Citations

Abstract Introduction Surface proteins in cancer not only reflect tumor–microenvironment interactions but also serve as targets for diagnostic flow cytometry and precision therapies, including monoclonal antibodies and CAR-T cell therapies. A better understanding of plasma cell immunophenotypes could inform flow cytometric prognostic assays and development of targeted therapies. Methods RNA-seq and Seq-FISH data from CD138-enriched bone marrow plasma cells, along with corresponding clinical annotations, were obtained from the Multiple Myeloma Research Foundation-CoMMpass Study. A curated list of surface genes was assembled by integrating three sources: the Human Protein Atlas (plasma membrane and cell junction annotations), the Gene-Set Enrichment Analysis membrane-associated gene set (Ontology:0016020), and the Cell Surface Protein Atlas (validated high-confidence category). A total of 4,579 genes coding for cell surface proteins were identified. Genes below the 25th variance percentile were removed. PCA (≥90% variance) followed by k-means (k=2, silhouette) and confirmed by hierarchical clustering. A Plasma Cell Maturity (PBM) score was computed using singscore on 84 mature plasma cell–associated genes to compare cluster phenotypes. Pathway analysis was done using GSEA software for Hallmark pathways. Clinical biomarkers and survival kinetics were compared between the clusters. Results 761 newly diagnosed patients were included. (Age: 27-93 years, median overall survival/OS: 29 months/mo). Clustering revealed two groups which we termed Atypical/Aggressive Cluster 1 (C1, n=105, 13.8%) and Classical Cluster 2 (C2, n=656, 86.2%), based on the patterns and clinical characteristics. Among non-missing cases, high-risk disease per the International Myeloma Society–International Myeloma Working Group (IMS–IMWG) definition was observed in 27.7% of patients in C2 (n = 552) and 24.7% in C1 (n = 90) (p = 0.4).C1 exhibited enrichment for t(14;16)-MAF (OR = 2.6, 95% CI: 1.1–6.1, p = 0.04) and t(11;14)-CCND1 (OR = 1.7, CI: 1.01–2.8, p = 0.04). In contrast, hyperdiploidy was more common in C2 (OR for C1 = 0.6, CI: 0.4–0.9, p = 0.04). Elevated LDH was observed in C1 (OR = 2.6, CI: 1.6–4, p < 0.001). Median serum Beta-2 microglobulin was lower in C1.(p=0.009) Upregulated genes in C1 in decreasing order of log Fold Change(logFC): AHNAK, MT-ND1, EEF2, EZR, HLA-B, TXNIP, HLA-E, TRIB1, MCL1, RHOB, CD74, CFLAR, HLA-A, HERPUD1, RPSA, ERN1, HSP90AB1, RAPGEF2, ADGRE5, and LAPTM5. Downregulated genes in C1 in descending order of |logFC|: B2M, SDC1 (CD138), HSP90B1, SEL1L, CALR, CANX, PECAM1, SLAMF7, STT3A, TNFRSF17 (BCMA), FCRL5, STT3B, PALM2AKAP2, CD53, PARP1, CCR2, RPN1, CD38, EDNRB, and LMAN2. Upregulated pathways in C1: proliferation (MYC, E2F, PI3K/AKT/mTOR, KRAS, Wnt); evasion of apoptosis (p53, TGF-β, Notch, NF-κB, IL6/JAK/STAT3); Epithelial to Mesenchymal Transition (angiogenesis, apical junction); inflammatory (interferon, TNF-α, complement, IL2/STAT5); metabolic reprogramming (oxidative phosphorylation, lipid/cholesterol); and stress (DNA repair, unfolded protein response). The PBM score for C1 was significantly lower, suggesting a less differentiated phenotype. C1 patients had inferior survival (n = 93, median OS 43.9 mo, p = 0.04) compared to those in the C2 cluster (n = 559, median OS 102.5 mo). Patients in the C1 + IMS–IMWG high-risk status had the shortest survival (20.7 mo), compared to C1+low (50 mo), C2/high (68.3 mo), and C2+low (not reached). In a multivariable analysis, C1 status (HR = 1.93; 95% CI: 1.1–3.4, p = 0.02) was an independent predictor, along with older age (1.05), UAMS70 (1.02), EMC-92 (1.4). In C1, early (<18 mo) progression occurred in 76.3% (n=71) (p < 0.001). In patients receiving first line of treatment(LOT1), median PFS was 39.7 mo in C1vs. 47.3 mo in C2 (p=0.8). Among patients who received stem cell transplant in LOT1, the median survival for the C2 was 102.5 mo, compared to 44.5 mo for C1 (n = 52) (p = 0.01). Among non-SCT patients on Immunomodulator + Proteasome Inhibitor therapy, C1 (n=28) had shorter survival of 50.0 vs. 71.7 C2 (n=137; p =0.8). Conclusion Our transcriptomic analysis identified a higher-risk group of patients (C1) exhibiting downregulation of myeloma specific markers (CD38, CD138, BCMA, SLAMF7, FCRL5) and inferior outcomes. It is important to diagnose and find appropriate therapy for these patients as they don't obtain the same benefit from the current standard of therapy as the remaining patients.

Abstract Background: Partial tandem duplications of the histone methyltransferase KMT2Agene(KMT2A-PTD) are the most common KMT2A-aberration in adult acute myeloid leukemia (AML). KMT2A-PTD AML represents a high-risk disease subset with a poor prognosis. However, KMT2A-PTD leukemia is under studied, likely due to a lack of experimental models, and therefore the underlying mechanisms of leukemogenesis remain elusive. Since KMT2A-PTD leukemias possess high-level expression of HOXAgenes, similar to KMT2A-rearranged (KMT2A-r) and NPM1c AML, patients with this type of AML are currently enrolled into several phase I/II trials assessing menin inhibitors (MIs). However, mechanistic or clinical evidence for treatment response is lacking. To date, no targeted therapeutic approaches for KMT2A-PTD leukemia are available. Results: To better understand KMT2A-PTD mediated leukemogenesis, we endogenously tagged the KMT2A-PTD or KMT2A-wildtype (WT) allele in EOL-1 cells with a dTAG that can be degraded with PROTACs. Targeted protein degradation showed that the KMT2A-PTD, but not the KMT2A-WT protein, is critical to maintain leukemia cell growth. We identified KMT2A-PTD specific genome-wide chromatin binding sites and direct target genes as assessed by changes in nascent RNA production that started to occur within 30 minutes of KMT2A-PTD degradation. KMT2A-PTD target genes identified in this study included HOXA9, HMX2, HMX3, CDKN2C, MYC and CDK6 among others. Having defined the KMT2A-PTD target gene program, we assessed the effect of MI on KMT2A-PTD function. In KMT2A-PTD cell lines, PDXs and cells from a published murine KMT2A-PTD/FLT3-ITD knockin model, we observed intrinsic resistance to revumenib characterized by retained chromatin binding of KMT2A-PTD, but not KMT2A-WT after MI treatment. We next defined critical domains for KMT2A-PTD function via a KMT2A domain scan. This revealed the CXXC domain and AT hooks as critical dependencies in EOL-1 cells. Overexpression of KMT2A or mutants with duplicated domains in 293T cells showed that a duplication of the CXXC domain or the AT hooks is sufficient to mediate retained KMT2A chromatin binding under MI. Therefore, the resistance to MIs is likely due to the duplicated protein of KMT2A subverting menin function at critical target loci. Given that KMT2A-PTD remains chromatin-bound upon menin inhibition, we focused on ENL as a potential regulator of leukemia gene expression programs. In KMT2A-r and NPM1c leukemia, the ENL protein has been shown to be a critical dependency as it associates with acetyl lysine via its YEATS domain. ENL/AF9 YEATS inhibitors reverse ENL-dependent gene expression including HOXA9 and MYC. Using the small molecules TDI-11055 and TM-7, we show that YEATS inhibition leads to loss of members of the super-elongation complex and DOT1L from KMT2A-PTD driven loci and downregulation of target gene expression. Treatment of KMT2A-PTD PDXs with YEATS inhibitors induced differentiation and significantly reduced leukemia burden in vivo. Interestingly, we show that in contrast to previous findings in KMT2A-r leukemia, loss of ENL alone is insufficient to abrogate leukemic proliferation of EOL-1 cells. Instead, by combining ENL degradation with CRISPR-Cas9 mediated knockdown of AF9, we find that both YEATS proteins, ENL and its paralogue AF9, support aberrant gene expression in KMT2A-PTD leukemia. Finally, we show that the novel combination of MI and YEATS inhibition (revumenib plus TDI-11055) synergistically affects proliferation and induces differentiation in cell line and PDX models of KMT2A-PTD leukemia, which in turn prolongs survival of mice with KMT2A-PTD leukemia. Conclusions: KMT2A-PTD leukemia is dependent on the mutated, but not the WT KMT2A allele. It is characterized by a relative, intrinsic resistance to MI monotherapy, which is mediated by a duplication of the CXXC domain and AT hooks of KMT2A. Targeting both, the ENL and AF9 YEATS domain, is a possible treatment strategy and when combined with revumenib, YEATS inhibition has synergistic effects and overcomes intrinsic MI resistance. However, based on our studies, MI monotherapy may not be effective for most patients with KMT2A-PTD leukemia. Given that numerous compounds targeting the ENL (and AF9) YEATS domain are under study and MIs have recently obtained FDA approval, the combination of MI and YEATS inhibition could be translated into clinical trials for patients with KMT2A-PTD leukemia in the relatively near future.

Abstract Background Secondary central nervous system lymphoma (SCNSL) is a rare but significant complication, affecting approximately 2–10% of patients with diffuse large B-cell lymphoma (DLBCL), often leading to poor outcomes. The CNS-International Prognostic Index (CNS-IPI) remains a widely adopted tool for estimating CNS relapse risk; however, recent advances in molecular profiling and evolving treatment paradigms have challenged the adequacy of CNS-IPI alone in guiding risk assessment. This study evaluates the prognostic relevance of CNS-IPI in conjunction with molecular and clinical factors, specifically cell-of-origin (COO), gene expression, and frontline treatment regimens. The aim is to refine risk stratification and identify patients at highest risk for SCNSL. Method Building on our previous study, we analyzed data from patients with newly diagnosed DLBCL between 2002 and 2023, enrolled in the Mayo Clinic/University of Iowa Lymphoma Molecular Epidemiology Resource. Patients with primary CNS lymphoma, CNS involvement at diagnosis, or who received CNS-directed therapy were excluded. COO was determined using the Hans algorithm and/or Nanostring profiling. Multivariate cause-specific Cox regression models were used to estimate hazard ratios (HR) and 95% confidence intervals (CIs) for predictors of CNS relapse that were measured at the time of initial DLBCL diagnosis. Cumulative incidence with competing risks and cause-specific Cox models were used to analyze relapse risk. Result We included 2137 patients in our analysis, median age at diagnosis was 63 (IQR 53-72), with 41.6% (n=890) females. The albumin level was below normal in 32.5% (n=350), 64.0% (n=1367) had CNS-IPI of intermediate/high, 37.5% (n=586) had non-germinal center B-cell (GCB) COO, and 14.5% (n=309) were double expressor positive. At a median follow-up of 83 months (IQR 42 -143), 82 (3.8%) SCNSL relapses were observed; the 3 and 5 yrs cumulative incidence for SCNSL from time of DLBCL diagnosis were 3.7% (95% CI 3.0-4.7) and 3.8% (95% CI 3.1-4.8) respectively. In models accounting for death as a competing risk, the 5-year cumulative SCNSL incidence estimate for patients with a CNS-IPI low was 1.5% (95% CI 0.8-2.7), Intermediate was 4.9% (95% CI 3.7-6.4), and high was 6.1% (95% CI 3.8-9.6). The 5-year cumulative SCNSL incidence estimate for patients with non-GCB COO was 5.2% (95% CI 3.6-7.4) compared to 2.4% (95% CI 1.6-3.6; p=0.001) for GCB patients, and the 5-year cumulative SCNSL incidence for double expressor positive patients was 8.6% (95% 5.8-12.6) compared to 1.5% (95% CI 0.8-2.7; p<0.001) for double expressor negative patients. In a multivariable model (including CNS-IPI, COO, double expressor, treatment group, extranodal involvement, and albumin group), CNS-IPI intermediate (HR 2.85 [1.58-5.14]; p<0.001) and high (HR 4.31 [2.15-8.65]; p<0.001), non-GCB COO (HR 2.36 [1.37-4.06]; p=0.002], double expressor (HR 5.56 [2.88-10.73]; p<0.001), and below normal albumin (HR 1.89 [1.02-3.50]; p=0.042) were independently associated with increased risk of SCNSL. The majority of the SCNSL relapse occurred within the first 2 years after DLBCL diagnosis; 81.7% (n=67), with only 6.1% (n=5) occurring after 5 years. For patients who developed SCNSL, the median OS from the time of SCNSL diagnosis was 24 months (95% CI 17-34), with 5 years OS of 31% (95% CI 22-43). These findings are being validated using an external, international cohort, and final analysis will be presented at the time of presentation at ASH. Conclusion In this large, prospectively followed cohort with long-term follow-up data, SCNSL remains a rare but devastating complication of DLBCL, with a 5-year cumulative incidence of 3.8% and it is associated with very poor long-term survival. While CNS-IPI remains a strong predictor of SCNSL risk, our study identifies non-GCB COO and double expressor phenotype as independent, additive molecular risk factors. These findings suggest that current risk stratification tools may underestimate the risk of CNS relapse in molecularly defined high-risk subgroups. Considering the poor outcomes linked to SCNSL and the absence of a connection with frontline treatment types, future research should aim to enhance risk prediction models through molecular profiling and explore prophylactic strategies to reduce the likelihood of SCNSL.

Abstract Anaplastic large cell lymphomas (ALCLs) are CD30+ T-cell lymphomas that share pathologic features but differ in presentation, outcome, and genetics. Current classification incorporates clinical presentation and anaplastic lymphoma kinase (ALK) status but inadequately addresses molecular heterogeneity and therapeutic vulnerabilities. We studied 689 patients with ALCL in the LLMPP (Lymphoma/Leukemia Molecular Profiling Project) and performed expert consensus review, genetic subtyping (ALK, DUSP22, TP63, and triple negative), and immunohistochemistry for phosphorylated STAT3Tyr705. RNA sequencing with unsupervised gene expression profiling in 393 patients identified 2 main molecular types of ALCL that could be predicted with 91% accuracy based on the presence (type I) or absence (type II) of phosphorylated STAT3Y705 expression. Type I ALCLs included ALK+ ALCL and a subset of triple-negative ALCLs (TN-I); type II ALCLs included tumors with DUSP22 and/or TP63 rearrangements and the remaining triple-negative ALCLs (TN-II). Type I ALCLs were enriched for JAK-STAT3, whereas type II ALCLs were enriched for non–tyrosine kinase pathways, particularly epigenetic regulators such as EZH2. Immunohistochemistry showed overexpression of EZH2 and its trimethylated substrate H3K27. Prognosis in systemic ALCL was favorable for DUSP22-rearranged ALCL (5-year overall survival, 95%) and ALK+ ALCL (88%), intermediate for triple-negative ALCL (TN-I, 52% and TN-II, 37%), and poor for TP63-rearranged ALCL (0%). We introduce an integrated molecular classification that preserves currently diagnosed ALCL entities but identifies 4 molecularly distinct ALK− ALCL subtypes (DUSP22-rearranged, TP63-rearranged, TN-I, and TN-II). This classification can be easily implemented on paraffin tissue in routine practice or clinical trials, and stratifies ALCL into diagnostically, prognostically, biologically, and potentially therapeutically relevant subtypes.

ABSTRACT Thogotoviruses are arthropod-borne viruses belonging to the genus Thogotovirus within the family Orthomyxoviridae . Like other orthomyxoviruses, such as the influenza A viruses (IAV), thogotoviruses replicate in the nucleus. As a result, progeny viral ribonucleoprotein complexes (vRNPs) must be exported to the cytoplasm prior to virion assembly and budding at the plasma membrane. In IAV, this export depends on binding of the viral nuclear export protein (NEP) to the cellular exportin chromosomal maintenance 1 (CRM1). In contrast, the mechanism of vRNP nuclear export, including identification of a protein with NEP functionality, has not been characterized for any thogotoviruses. Here, we characterized vRNP nuclear export in Dhori virus (DHOV), a prototypic member of the Thogotovirus genus. DHOV replication and nuclear export of the viral nucleoprotein were inhibited by the canonical CRM1 inhibitor leptomycin B (LMB), suggesting that DHOV vRNP export also utilizes CRM1. Interestingly, LMB treatment led to nuclear retention of the DHOV matrix (M) protein in both infected and transfected cells. Using a mammalian two-hybrid system, we found that DHOV M interacts with CRM1 through a nuclear export sequence (NES) located between amino acids 111 and 128. Mutation of hydrophobic residues within this NES reduced M-CRM1 interaction, abolished the NES phenotype when fused to a fluorescent protein, and impaired rescue of recombinant DHOV by reverse genetics. Together, our results reveal that DHOV vRNP nuclear export is CRM1-dependent and mediated by the M protein rather than a dedicated NEP-like protein, providing the first mechanistic insight into vRNP egress in the genus Thogotovirus . IMPORTANCE Dhori virus (DHOV) is a pathogenic tick-borne virus in the genus Thogotovirus , in the family Orthomyxoviridae. Despite evidence of DHOV exposure in various mammals, including humans, its basic biology is not well understood. We investigated how DHOV’s progeny genome and protein complexes—viral ribonucleoprotein complexes (vRNPs)—are transported out of the nucleus. Our findings show that DHOV, like the influenza viruses, uses the cellular protein chromosomal maintenance protein 1 (CRM1) for vRNP export. We found that chemically inhibiting CRM1 completely blocked DHOV vRNP export, preventing the production of progeny viruses from infected cells. Screening of all known DHOV proteins revealed that the matrix protein, which forms the virus’ scaffold, interacted with CRM1, suggesting it may link CRM1 to the vRNPs. These results advance our understanding of DHOV replication and suggest that chemically inhibiting vRNP export could be a way to treat thogotovirus infections.

ABSTRACT Central venous catheters (CVCs) are a cornerstone of hematopoietic stem cell transplantation (HSCT), facilitating the delivery of chemotherapy, parenteral nutrition, medications, and blood products. Despite CVCs’ essential role, prolonged use can lead to complications such as increased risk of infection, thrombosis, mechanical issues, and psychosocial burden. However, the timing of CVC removal remains highly variable across institutions. Additionally, there are no standardized guidelines to balance the benefits of extended access against the risks of prolonged use. This narrative review examines the existing literature on CVC management post‐HSCT, highlighting key factors influencing the removal timing, such as patient characteristics, disease‐specific considerations, and institutional practices. The review emphasizes the urgent need for multi‐institutional research and standardized protocols to improve outcomes, reduce complications, and enhance the quality of care for HSCT patients.

Abstract BACKGROUND Gaseous hydrogen sulfide (H2S), a by-product of cysteine metabolism, inhibits cancer cell behavior and growth in glioblastoma (GBM) models. H2S production capacity (HPC) is decreased in human GBM specimens compared to non-tumor controls. Thus, boosting HPC is a novel strategy for GBM treatment. Suppression of thyroid hormone signaling increases production of H2S. Hypothesis: methimazole-induced hypothyroidism will increase tumor HPC to enhance chemotherapy efficacy in GBM. GOAL Proof of concept that methimazole, by reducing thyroid hormone signaling, can increase HPC in patients with recurrent/progressive GBM (rGBM). PRIMARY ENDPOINTS 10% increase in HPC and a 1.5-fold increase in peripheral blood sulfhydration signaling. METHODS This window of opportunity trial evaluates safety, HPC in plasma and tumor, and efficacy of methimazole + chemotherapy in patients with rGBM. rGBM patients planned for a resection begin methimazole 15 mg/d 5-7 days pre-op with investigator’s choice chemotherapy added 10-28 days post-op. Patients receive combination until progression. Pre- and post-op plasma and resected tumor tissue are assayed for HPC and proteins relevant to H2S production. Key eligibility: rGBM for whom a clinically-indicated resection is planned; normal thyroid function with no history of thyroid dysfunction. Patients may have received unlimited prior regimens including bevacizumab. RESULTS To date 15 patients (8 male), median age 56 years, enrolled. The trial was amended to increase methimazole to 25 mg/d; 3 patients have received this dose. Median TSH rose from 1.3 mU/ml to 20.5 at cycle 6. Free T3 and T4 did not fall significantly. Median plasma HPC rose 3-fold while tumor HPC did not rise significantly. No treatment-related grade 3-5 toxicities. Efficacy: PFS6 – 15% and OS12 – 21%. CONCLUSIONS Induction of subclinical hypothyroidism is feasible and safe in rGBM with significant increases in plasma but not tumor HPC. Further tumor correlative data for the dose-escalated methimazole will be presented.

Abstract This brief report details the initial findings from a Phase 1b/2 trial of TN-201, an adeno-associated virus serotype 9 (AAV9) gene therapy for MYBPC3-associated hypertrophic cardiomyopathy (HCM), a condition with significant morbidity, increased risk of mortality, and no approved therapy for the majority of patients. TN-201 was well tolerated, and changes to the management of potential immune responses resulted in a shorter period of immunosuppression. These results show consistent transduction and expression of TN-201 in cardiomyocytes, corresponding with increases in MyBP-C levels, reductions or stabilization of cardiac biomarkers, and reductions in key measures of left ventricular (LV) hypertrophy.

Abstract Background The associations between different types of diabetes, characterized by distinct pathophysiology and genetic architecture, and pancreatic ductal adenocarcinoma (PDAC) risk are not understood. Methods We investigated associations of genetic susceptibility to type 2 diabetes (T2D), 8 T2D mechanistic clusters, type 1 diabetes (T1D), and maturity-onset diabetes of the young (MODY) with PDAC risk. We used genome-wide association study (GWAS) summary-level statistics for T2D (242 283 cases, 1 569 734 controls), T1D (18 942 cases, 501 638 controls), and PDAC (10 244 cases and 360 535 controls) in individuals of European ancestry. Results Two-sample Mendelian randomization (MR) using the Robust Adjusted Profile Score (MR-RAPS) method indicated that genetically predicted T2D was associated with PDAC risk (OR = 1.10; 95% CI = 1.05 to 1.15), particularly the T2D obesity (OR = 1.28; 95% CI = 1.15 to 1.42) and lipodystrophy (OR = 1.25; 95% CI = 1.03 to 1.51) clusters. No association was observed for T1D with PDAC risk (OR = 1.01; 95% CI = 0.99 to 1.02). Pathway/gene-set analysis using the summary-based Adaptive Rank Truncated Product (sARTP) method revealed a significant association between the MODY gene-sets and PDAC risk (P = 1.5 × 10−8), which remained after excluding 20 known PDAC GWAS loci (P = 7.6 × 10−4). HNF1A, FOXA3, and HNF4A were the top contributing genes after excluding the previously identified GWAS loci regions. Conclusions Our results from this genetic association study support that T2D, particularly the obesity and lipodystrophy mechanistic clusters, and MODY genomic susceptibility regions play a role in the etiology of PDAC.