. Thus, we conclude p.R525H has a dominant-negative effect on certain non-truncating DDX41 variants. This is consistent with the emerging idea that the presence of an acquired hotspot DDX41 co-mutation is sufficient to classify a non-truncating DDX41 variant as pathogenic.Our results demonstrate that many DDX41 missense variants retain protein function when overexpressed. However, at endogenous expression levels, some P/LP variants are unable to support cell proliferation, indicative of hypomorphic effects on protein function. In patients, acquisition of the p.R525H mutation in the contralateral allele disrupts the functionality of P/LP variants through dominant-negative effects, leading to hematopoietic progenitor defects that are hallmark of the DDX41 pathogenesis.

Abstract BACKGROUND Ivosidenib is an oral inhibitor of mutant isocitrate dehydrogenase type I (IDH1) currently approved for the treatment of IDH1 mutated acute myeloid leukemia and myelodysplastic syndrome (MDS). Hematopoietic stem and progenitor cells carrying preleukemic mutations, referred to as clonal hematopoiesis (CH), are the origin of myeloid neoplasms (MN). Individuals who have cytopenias and CH, but do not meet diagnostic criteria for a hematologic malignancy, are classified as having Clonal Cytopenias of Undetermined Significance (CCUS), a condition associated with a high risk of progression to MN. While CCUS patients (pts) can have multiple mutations, they show lower mutational burden on average compared to MN. Thus, we hypothesized that treatment with ivosidenib would improve cytopenias in IDH1-mutant CCUS. METHODS; We performed a decentralized phase II single-arm study to characterize the safety and efficacy of ivosidenib in IDH1-mutant CCUS (NCT0503044). Drug was shipped to pts with local oncologists performing standard-of-care clinical exams supplemented by study team lead interviews for adverse event monitoring. Research labs were drawn by local providers or through Quest. QT corrected interval (QTc) was monitored through a mobile electrocardiogram device (AliveCor). Eligible patients were aged ≥ 18 years and had confirmed IDH1-mutant CCUS with at least 6 months of unexplained cytopenias (hemoglobin<10 g/dL, platelets<100 x109/L or absolute neutrophil count <1.8 x109/L). The primary endpoint was hematologic response of at least 8 weeks in duration based on the IWG 2006 criteria for MDS. RESULTS 20 pts with IDH1-mutant CCUS have been enrolled. Most were male (70%) with a median age of 66 (range 41-79). Overall, 74% had a self-reported race of non-Hispanic white, 11% of Hispanic white, 5% of Asian and 11% of black or African American. Most pts presented with neutropenia (95%) including some with co-occurring thrombocytopenia (21%). One pt presented with anemia and thrombocytopenia without neutropenia. Prior to treatment, the average number of co-mutations beyond IDH1 was 2 (range 0-3), with most pts (74%) harboring a co-occurring spliceosome gene mutation. The IDH1 variant allele fraction (VAF) was lower in the blood (mean=19%, range 3-35%) than in the bone marrow (mean=31%, range 18-43%) in most (93%) patients. Out of the 20 enrolled pts, 17 received at least 8 weeks of therapy at the time of our data cutoff (7/29/2025) and were included in the efficacy analysis. Grade ≥3 adverse events (AEs) occurred in five patients (26%) including two with grade ≥3 treatment-related adverse events (pancytopenia and sepsis in the first pt, rash in the second pt). The most common all-grade treatment-related adverse events were nausea (n=5, 26%), prolonged QTc (n=3, 16%), anemia (n=3, 16%), and diarrhea (n=3, 16%). There were no instances of reported differentiation syndrome. Overall, 82% of pts achieved a hematologic response (14/17) including improvement in neutropenia (88%) and thrombocytopenia (75%). With a median follow-up of 16 months (range 0.6-24 months), the median duration of hematologic response was not reached. Among responders, 86% had a continued response at one year. Two pts progressed to MDS after 4 and 17 months of treatment characterized by recurrence of cytopenias and the emergence of new clones. A surveillance bone marrow biopsy was performed at 18 cycles for the 8 pts who remained on treatment with none showing disease progression. Most pts (90%, N=9/10) treated for at least 12 months had a decrease in IDH1-mutant CH VAF over time and 40% (N=4/10) showed IDH1 mutation clearance (VAF <2%) with a median time to clearance of 9 months. Among those with decreasing IDH1 clonal burden, all had a corresponding decrease in other co-occurring mutations present at baseline with one responder showing emergence of a newly detectable CHEK2 mutation without disease progression. CONCLUSIONS Decentralized trials represent a feasible solution for the conduct of clinical trials in rare hematologic neoplasms and precursor conditions. Ivosidenib was well-tolerated and induced durable hematologic remissions in IDH1-mutant CCUS. Most pts showed a reduction in clonal burden with mutation clearance commonly seen with long-term treatment demonstrating that ivosidenib modifies the natural history of IDH1-mutant CCUS.

Abstract Introduction: TERT promoter (pTERT) variants are among the most frequent genetic alterations in human cancers, where they drive oncogenesis through telomerase reactivation. However, somatic, pathogenic pTERT variants have also been seen in non-cancerous conditions such as telomere biology disorders (TBD), where they attempt to rescue the bone marrow failure phenotype (adaptive compensation). We conducted this study to assess the phenotype and outcomes of pTERT mutations in TBD patients. Methods: After IRB approval, the Mayo Clinic institutional TBD database was queried to identify all patients with somatic pTERT mutations. We have designed a customized error corrected sequencing panel that covers somatic mutations (52 genes) associated with adaptive and maladaptive outcomes in TBD patients. This covers the promoter region for TERT and can detect variants down to 0.5% variant allele fraction (VAF) with 10,000 X sequencing depth. Clinical data was retrospectively abstracted. Results: We identified 7 pTERT variants (3 hotspots) in 6 (two females (33%), mean age 61 years, 4 alive). The three hotspots were: (1) c.-57A>C (2 individuals, mean VAF 17.1%; range 11.6%-22.6%), (2) c.-124C>T (4 individuals, mean VAF 12.9%; range 1.9%-41.3%), and (3) c.-146C>T (1 individual, VAF 1.2%). One individual had both the c.-124C>T (VAF 41.3%) and the c.-146C>T somatic pTERT variants, occurring in the context of a germline TERT variant. The median VAF for all 7 pTERT variants was 6.1% (range 1.2%-41.3%). The hotspot, c.-57A>C, occurred in the context of pathogenic germline TERT (VAF 49.9%) variants with pathogenic somatic co-variants in PPM1D (avg. VAF 1.5%). The second hotspot, c.-124C>T, occurred in the context of germline TERT (avg. VAF 49.6%) and RTEL1 (VAF 47.3%) variants with pathogenic somatic co-variants including ASXL1 (VAF 1%), DNMT3A (VAF 8%), and PPM1D (VAF 4%). Five of six assessable patients with pTERT variants had shortened telomere lengths (TL), with results pending for one individual. Among those with the c.-57A>C variant, granulocyte TLs were at or below the 10th percentile, while lymphocyte TLs were below the 10th percentile in one patient and below the 1st percentile in another. For those with the c.-124C>T variant, all granulocyte TLs were below the 1st percentile. Lymphocyte TLs in this group included one at the 10th percentile and two at or below the 1st percentile. The median follow up for all patients was 2 years. Hotspot 1 (c.-57A>C) variants were associated with normocellular bone marrow biopsies with one patient having normal blood counts and the other having chronic macrocytic anemia (grade 2) and thrombocytopenia (< grade 1). In patients with hotspot 2 and 3 somatic variants, bone marrow cellularity ranged from 15–50% (1 patient had grade 2-3 hypocellularity), with normal bone marrow morphology, except for polytypic plasma cells (10–15%) identified in a patient with IgG kappa multiple myeloma (currently MRD negative on maintenance therapy). This patient also had a history of head and neck cancer and follicular lymphoma. Of these four patients, only one had normal blood counts (co-occurring c.-146C>T variant); the rest had cytopenias (n=3, the worst being grade 2 thrombocytopenia), progressive macrocytosis (n=3), or eosinophilia (n=1). Comorbidities encountered in these patients included myasthenia gravis (1), hypogonadism (1), and sarcoidosis (1). Moreover, four patients (2 each for hotspots 1 and 2) presented with idiopathic pulmonary fibrosis, while liver fibrosis was seen in 4 patients (also 2 each for hotspots 1 and 2). At last follow up, none of these patients had documented progression to myelodysplastic syndrome or acute myeloid leukemia. Conclusions: We describe the spectrum and clinical features of somatic pTERT mutations in TBD patients. pTERT mutations involved the following hotspot regions, c.-124C>T, c.-146C>T, and c.-57A>C, and co-occurred with other somatic variants (i.e., PPM1D and DNMT3A). None of the 6 patients with pTERT mutations had a severe bone marrow failure phenotype or developed myeloid neoplasms at last follow up, exemplifying a unique mechanism of adaptive somatic rescue.