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Background The prevalence and impact of right ventricular dysfunction (RVD) in degenerative mitral regurgitation (DMR) is unknown. We aimed to determine whether RVD assessed by echocardiography in routine clinical practice is independently associated with mortality in patients with DMR. Methods and Results We used data from the MIDA‐Q (Mitral Regurgitation International DAtabase‐Quantitative) registry, which included patients with isolated DMR due to mitral valve prolapse from January 2003 to January 2020 from 5 tertiary centers across North America, Europe, and the Middle East. A cohort of 2917 (mean age: 66 years, 70.8% male patients, follow‐up: 5.2 [3.3–8.3] years) consecutive patients with severe DMR was included and long‐term mortality was analyzed. RVD, identified in 426 (14.6%) patients, was associated with reduced 8‐year survival (55%±3% versus 77%±1%; P <0.001), overall and in all subgroups of patients, even after comprehensive adjustment including left ventricular dilatation and dysfunction, DMR severity, pulmonary pressures, and surgery (adjusted hazard ratio, 1.44 [95% CI, 1.17–1.77]; P <0.001). This excess mortality was observed under medical management (adjusted hazard ratio, 1.57 [95% CI, 1.20–2.05]; P =0.001) and after surgical correction of mitral regurgitation (adjusted hazard ratio, 1.45 [95% CI, 1.02–2.05]; P =0.039). Patients with RVD undergoing surgery within 3 months of diagnosis experienced a better 8‐year survival (73%±4% versus 43%±4%; P <0.001), even after adjustment (adjusted hazard ratio, 0.44 [95% CI, 0.29–0.67]; P <0.001) despite an increase of 1‐month postoperative mortality (7.1% versus 0.5% for patients without RVD; P <0.001). Conclusions RVD is observed in 14.6% of severe DMR and exhibits a powerful and independent association with excess mortality partially attenuated by mitral surgery. Therefore, assessment of right ventricular systolic function should be included in routine DMR evaluation and in the clinical decision‐making process.

Abstract The interactions between transcription factors (TFs) and the target genes could provide a basis for constructing gene regulatory networks (GRNs) for mechanistic understanding of various biological complex processes. From gene expression data, particularly single-cell transcriptomic data containing rich cell-to-cell variations, it is highly desirable to infer TF–gene interactions (TGIs) using deep learning technologies. Numerous models or software including deep learning–based algorithms have been designed to identify transcriptional regulatory relationships between TFs and the downstream genes. However, these methods do not significantly improve predictions of TGIs due to some limitations regarding constructing underlying interactive structures linking regulatory components. In this study, we introduce a deep learning framework, DeepTGI, that encodes gene expression profiles from single-cell and/or bulk transcriptomic data and predicts TGIs with high accuracy. Our approach could fuse the features extracted from Auto-encoder with self-attention mechanism and other networks and could transform multihead attention modules to define representative features. By comparing it with other models or methods, DeepTGI exhibits its superiority to identify more potential TGIs and to reconstruct the GRNs and, therefore, could provide broader perspectives for discovery of more biological meaningful TGIs and for understanding transcriptional gene regulatory mechanisms.

Introduction: The prognosis for CLL/SLL has improved with the advent of novel therapeutic classes, including BTKis. While comparative data for several BTKis have been published, there are limited data on patient preferences in BTKi treatment selection. Understanding and integrating patient perspective in the BTKi treatment selection process is crucial to shared decision-making and attaining optimal treatment outcomes. To understand patients' priorities for different treatment attributes that impact their treatment decisions, a comprehensive quantitative analysis of patient preferences on BTKi treatment attributes was conducted. Methods: A patient survey with a discrete-choice experiment (DCE) design was conducted from March to June 2024 among USA adults (≥18 years) with confirmed diagnosis of CLL/SLL, recruited through online patient panels, physician referrals, and support groups. BTKi treatment attributes were selected based on results of a targeted literature review and clinical inputs. Patients responded to DCE questions on attributes related to efficacy, safety (eg, impacts of diarrhea, headache, atrial fibrillation, and hypertension on quality of life [QoL]), formulation type, and dosing frequency. The impact of adverse events (AEs) on QoL was defined as the extent to which AEs caused interruptions in patients' ability to engage in their usual day-to-day activities. A conditional logistic regression model was used to calculate the relative importance of each attribute, as well as patient willingness to trade off specified BTKi treatment attributes. Results: A total of 200 patients with CLL/SLL completed the survey (median age: 61 years; 78% White; 55% female; 60% commercially insured; 82% suburban/urban residence). Less than half (43%) were diagnosed ≥5 years ago, and 61% received ≥3 lines of therapy. Almost all (89%) patients reported having experienced ≥1 AE from treatment previously, with the most common AEs being fatigue (76%), diarrhea (51%), headache (51%), and nausea and/or vomiting (51%). When considering the importance of efficacy measures, most patients prioritized CLL/SLL treatments that extended life expectancy (93%), followed by those that increased the likelihood of remission or cure (84%) and those that paused the progression of disease (67%). Patients preferred treatments with higher efficacy, less impact of AEs on QoL, and lower dosing frequency (P&lt;.001). The top 3 treatment attributes with the highest relative importance to patients were impact of atrial fibrillation on QoL (24%), progression-free survival (PFS; 19%), and impact of headache on QoL (18%), followed by impact of diarrhea (14%) and hypertension (14%) on QoL, dosing frequency (9%), and formulation type (3%). On average, patients were willing to accept a reduction of 2.6, 1.9, 1.4, and 1.4 years of PFS to receive a treatment with less (none or mild vs significant) impact of atrial fibrillation, headache, diarrhea, and hypertension on QoL, respectively. Patients were willing to accept a reduction of 1.0 year of PFS to receive once-daily vs twice-daily treatment. Conclusions: Findings from this patient preference survey suggested that impact of atrial fibrillation on QoL, PFS, and impact of headache on QoL were the most important attributes of BTKi treatment for patients with CLL/SLL in the USA. Shared decision-making in CLL/SLL treatment selection should include an informed discussion about AEs, as besides efficacy comparisons, patients may prefer treatments with less impact of AEs on their QoL. Future prospective studies evaluating the effects of shared treatment decision-making on treatment adherence and outcomes are needed to better understand their impact on CLL/SLL patient care and inform clinical practice.

Multiple myeloma (MM), an incurable hematologic malignancy, presents significant challenges in managing its recurrence. The bone marrow tumor microenvironment (BM-TME) is critical to MM progression. However, classical immune checkpoint blockade (ICB) therapies, like anti-PD1, have shown limited efficacy in MM. Therefore, elucidating the compositional features and regulatory mechanisms of the TIME in MM is crucial for developing novel immunotherapeutic targets. Tissue-resident memory CD8+ T cells (CD8+ TRMs) reside indefinitely at multiple anatomical locations like the skin, intestine, and bone marrow, functioning as frontline responders against reencountered pathogens and tumors. Whether CD8+ TRMs within BM-TME are involved in the MM cell immune escape and pathogenesis has not been systematically elucidated. Firstly, we leverage single-cell RNA sequencing (scRNA-seq) to dissect the BM CD8+ T cells across patients at different stages of MM, and identify that CD69+CD8+ T subsets were BM residents, and the proportion of BM CD8+ TRMs between health donors and MM patients was comparable. Moreover, our findings indicated that BM CD8+ TRMs exhibit exhausted features and enrichment of NK genes with MM progresses. Importantly, we observed a considerable elevation of the NK gene KLRB1 and its encoded protein CD161 in BM CD8+ TRMs in MM patients. Immunofluorescence labeling of BM biopsy samples from MM patients confirmed the infiltration of the BM-TME with CD3+CD8+CD69+CD161+ cells. Then, we found that KLRB1 expression in BM CD8+ TRMs was higher than that of other classical inhibitory receptor genes (e.g., PDCD1, CTLA4, LAG3), and CLEC2D (encodes the ligand of CD161) was also markedly expressed in patients' MM cells, exhibiting considerably higher than classical immunosuppressive receptor ligand genes (e.g., PDL1, CD80, CD86). Moreover, patients with higher CLEC2D expression had unfavorable overall survival. We further found that the CD161 expression was higher in CD69+CD8+ TRMs compared to circulating CD69-CD8+ T cells, and the percentage of BM CD161+CD8+ TRMs in MM patients was significantly higher than in healthy donors, while there was no difference for PD-1, LAG3, and TIM3 expression. Notably, only a small fraction of BM CD8+ TRMs have mucosal-associated invariant T cell phenotypes (identified by CD161+TCR-Vα7.2+). Additionally, the CLEC2D expression of BM cells was analyzed, and the highest level of CLEC2D expression was observed in B cells from MM patients, followed by plasma cells. Importantly, CLEC2D expression in MM patients was significantly higher than in plasma cells from healthy donors. Next, to investigate whether the blockade of CD161 could restore the function of CD8+ TRMs, the primary BM cells from MM patients were isolated and stimulated ex vivo. Compared to the anti-PD-1 and isotype group, CD161 blocking presents enhanced CD8+ TRMs proliferation and cytokine secretion levels (TNF-α, IFN-γ, IL2), increasing MM cells apoptosis. Chimeric antigen receptor T (CAR-T) cell therapy has achieved impressive success in treating relapsed/refractory MM. How to prevent CAR-T cell exhaustion and enhance function remains a significant challenge. Therefore, we next set out to investigate the impact of CD161 on CAR-T cells. Our results demonstrated that CD161 was highly expressed in early peripheral blood (PB) CAR-T cells after infusion in MM patients but decreased with time. Moreover, the CD161 expression of CAR-T cells was considerably higher than endogenous T cells. Notably, BM-derived CAR-T cells have higher CD161 expression than PB counterparts for the same patient, suggesting CD161 may have BM-specific expression enrichment. After co-culturing MM and CAR-T cells in vitro for 24 hours, we found that blocking CD161 led to an augmented proportion of CAR-T cells, increased IFN-γ secretion, and a notable elevation in tumor cell apoptosis compared to the anti-PD-1 and isotype groups. Taken together, we demonstrated that CD8+ TRMs constitute a vital anti-tumor cell subset in the MM BM-TME, which exhibits a high expression of the inhibitory CD161 receptor, binding to the CLEC2D expressed by MM cells, thereby mediating the dysfunction of CD8+ TRMs. Blocking the CD161-CLEC2D pathway is expected to become a novel target for MM immunotherapy. The combination of CD161 inhibitors and CAR-T cell therapy can potentially enhance the anti-myeloma function of CAR-T cells.

Background: Immune dysfunction is a hallmark of chronic lymphocytic leukemia (CLL), and several studies suggest that hypogammaglobulinemia at the time of CLL diagnosis may predict shorter time to first therapy (TTFT; Parikh et al, 2015). However, it is unclear if hypogammaglobulinemia can predict TTFT independent of the CLL-International Prognostic Index (CLL-IPI) and the tumor mutational load (TML). We sought to determine if serum immunoglobulin (Ig) levels at diagnosis can independently predict outcomes in patients with CLL and its precursor, high-count monoclonal B-cell lymphocytosis (MBL). Methods: We used the Mayo Clinic CLL Database to identify newly diagnosed CLL/MBL consented within 2 years of diagnosis. Next generation sequencing (NGS) was performed using a 59 gene panel (SureSelect) to detect mutated CLL genes. Serum Ig levels were quantitated by radial immunodiffusion (Immunoplates). Serum Ig levels below the lower limit of normal were defined as hypogammaglobulinemia. We used Chi-squared or Fisher's exact tests to compare discrete variables and the Kruskal Wallis test for continuous variables. TTFT was calculated from date of diagnosis to date of first treatment or date last known to be untreated. We used Cox regression models to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for TTFT and overall survival (OS) associations. Results: We identified 895 newly diagnosed patients (588 CLL and 307 MBL) who had undergone NGS for recurrent somatic mutations and had serum Ig levels available at the time of diagnosis. The median absolute B-cell count was 6.7 x109/L; 613 (69%) were male, 375 (42%) had unmutated IGHV genes, and 81 (9%) had TP53 disruption. Based on CLL-IPI, 412 (46%) patients had low risk, 285 (32%) had intermediate risk, and 198 (22%) had high/very high risk. The most commonly mutated genes were NOTCH1 (14%), SF3B1 (11%), TP53 (10%), NFKBIE (8%), ATM (6%), and BIRC3 (6%). Based on the number of genes with high impact or hotspot mutations, we classified 40%, 29%, and 31% patients with TML scores of 0, 1, or 2+, respectively. At CLL/MBL diagnosis, the median serum IgG, IgA, and IgM was 891 mg/dL (111-2620), 121 mg/dL (1-1150), and 44 mg/dL (5-1320), respectively; 284 (32%) patients had low serum IgG, 128 (17%) had low serum IgA, and 322 (42%) had low serum IgM. Low serum IgA was associated with mutations in NOTCH1, SF3B1, ATM, BIRC3 and NFKBIE, low IgM was associated with SF3B1 and BIRC3 mutations (all comparisons, P &lt; .05), and low IgG was associated with BIRC3 mutation (P = .05). The median follow-up for the cohort was 8.4 years. A total of 359 patients progressed requiring therapy (299 CLL and 60 MBL), and 265 patients died (177 CLL and 88 MBL). The TTFT was significantly shorter for patients with low serum IgG compared to normal serum IgG at diagnosis (median 4.4 vs 10.8 years) and similar findings were observed in individuals with low serum IgA (1.7 vs 10.8 years) and those with low serum IgM (4.6 vs 11.1 years). On univariable analysis, the following were associated with a shorter TTFT: low serum IgG (HR: 1.8, 95% CI 1.4-2.2), low serum IgA (HR: 3.5, 95% CI 2.7-4.4), low serum IgM (HR: 1.9, 95% CI 1.5-2.3), TML score of 1 (HR: 1.7, 95% CI 1.3-2.2), TML of 2+ (HR: 4.4, 95% CI 3.4-5.7), CLL-IPI intermediate risk (HR: 3.7, 95% CI 2.8-4.8), and CLL-IPI high/very high risk (HR: 7.6, 95% CI 5.8-10.1) (all comparisons, P &lt; .0001). In multivariable analyses after adjusting for CLL-IPI and TML, low serum levels of IgG (HR: 1.8, 95% CI: 1.5-2.3), IgA (HR: 2.4, 95% CI: 1.8-3.0), and IgM (HR: 1.8, 95% CI: 1.5-2.3) were independently associated with a shorter TTFT (all comparisons, P &lt; .0001). No significant differences in OS were detected between patients with low and normal serum IgG, IgM, and IgA on univariate analysis. Similar results for TTFT and OS were observed after adding clonal B-cell count to the Cox model. Conclusions: Our study shows that low serum Ig levels at the time of initial diagnosis is predictive of TTFT independently of the CLL-IPI and TML, which can further risk stratify individuals with newly diagnosed CLL/MBL. Additionally, low serum IgA, IgM, and IgG levels at diagnosis are significantly associated with specific somatic mutations in individuals with newly diagnosed CLL/MBL.

Background: Multiple myeloma (MM) is an incurable plasma cell malignancy with several recurrent primary cytogenetic abnormalities including t(11,14)(q13;q32), resulting in increased expression of CCND1. Although 40% of patients with t(11;14) MM respond favorably to the BCL-2 inhibitor venetoclax (ven), 60% fail to achieve an objective response. Previous studies have suggested upregulation of PMAIP1, encoding the pro-apoptotic NOXA protein, in association with ven sensitivity (Leblay, Blood, 2024). Here we sought to evaluate the role for NOXA in ven response in t(11;14) MM. Methods: We analyzed whole exome, whole genome and RNA sequencing data of CD138+ tumor cells from 1,359 patients with MM in the CoMMpass and Mayo Clinic cohorts. The histone mark H3K27ac was assessed in t(11;14)+ KMS12PE and U266B1 human myeloma cell lines using ChIP-seq. Gene expression and protein levels of PMAIP1 (NOXA) were also detected by qRT-PCR and Western blot, respectively. Live cell detection was evaluated by Annexin V and PI using flow cytometry and by YoYo3 dye using IncuCyte following treatment with ven. Results: The t(11;14) MM subtype was associated with a 1.6-5.5-fold increased expression of PMAIP1 compared to non-t(11,14) MM in the CoMMpass and Mayo Clinic cohorts (p&lt;0.0001). These findings are consistent with a significant correlation between CCND1 and PMAIP1 expression in both cohorts (p&lt;0.001). To evaluate whether cyclin D1 is directly associated with increasing expression of PMAIP1 in t(11;14) MM, we generated a cyclin D1 knock out (KO) version of the U266B1 line using CRISPR/cas9. Two independent U266B1 KO cell lines showed reduced expression of PMAIP1 and NOXA protein compared to the WT U266B1 consistent with a role for cyclin D1 in regulating PMAIP1 expression. In addition, the KO lines had a 4.8-fold reduced H3K27ac signal at the PMAIP1 locus in comparison to the WT control suggesting a role for cyclin D1 in promoting H3K27ac. We previously observed increased expression of CCND1 in association with the G allele compared to the A allele of rs9344 in both the CoMMpass and Mayo Clinic cohorts (Leukemia, in press). We next asked whether the G risk allele of rs9344 within CCND1 impacted gene expression and H3k27ac levels at the PMAIP1 locus. To study the allele specific effect of CCND1, we used the CRISPR/cas9 edited KMS12PE WT (rs9344 AA) and Knock In (KI) (rs9344 GG) cell lines. In the KI cells, the G allele was accompanied by an ~2-fold increased expression of PMAIP1 and NOXA protein detected by western blot (&lt;0.05). Increased PMAIP1 expression in KI lines was also accompanied by a 2.2-fold increased H3K27ac further suggesting a role for the G allele of rs9344 in promoting H3K27ac and gene expression at the PMAIP1 locus. Finally, we evaluated the consequence of PMAIP1 expression levels in relation to ven response. Increased expression of PMAIP1 and elevated levels of NOXA protein in the KMS12PE KI lines was associated with increased sensitivity to ven resulting in ~50% increase in cell death of KI vs. WT lines (p&lt;0.02). Conclusion: We demonstrate a role for cyclin D1 in regulating PMAIP1 expression through H3K27ac resulting in increased NOXA protein. Levels of NOXA are associated with the G allele of rs9344 and increased venetoclax response.

Introduction: ASXL1-mutant Chronic Myelomonocytic Leukemia (CMML) is a high-risk myeloid neoplasm characterized by epigenetic remodeling and overexpression of leukemogenic driver genes. DLK1 (delta-like homolog 1) is a non-canonical Notch ligand, crucial for the proliferation of early hematopoietic progenitor cells and its expression is controlled by maternal imprinting. DLK1 expression is restricted to select progenitor populations, but was found to be overexpressed in several malignancies including ASXL1-mutant CMML. Here we investigate the molecular mechanisms that drive the aberrant re-expression of DLK1 and postulate potential targeted therapeutic interventions. Methods: We performed bulk RNA- and ChIP-seq (H3K4me1/3, H3K27ac/me3, H2AK119ub, H2BK20ac) on bone marrow mononuclear cells from 20 patients with CMML (11 ASXL1-mutant, 9 -wildtype). All libraries were sequenced on an Illumina NovaSeq instrument. Differential gene expression and histone modification occupancy between ASXL1-mutant and -wildtype patients were assessed. Single-cell RNA-seq was performed for a subset of patients to investigate the cell populations of interest for DLK1 expression. To assess DLK1 allelic expression, we identified a single nucleotide polymorphism (SNP) in the coding region of DLK1 (rs1802710) and used cases which were confirmed heterozygous by Sanger sequencing. DLK1 transcript levels were quantified by RT-PCR, and the relative abundance of alleles was measured using digital droplet PCR. We designed primers to amplify the region around our SNP of interest and utilized high mismatch discrimination locked nucleic acid (LNA) probes labeled with FAM (reference SNP allele) and HEX (alternate SNP allele) to quantify specific alleles. The number of RNA molecules originating from each allele was quantified by counting the number of droplets that fluoresced with the corresponding probe colors. Illumina 850K EPIC microarrays were used to evaluate DNA methylation. Drug studies were carried out in progenitor colony forming assays derived from ASXL1-mutant patients (bone marrow mononuclear cells) with the dual BRD4 and p300 / CBP inhibitor EP31670 (62 nM, 24-hour exposure), quantifying DLK1 expression by real-time RT-PCR. Results: This study included 20 patients with CMML (median age at diagnosis 74 years). All ASXL1 mutations were typical hotspot mutations (most commonly Gly646Trpfs*12) and the variant allele frequencies were compatible with heterozygosity (median 0.41). The spectrum of co-mutations was typical and included TET2 (23%), SRSF2 (16%), CBL (7%), among others. DLK1 was strongly overexpressed in ASXL1-mutant patients (log2 fold-change +4.0, FDR &lt; 0.001). Allele-specific gene expression studies (n = 3) revealed the re-expression of the imprinted maternal DLK1 allele in ASXL1-mutant patients. Single-cell gene expression studies (n = 5) demonstrated that the DLK1 overexpression is restricted to the hematopoietic progenitor cell population. Differential methylation analysis between patients with ASXL1-mutant clonal hematopoiesis (n = 4) and matched controls (n = 8) identified two hypermethylated CpG islands in the DLK1 promoter region (cg18122767, Δß = +8.6%, p = 0.021 and cg15831296, Δß = +5.8%, p = 0.008). Histone modification analysis identified DLK1 as a p300 target gene by mapping H2BK20ac onto established ASXL1-mutant-specific enhancer regions (H3K4me1 + H3K27ac co-occupancy). The distal enhancer EH38D2760182 was predicted to bind p300 and to govern the expression of DLK1. ChIP-seq experiment in K-562 and Kasumi-1 cells showed the binding of BRD4 and p300 to EH38D2760182, respectively. Targeting BRD4 and p300 using EP31670 led to the downregulation of DLK1 expression (mean fold-change = 0.569, p &lt; 0.001, n = 3) in progenitor colony forming assays. Conclusions: We observed the aberrant re-expression of the maternally imprinted DLK1 allele in patients with ASXL1-mutant CMML. Both DLK1 promoter hypermethylation and the genotype-specific activation of enhancers by p300 were identified as putative regulatory mechanisms. The distal enhancer EH38D2760182 was found to bind BRD4 and p300 and the pharmacologic disruption of BRD4 / p300 activity in model systems led to the downregulation of DLK1. The clinical-grade dual inhibitor of BRD and CBP / p300 EP31670 is currently being investigated in patients with ASXL1-mutant chronic myeloid neoplasms (NCT05488548).

Introduction: Cyclin D1, encoded by the CCND1 gene, is primarily known as a major regulator of cell cycle progression. Emerging studies have demonstrated a role for cyclin D1 in regulating gene transcription. In mantle cell lymphoma with t(11;14), cyclin D1 strongly binds to the promoters of highly transcribed genes and its overexpression led to genome-wide transcriptional downregulation. However, the transcriptional role for cyclin D1 in t(11;14) MM remains undefined. This study aims to elucidate the global chromatin and transcriptional changes induced by cyclin D1 in t(11;14) MM. Methods: Knockout (KO) of CCND1 in U266B1, a MM cell line carrying t(11;14), was performed by the Synthego (Redwood City, CA) using CRISPR/Cas9, which generated a frameshift insertion of base pair (bp) “A” after 69,641,478 bp within exon 1. Two independent KO clones were used for downstream analysis. ChIP-seq and ATAC-seq were performed for KO (n=2) and wild-type clones (WT, n=2). ChIP-seq used antibodies against H3K4me3 (promoter) and H3K4me1 and H3K27ac (enhancer). Libraries were sequenced to 2x51 bp on the Illumina NextSeq 2000 platform. Total RNA libraries (in triplicate) were sequenced to 2x150 bp. ChIP-seq and ATAC-seq reads were mapped to hg38 with BWA, and peaks were identified by MACS2 at FDR 0.01. RNA-seq reads were mapped to hg38 with STAR and gene raw counts were estimated using featureCounts. Differential peaks and differentially expressed genes between KO and WT were identified using edgeR at FDR 0.05 and fold-change 2. Only peaks present in at least 2 samples and genes having reads-per-million value 0.1 in at least 1 sample were included, excluding those from chrY. Pathway analysis was performed with the Enrichr package. Results: Differential expression analysis identified 2-fold more genes that were down-regulated than up-regulated in KO compared to WT (467 vs. 233). Pathway analysis revealed an enrichment of TNF-alpha signaling via NF-kappaB, inflammatory response, and apoptosis in association with down-regulated genes, while up-regulated genes are enriched in myogenesis, KRAS signaling, and epithelial mesenchymal transition pathway. In parallel, differential chromatin analysis identified 2.5% (1,161) of the peaks from H3K27ac and 0.5-1% (359-610) of the peaks for the other 3 marks that showed significant changes of signal levels between KO and WT. For the promoter mark H3K4me3, there are largely a comparable number of peaks showing increased (191 peaks) and decreased (168 peaks) signals, respectively, in KO compared to WT. However, for ATAC-seq and H3K4me1, about 70% of the differential peaks showed an increased signal in KO, in contrast with H3K27ac for which 60% of differential peaks showed decreased signal in KO. The preferential loss of H3K27ac occupancy is consistent with the observation of a higher proportion of genes being down-regulated in KO. These results indicated that knockout of CCND1 led to a global increase of chromatin accessibility, but a reduction of H3K27ac and gene expression. Further annotation revealed that, for H3K27ac and H3K4me1/ATAC-seq, 92% and 97% of the differential peaks were located &gt;2kb away from the transcription start sites (TSSs) of expressed genes. Even for H3K4me3, 88% of the differential peaks are &gt;2kb away from TSSs. The results suggest that the changes of chromatin upon CCND1 knockout predominantly occurred at distal regulatory regions. For up- and down-regulated genes, we estimated ChIP-seq and ATAC-seq signals in the TSS 2kb regions, revealing that up-regulated genes were overall associated with increased signals. Further analysis found that, for ATAC-seq and H3K4me3, 44% and 59% of the differential peaks located in the promoter regions were associated with differentially expressed genes, which dropped to ~20% for the two enhancer marks. These data indicate that changes in chromatin state impact the expression of the associated genes. Conclusion: Knockout of CCND1 impacts local chromatin state, particularly at enhancer regions, and the transcriptional program. In promoter-proximal regulatory regions, the changes of chromatin accessibility and H3K4me3 are strongly correlated with the expression changes of nearby genes. Further studies will identify the genes targeted by the differential enhancers and their possible roles in MM pathogenesis mediated by cyclin D1 following the t(11;14) event.

Introduction Patients with lower-risk (LR) myelodysplastic syndrome (MDS) and chronic myelomonocytic leukemia (CMML) experience shortened survival and significant unmet medical need due to limited disease-modifying treatments. The NLRP3 pathway is activated in hematopoietic stem and progenitor cells and in the marrow microenvironment in myeloid neoplasms, contributing to ineffective hematopoiesis and clonal progression. DFV890, a small molecule NLRP3 inhibitor, blocks IL-1β and IL-18 secretion and pyroptotic cell death. Thus, DFV890 may disrupt the smoldering inflammation and provide disease-modifying benefits to patients by restoring normal hematopoiesis and suppressing clonal myeloproliferation. Methods This open-label, phase 1b, multicenter study evaluates DFV890 in patients with very low, low, or intermediate risk MDS per revised International Prognostic Scoring System (IPSS-R) criteria and low or intermediate-1 risk CMML per CMML-specific Prognostic Scoring System (CPSS) criteria (NCT05552469). The study comprises 2 parts: dose optimization and dose expansion. Eligible patients ≥18 years, with ECOG performance status ≤2, carrying a diagnosis of (a) IPSS-R-defined LR-MDS or (b) CPSS-defined LR-CMML, and have failed to respond to or not tolerated established first-line therapies as defined in the protocol. Key exclusion criteria include previous treatment with agents targeting the NLRP3 inflammasome and IL-1 pathway. DFV890 is administered orally twice daily (BID) for a minimum of 24 weeks (6 cycles of treatment) until treatment discontinuation. In the dose-optimization part, patients are randomized to receive either low- or high-dose, stratified by indication. Primary objectives are to assess safety and tolerability and determine the optimal for DFV890. Secondary objectives include assessment of pharmacokinetics, and evaluation of preliminary efficacy of DFV890 based on hematologic improvement (Garcia-Manero, Blood 2023). Exploratory objectives include assessment of peripheral cytokines and genetic alterations in blood and bone marrow, and patient-reported symptoms. Results As of April 15, 2024, 39 patients (median age, 74 years) with a median of 2 prior lines of therapy (range: 1-5) were treated with DFV890 in the dose-optimization part. Based on an 8-week screening period, 8 patients (20.5%) were RBC transfusion independent at baseline. Eighteen patients received low dose (17 with LR-MDS; 1 with LR-CMML), and 21 patients received high dose (18 with LR-MDS; 3 with LR-CMML). At data cutoff, 10 (25.6%) patients had discontinued treatment. Median duration of exposure was 10.7 weeks (range, 0.6-42.0 weeks). Adverse events (AEs) leading to study drug discontinuation were only reported in the high dose arm (2 patients, grade ≥3 neutropenia, n=1 and blood bilirubin increased, n=1). Treatment-related AEs (TRAEs) were reported in 10 patients (25.6%), with 4 (10.3%) experiencing grade ≥3 TRAEs (anemia [n=2], neutropenia, and rash [n=1 each]). No serious AEs related to DFV890 were reported. Peripheral cytokines were assessed as a marker of preliminary activity. Decrease in plasma IL-18 and IL-1RA levels observed in most patients, with a higher frequency in the low dose arm (IL-18 decreased in 8/8 patients in low dose arm vs. 4/7 in high dose arm; IL-1RA in 7/8 vs. 5/7), potentially due to less frequent dose interruptions. Changes in serum IL-6 levels were more heterogeneous; notably, among the patients with complete mutation and biomarker data, both patients with mutations in TET2 showed dramatic decreases in serum IL-6; IL-18 and IL-1RA also decreased in those patients. In addition, out of 8 patients who were transfusion-independent at baseline, 6 reported an increase in hemoglobin with treatment, 4 of whom with an increment &gt;10% from baseline. Updated data including hematologic response assessment according to IWG will be presented at the meeting. Conclusions Preliminary findings from this ongoing study show a favorable safety profile in patients with LR-MDS and LR-CMML, in line with prior human studies with DFV890. Analysis of peripheral cytokines and hematologic parameters showed early indications of activity in a subset of patients, particularly those with mutations in TET2 and those transfusion independent at baseline. These findings will require confirmation with longer follow-up and in the dose expansion phase of the study.