Cladribine indirectly downregulates methylation of DNA, RNA, and histones by blocking the transfer of methyl groups from S-adenosyl-methionine. The cladribine and rituximab combination showed a synergetic effect in treating B-cell lymphomas. Bortezomib (Velcade) is a Food and Drug Administration (FDA)-approved proteasome inhibitor for treating mantle cell lymphoma (MCL). In this single-arm, phase I study, the safety, dose-limiting toxicity, and clinical activity of bortezomib, cladribine, and rituximab (VCR) combination treatment were evaluated in elderly MCL patients. Potential DNA methylation biomarkers for VCR treatment were also proposed. A standard 3 + 3 dose-escalation scheme was designed to determine the maximum tolerated dose of cladribine. The therapy consisted of six 28-day cycles. Most patients tolerated this regimen well. The overall response (OR) rate was 84.6%, and the complete remission (CR) rate was 84.6%. In the newly diagnosed subject cohort, the OR and CR were 100%, the 2-year overall survival rate was 84.6%, and the progression-free survival rate was 76.9%. The median age was 64 (54–81). The median time to first response was 3 (2.1–7.4) months. The median follow-up time was 43 (9–60) months. Low-grade hematological toxicity and mild fatigue were observed. No severe systemic toxicity was observed. Five hypermethylated regions located at gene promoters were identified as potential biomarkers for an effective treatment response. In conclusion, the VCR combination is a well-tolerated, low-toxicity, and highly effective regimen for the elderly with untreated MCL.Clinical Trial RegistrationClinicalTrials.gov, identifier NCT01439750.

ObjectivesLarge granular lymphocyte (LGL) leukemia is a rare hematologic malignancy characterized by clonal expansion of cytotoxic T-cells frequent somatic activating STAT3 mutations. Based on the disease overlap between LGL leukemia rheumatoid arthritis (RA)a putative role for CD8+ T-cells in RA we hypothesized that STAT3 mutations may be detected in RA patient CD8+ T-cells correlate with clinical characteristics.MethodsBlood samples, clinical parameters, and demographics were collected from 98 RA patients and 9 healthy controls (HCs). CD8+ cell DNA was isolated and analyzed via droplet digital (dd)PCR to detect STAT3 mutations common in LGL leukemia: Y640F, D661Y, and the S614 to G618 region. STAT3 data from 99 HCs from a public dataset supplemented our 9 HCs.ResultsRA patients had significantly increased presence of STAT3 mutations compared to controls (Y640F p=0.0005, D661Y p=0.0005). The majority of these were low variant allele frequency (VAF) (0.008-0.05%) mutations detected in a higher proportion of the RA population (31/98 Y640F, 17/98 D661Y) vs. HCs (0/108 Y640F, 0/108 D661Y). In addition, 3/98 RA patients had a STAT3 mutation at a VAF >5% compared to 0/108 controls. Serological markers, RF and anti-CCP positivity, were more frequently positive in RA patients with STAT3 mutation relative to those without (88% vs 59% RF, p=0.047; 92% vs 58% anti-CCP, p=0.031, respectively).ConclusionsSTAT3 activating mutations were detected in RA patient CD8+ cells and associated with seropositivity. Thus, STAT3 activating mutations may play a role in disease pathogenesis in a subset of RA patients.

ABSTRACT Despite early optimism, therapeutics targeting oxidative phosphorylation (OxPhos) have faced clinical setbacks, stemming from their inability to distinguish healthy from cancerous mitochondria. Herein, we describe an actionable bioenergetic mechanism unique to cancerous mitochondria inside acute myeloid leukemia (AML) cells. Unlike healthy cells which couple respiration to the synthesis of ATP, AML mitochondria were discovered to support inner membrane polarization by consuming ATP. Because matrix ATP consumption allows cells to survive bioenergetic stress, we hypothesized that AML cells may resist cell death induced by OxPhos damaging chemotherapy by reversing the ATP synthase reaction. In support of this, targeted inhibition of BCL-2 with venetoclax abolished OxPhos flux without impacting mitochondrial membrane potential. In surviving AML cells, sustained polarization of the mitochondrial inner membrane was dependent on matrix ATP consumption. Mitochondrial ATP consumption was further enhanced in AML cells made refractory to venetoclax, consequential to downregulations in both the proton-pumping respiratory complexes, as well as the endogenous F 1 -ATPase inhibitor ATP5IF1 . In treatment-naive AML, ATP5IF1 knockdown was sufficient to drive venetoclax resistance, while ATP5IF1 overexpression impaired F 1 -ATPase activity and heightened sensitivity to venetoclax. Collectively, our data identify matrix ATP consumption as a cancer-cell intrinsic bioenergetic vulnerability actionable in the context of mitochondrial damaging chemotherapy.

Abstract Acute myeloid leukemia (AML) has been extensively studied at the genomic level, resulting in various genomic classifications. Despite the progress, three key challenges remain: 1) a significant proportion of patients lack identified genomic features, 2) a discrepancy exists between genomic risk classification and clinical outcomes, and 3) many mutated targets remain non-druggable. There is an urgent need for an enhanced AML risk classification that goes beyond genomic aberrations to guide effective therapeutics. Recent research, including our own, has increasingly linked AML pathogenesis and therapeutic resistance with dysfunctional sphingolipid metabolism, a family of bioactive molecules crucial for cellular functions. In a recent manuscript, we identified two robust sphingolipidomic clusters in AML, characterized by reciprocal abundances of hexosylceramide (Hex) and sphingomyelin (SM) species (HexloSMhi, HexhiSMlo). These clusters correlate with latent transcriptional states and stratify patient groups in multiple independent datasets such as TCGA, and BeatAML, with the HexloSMhi cluster representing a high-risk subgroup associated with poor clinical outcomes. These findings underscore the role of sphingolipids in refining AML risk assessment and creating avenues for discovery and therapeutic intervention. However, the signaling states driving these sphingolipidomic clusters and the mechanisms elevating risk in the HexloSMhi cluster require further investigation. To identify regulatory genes for the AML subtypes, we constructed gene regulatory networks using differentially expressed genes. Focusing on the high-risk subtype, we identified highly connected genes ranked by connectivity, including KDM1A, GSK3β, LCK, and STAT5A. We found that higher STAT5A abundances in the HexloSMhi subtype, particularly correlated with pro-survival Bcl-xL proteins. Furthermore, we identified STAT5 protein abundance as a key variable associated with drug sensitivity from pharmacological screening with sphingolipid pathway inhibitors and AML therapeutics 30 AML cell lines and patient samples. This is encouraging as STAT5 is druggable as evidenced in the NIH-Pharos druggable genome database, and several small-molecule inhibitors are currently in clinical trials. Analysis of gene expression data suggest that STAT5 inhibition, through genetic or pharmacological means, downregulates cell cycle-related genes and significantly alters sphingolipid gene expression. Recent work by others indicates that sphingolipid-catalyzing enzymes regulate STAT5 activity in leukemias, with ceramides acting as a second messenger in cells. Taken together, this suggests a possibility of a positive feedback loop between sphingolipid homeostasis and activity of STAT5; the details of this interaction require further investigation. Citation Format: B Bishal Paudel, Su-Fern Tan, Johnson Ung, David Claxton, David J. Feith, Thomas P. Loughran, Kevin A. Janes. Uncovering the molecular basis for clinically relevant sphingolipidomic subtypes in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4947.

Histone deacetylase (HDAC) inhibitors are a widely recognized and valued treatment option for patients with relapsed or refractory peripheral T cell lymphomas (PTCL). Romidepsin is a relatively selective Class I HDAC inhibitor originally approved for patients with relapsed or refractory (R/R) cutaneous T cell lymphoma (CTCL) and subsequently R/R PTCL. Unfortunately, the FDA approval of romidepsin for R/R PTCL was withdrawn due to a negative Phase 4 post-marketing requirement (PMR), diminishing further the treatment options for patients with PTCL. Herein we describe the development of a first-in-class polymer nanoparticle of romidepsin (Nanoromidepsin) using an innovative amphiphilic di-block copolymer-based nanochemistry platform. Nanoromidepsin exhibited superior pharmacologic disposition, with improved tolerability and safety in murine models of T-cell lymphoma. Nanoromidepsin also exhibited superior anti-tumor efficacy in multiple models including in vitro T cell lymphoma (TCL) cell lines, ex vivo LGL leukemia primary patient samples, and murine TCL xenografts. Nanoromidepsin demonstrated greater accumulation in tumors and a statistically significant improvement in overall survival (OS) compared to romidepsin in murine xenograft models. These findings collectively justify the clinical development of Nanoromidepsin in patients with T-cell malignancies.

Background: Mantle cell lymphoma (MCL) is a moderately aggressive and incurable small to medium size B cell lymphoma. In this phase 1 study, we evaluated the safety and efficiency of Valcade, Cladribine, and Rituximab (VCR) combination treatment in MCL. Patients and Methods: This is a single arm, open label, investigator-initiated Phase 1 study. This study employed a standard 3+3 dose escalation scheme designed to determine the maximum tolerated dose (MTD) of Cladribine in VCR regimen. The treatment scheme and Cladribine dose escalation levels (1, 2, and 3) are as follows: the therapy consisted of 6 28-day cycles. At first cycle of the treatment, Rituximab 375 mg/m2 infusion started on day 5 of the first week and then given weekly for 3 weeks; in the next 5 cycles, Rituximab was given on day 5 of each cycle, and then every 2 months as the maintenance therapy. Cladribine 35 mg/m2 (3 mg/m2 for level 1, 4 mg/m2 for level 2, and 5 mg/m2 for level 3) infusion was given on days 1 to 5 for 6 cycles. If the patient was older than 70 years old, Cladribine was only given on days 1 to 3 of each cycle. Velcade 1.6 mg/m2 subcutaneous injection was given on days 12, 19 and 26 for cycles 1 to 3, then Day 5 and 19 during Cycles 4 to 6, then once per month as maintenance therapy until toxicity or progression of the disease. The primary endpoint of this study was to investigate the dose limiting toxicity (DLT), safety, and efficiency of this regimen in patients with MCL. The secondary endpoints included remission rate (RR), progression free survival (PFS) and overall survival (OS). This study is registered with clinicaltrials.gov (NCT01439750). Results: No subject experienced dose limited toxicity (DLT) at either level 1 or 2, one possible DLT (infectious colitis) was observed on a subject during 2nd cycle at level 3. Then no additional DLTs were seen in 3 subjects added to level 3. Overall, this study recruited 13 subjects, with a median age of 64 years old (range from 55 to 83), and a total of 11 male and 2 females. Ten subjects were never previously treated, while 3 either relapsed or failed previous treatments. The majority of subjects tolerated this regimen well. Two relapsed patients experienced disease progression after received two cycles of treatments and died in 5 and 7 months after initiating the treatment. Another patient died 15 months after starting treatment. The overall remission (OR) rate was 77% (10/13) and complete remission (CR) rate was 85% (10/13). In newly diagnosed subject cohort, the RR and OS rates were 90% (9/10), PFR was 80% (8/10), and CR rate was 100% (10/10), of which 3 patients have been followed for more than 4 years, 3 other patients for more than 3 years, and 3 others for over 2 years. However, in relapsed/refractory subject cohort, 1 subject achieved CR for 7 months but then relapsed, 2 subjects had no response. There were 2 blastoid subjects, one was newly diagnosed and achieved CR.No severe systemic toxicity was observed in this study. Bone marrow suppression caused prolonged anemia and thrombocytopenia were the most common toxicity (3/13 with ≤grade 2). Low grade peripheral neuropathies (≤grade 2) were observed in 15% (2/13). Mild fatigue was a frequent complaint. Conclusions: The VCR combination is a well-tolerated, low toxicity and effective regimen for for untreated MCL. Cladribine 5 mg/m2 is a tolerable dose with manageable toxicity. Citation Format: Jeffrey J. Pu, Kristin Berger, David Claxton, Joseph Drabick, Thomas Loughran, Elliot Epner. The final results of a phase I study using velcade (bortezomib), cladribine, and rituximab (VCR) in treating elderly patient with mantle cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT145.

Supplementary Methods and Figures

AbstractPurpose: Develop a novel therapeutic strategy for patients with subtypes of mature T-cell and NK-cell neoplasms. Experimental Design: Primary specimens, cell lines, patient-derived xenograft models, commercially available, and proprietary anti-KLRG1 antibodies were used for screening, target, and functional validation. Results: Here we demonstrate that surface KLRG1 is highly expressed on tumor cells in subsets of patients with extranodal NK/T-cell lymphoma (ENKTCL), T-prolymphocytic leukemia (T-PLL), and gamma/delta T-cell lymphoma (G/D TCL). The majority of the CD8+/CD57+ or CD3−/CD56+ leukemic cells derived from patients with T- and NK-large granular lymphocytic leukemia (T-LGLL and NK-LGLL), respectively, expressed surface KLRG1. The humanized afucosylated anti-KLRG1 monoclonal antibody (mAb208) optimized for mouse in vivo use depleted KLRG1+ TCL cells by mechanisms of ADCC, ADCP, and CDC rather than apoptosis. mAb208 induced ADCC and ADCP of T-LGLL patient-derived CD8+/CD57+ cells ex vivo. mAb208 effected ADCC of subsets of healthy donor-derived KLRG1+ NK, CD4+, CD8+ Tem, and TemRA cells while sparing KLRG1− naïve and CD8+ Tcm cells. Treatment of cell line and TCL patient-derived xenografts with mAb208 or anti-CD47 mAb alone and in combination with the PI3K-δ/γ inhibitor duvelisib extended survival. The depletion of macrophages in vivo antagonized mAb208 efficacy. Conclusions: Our findings suggest the potential benefit of a broader treatment strategy combining therapeutic antibodies with PI3Ki for the treatment of patients with mature T-cell and NK-cell neoplasms. See related commentary by Varma and Diefenbach, p. 2300

Abstract Acute myeloid leukemia (AML) is an aggressive hematologic malignancy in urgent need of improved therapeutic strategies. AML blasts frequently rely on the anti-apoptotic protein, Bcl-2, for survival. The specific Bcl-2 inhibitor, venetoclax (VEN), is FDA-approved in combination with low-dose cytarabine (LDAC) or azacitidine for patients unfit for intensive induction chemotherapy. Unfortunately, responses are transient due to upregulation of compensatory survival proteins (e.g., Bcl-xL or Mcl-1) or resistance characterized by reprogrammed mitochondrial bioenergetics. Our research aims to improve current AML treatments and understanding of AML pathogenesis by targeting dysregulated sphingolipid metabolism. Ceramides are tumor-suppressor sphingolipids that mediate therapy-induced cell death. Sphingolipid dysregulation that results in decreased ceramide content and/or enhanced ceramide catabolism is an emerging AML hallmark. We’ve previously shown that acid ceramidase (AC), a ceramide catabolizing lysosomal enzyme, is overexpressed in AML and contributes to drug resistance. Here, we demonstrated that AC inhibition enhanced VEN cytotoxicity. Combining the AC inhibitor/ceramide analog, SACLAC, with VEN resulted in synergistic lethality in multiple AML cell lines in cell viability and apoptosis assays. Genetic inhibition of AC also improved VEN cytotoxicity. The SACLAC+VEN combination achieved Bliss scores (SynergyFinder 2.0) between 22 and 32 in cell lines, which indicate a highly synergistic combination. SACLAC+VEN efficacy was comparable to the FDA-approved combination of VEN+LDAC when tested in 67 primary AML patient samples. Pharmacological inhibition of AC also increased the efficacy of the VEN+LDAC combination. Mechanistically, the observed synergistic lethality was independent of changes to Bcl-2, Mcl-1, and Bcl-xL protein levels. Combined AC and Bcl-2 inhibition resulted in synergistic ceramide accumulation, integrated stress response (ISR) activation, and caspase-dependent apoptosis characterized by impaired mitochondrial function. Pretreatment with the pan-caspase inhibitor, zVAD-FMK, or ISR inhibitor, ISRIB, significantly rescued cell death. Ongoing studies aim to further characterize mitochondrial impairment and ISR activation induced by inhibiting AC and Bcl-2. Taken together, these results detail the first report of ISR activation and mitochondrial defects elicited by combined AC and Bcl-2 inhibition as contributory to cytotoxic impact (mechanism) and warrant additional studies of AC inhibitors with frontline AML therapeutics. Citation Format: Johnson Ung, Su-Fern Tan, Jeremy J. Shaw, Todd E. Fox, Maansi Taori, David F. Claxton, Kelsey H. Fisher-Wellman, Myles C. Cabot, David J. Feith, Thomas P. Loughran. Acid ceramidase inhibition enhances venetoclax sensitivity in preclinical models of acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4740.

Lipid amidases of therapeutic relevance include acid ceramidase (AC), N-acylethanolamine-hydrolyzing acid amidase, and fatty acid amide hydrolase (FAAH). Although fluorogenic substrates have been developed for the three enzymes and highthroughput methods for screening have been reported, a platform for the specific detection of these enzyme activities in intact cells is lacking. In this article, we report on the coumarinic 1-deoxydihydroceramide RBM1-151, a 1-deoxy derivative and vinilog of RBM14-C12, as a novel substrate of amidases. This compound is hydrolyzed by AC (K-app(m) = 7.0 mu M; V-app(max) = 99.3 nM/min), N-acyle-thanolamine-hydrolyzing acid amidase (K-app(m) = 0.73 mu M; V-app(max) = 0.24 nM/min), and FAAH (K-app(m) = 3.6 mu M; V-app(max) = 7.6 nM/min) but not by other ceramidases.(jlr) We provide proof of concept that the use of RBM1-151 in combination with reported irreversible inhibitors of AC and FAAH allows the determination in parallel of the three amidase activities in single experiments in intact cells.

Abstract Introduction: Histone Deacetylase inhibitors (HDACi) are important drugs for the treatment of patients with PTCL (peripheral T-cell lymphoma). Romidepsin (R), a potent Class I HDACi, is given intravenously, weekly for three to four consecutive weeks. R has a half-life of three hours and is extensively protein bound. The indication for R in PTCL was recently withdrawn due to a failed Phase 4 study. Given the need for new drugs in PTCL, and the importance of epigenetically targeted drugs for the disease, we developed a first-in-class nanoparticle of R (NR) deploying a proprietary nanochemistry platform. Methods: We modified the bulk nanoprecipitation method with FDA approved and Generally Recognized as Safe (GRAS) materials, specifically including PEGylated amphiphilic diblock copolymers, to develop NR combinatorially. By combining a drug and polymer solution with an anti-solvent, we produced core-shell structured NR particles with “stealth” properties. To achieve high R loading, stability, purity, scalability, and reproducibility, we devised a multi-pronged optimization system by modulating parameter sets in tandem. We determined the optimal parameters for the "lockdown" formulation. We purified NR by using centrifugal filters and determined stability by storing at 4°C. We used Cryo-electron microscopy (cryo-EM), Dynamic Light Scattering (DLS), and Liquid Chromatography-Mass Spectrometry (LC-MS) to determine the morphology, size, PDI, and drug concentration of NR. We developed fluorescent-NR with DiO dye to test bioavailability. We tested NR in T-cell lymphoma cell lines for histone acetylation and apoptosis induction. Furthermore, we investigated the in vivo pharmacokinetics and toxicity of NR in PTCL xenograft mouse model and quantified the drug by LC-MS. Results: The physiochemical analysis of NR demonstrated that the particles were spherical, with a hydrodynamic diameter of 46 ±5 nm and PDI of 0.15 - 0.2. NR had a negative zeta potential and an exceptional drug encapsulation efficiency of over 50% (>500 µg/mL). NR exhibited high stability with respect to size, PDI and drug concentration for over two years. Flow cytometry and western blot analyses indicate NR induces apoptosis and histone acetylation in a time and dose-dependent manner, equivalent to or better than that observed for R. NR’s AUC increased 25-fold when administered intravenously. NR had superior tolerability, and DiO-NR confirmed superior biodistribution in tumor in a PTCL xenograft mouse model. Conclusion: We developed a cutting-edge approach with minimum excipients, which enabled NR scale up with batch-to-batch reproducibility and high quality co-packaging of fluorescent dye and drug. NR improved R’s pharmacokinetic profile and efficacy in pre-clinical xenograft mice models. Our versatile technology enables Chemistry Materials and Controls products, an essential step in clinical product development. Citation Format: Samir Zuberi, Deepthi P. Damera, Ipsita Pal, Susan Walker, Ramesh Katla, Colin Haws, Akhil Gajjala, Andrea Joyner, Kallesh D. Jayappa, David J. Feith, Todd E. Fox, Thomas P. Loughran, Owen A. O'Connor, Anuradha Illendula. Chemical fabrication and characterization of a novel nanoparticle of the histone deacetylase (HDACi) romidepsin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3207.

Large granular lymphocytic (LGL) leukemia is a rare lymphoproliferative chronic disorder characterized by expansion of either T- or NK- cytotoxic cells. Contrary to EBV-induced aggressive NK-LGL leukemia, chronic T- and NK-LGL leukemia are indolent diseases affecting elderly patients with a median age of 66.5 years old. LGL leukemia is frequently associated with autoimmune disorders, most frequently rheumatoid arthritis. An auto/allo antigen is tentatively implicated in disease initiation. LGLs expansion is then triggered by proinflammatory cytokines such as interleukin (IL) IL-15, MIP-1, and RANTES. This proinflammatory environment contributes to deregulation of proliferative and apoptotic pathways. Following the initial description of the JAK-STAT pathway signaling activation in the majority of patients, recurrent STAT3 gain of function mutations have been reported. The JAK-STAT pathway plays a key role in LGL pathogenesis by promoting survival, proliferation and cytotoxicity. Several recent advances have been made towards understanding the molecular landscapes of T and NK LGL leukemia, identifying multiple recurrent mutations affecting the epigenome, such as TET2 or KMT2D, and crosstalk with the immune microenvironment, such as CCL22. Despite an indolent course, published series suggest that the majority of patients will eventually need treatment. However, it is noteworthy that many patients may have a long-term observation period without ever requiring therapy. Treatments rely upon immunosuppressive drugs, namely cyclophosphamide, methotrexate and cyclosporine. Recent advances have led to the development of targeted approaches, including JAK-STAT inhibitors, cytokine targeting and hypomethylating agents, opening new developments in a still-incurable disease.

Background: Mantle cell lymphoma (MCL) is a moderately aggressive and incurable small to medium sized B cell lymphoma. No standardized treatment exists for this disease. Cladribine is a hypomethylating agent that indirectly down-regulate DNA methylation to suppress tumorigenesis. Combination of Cladribine and Rituximab showed a synergetic effect in treating B cell lymphomas. Bortezomib (Velcade) is an FDA approved proteasome inhibitor to treat relapsed/refractory MCL. In this study, we evaluated the safety and efficacy of Valcade, Cladribine, and Rituximab (VCR) combination treatment in newly diagnosed and relapsed/refractory MCL. Patients and Methods: This is a single arm open label phase I trial. This study employed a standard 3+3 dose escalation scheme designed to determine the maximum tolerated dose (MTD) of Cladribine in VCR regimen. Briefly, the treatment scheme was consisted of 6 28-day cycles. At first cycle of the treatment, Rituximab 375 mg/m 2 infusion started on day 5 of the first week and then given weekly for 3 weeks; in the next 5 cycles Rituximab was given on day 5 of each cycle, and then every 2 months as the maintenance therapy. Cladribine 3 to 5 mg/m 2 (3 mg/m 2 for level 1, 4 mg/m 2 for level 2, and 5 mg/m 2 for level 3) infusion was given on days 1 to 5 for 6 cycles. For patient older than 70 years old, Cladribine was only given on days 1 to 3 of each cycle. Velcade 1.6 mg/m 2 subcutaneous injection was given on days 12, 19 and 26 for cycles 1 to 3, Days 5 and 19 for Cycles 4 to 6, then once per month as maintenance therapy. The primary endpoint of this study was the dose limiting toxicity (DLT), safety, and efficacy of this regimen in patients with MCL. The secondary endpoints included remission rate (RR), progression free survival (PFS) and overall survival (OS) (Figure 1). The analysis was done by intent to treat. Differentially methylated region (DMR) analysis and cytokine assay were performed to explore biomarkers differentiating good-responders from poor-responders. Results: This study recruited 13 patients, with a median age of 64 years old (range from 55 to 83) and including 11 males and 2 females. Ten patients were never previously treated, other 3 either relapsed or failed from previous treatments. Most patients tolerated this regimen well. No patient experienced DLT at either level 1 or 2, one possible DLT (infectious colitis) was observed during 2nd cycle at level 3. Two relapsed patients experienced disease progression after received two cycles of treatment and died in 5 and 7 months. Another patient died in 15 months after receiving treatment. The overall remission (OR) rate was 85% (11/13) and complete remission (CR) rate was 77% (10/13). In newly diagnosed patient cohort, CR rate was 100% (10/10), OS rates were 90% (9/10), and PFS was 80% (8/10), of which 3 patients have been followed for more than 4 years, 3 other patients for more than 3 years, and 3 others for over 2 years (Fig.1). In relapsed/refractory patient cohort, 1 achieved CR for 7 months but then relapsed, 2 had no response. There were 2 blastoid patients, 1 of these 2 patients was newly diagnosed and achieved CR. Bone marrow suppression caused prolonged anemia and thrombocytopenia were the most common toxicity (3/13 with ≤grade 2). Low grade peripheral neuropathies (≤grade 2) were observed in 15% (2/13). Mild fatigue was a frequent complaint. Cytokine assay showed decreased CXCL12 level in the good responders. Though global methylation pattern showed no difference, DMRs were identified in the good responders and the poor responders. DMRs-related genes involved in CXCL2 pathways were further extracted and enriched biological process analysis revealed the pathway profile difference between good responders and poor responders. Good responders exhibited alternation of apoptotic and Wnt signaling pathways (Fig.2). Conclusions: The VCR combination is a well-tolerated, low toxicity and effective regimen for MCL, especially for untreated MCL. Cladribine 5 mg/m 2 is a tolerable dose with manageable toxicity. Individual patient methylation profile may affect response to VCR therapy.

T-cell large granular lymphocytic leukemia (T-LGLL) is a clonal proliferation of cytotoxic T lymphocytes that can result in severe neutropenia, anemia, and bone marrow failure. Strong evidence from patients and mouse models demonstrate the critical role of interleukin-15 (IL-15) in T-LGLL pathogenesis. BNZ-1 is a pegylated peptide that selectively inhibits the binding of IL-15 and other gamma c cytokines to their cellular receptor complex, which has demonstrated efficacy in ex vivo T-LGLL cells and transgenic mice in preclinical studies. We conducted a phase 1/2 trial of BNZ-1 in patients with T-LGLL who had hematocytopenias (anemia or neutropenia) and required therapy. Clinical responses were assessed using hematologic parameters (improvement in hematocytopenias) based on response criteria from the Eastern Cooperative Oncology Group 5998 T-LGLL trial. BNZ-1 demonstrated clinical partial responses in 20% of patients with T-LGLL with mini-mal toxicity and the maximum tolerated dose was not reached. Furthermore, T-LGL leukemic cells showed significantly increased apoptosis in response to BNZ-1 treatment as early as day 2, including in clinical nonresponders, with changes that remained statistically different from baseline throughout treatment (P < .005). We report first-in-human proof that T-LGL leukemic cells are dependent on IL-15 and that intervention with IL-15 inhibition with BNZ-1 in patients with T-LGLL shows therapeutic effects, which carries important implications for the understanding of the pathogenesis of this disease. This trial was registered at www.clinicaltrials.gov as #NCT03239392.

Large granular lymphocytic (LGL) leukemia is an uncommon lymphoproliferative disorder characterized by a clonal expansion of greater than 0.5 × 109/L circulating neoplastic T cells (CD3+CD8+ and either CD57+ or CD16+) or NK cells (CD3-CD8+CD16+ and/or CD16+CD56+).1 There is an association with STAT3 mutations and inflammation caused by autoimmune diseases, such as rheumatoid arthritis and pure red cell aplasia (PRCA), as well as chronic viral infections, such as hepatitis B and hepatitis C.1, 2 Treatment consists of immunosuppression and is reserved for patients with the following indications: (1) severe neutropenia, defined as an absolute neutrophil count (ANC) <0.5 × 109/L, (2) moderate neutropenia (ANC >0.5 × 109/L) with recurrent infections, (3) symptomatic or transfusion dependent anemia, and (4) autoimmune conditions necessitating therapy. Methotrexate has been used as first line therapy due to its efficacy in both LGL leukemia and comorbid conditions, that is, rheumatoid arthritis. In the setting of PRCA, cyclophosphamide has been recommended because of higher response rates (6/8 patients responded) compared to cyclosporine A or prednisolone.2 Military exposures may be associated with the development of lymphoid malignancies, but an association has not been well described in LGL leukemia. Herein we describe the characteristics and outcomes of patients diagnosed with LGL leukemia (30% of whom potentially had military exposures) and managed in the national Veteran Affairs (VA) Healthcare System. This is a retrospective, secondary analysis of electronic health records of a VA cohort of patients diagnosed with LGL leukemia from January 1, 1998 to December 31, 2020 using the VA informatics infrastructure.3 The VA is the largest integrated healthcare system in the United States with sites also in American Samoa, Guam, Philippines, Puerto Rico, and the Virgin Islands. The diagnosis of LGL leukemia was made by the detection of monoclonal population of at least 0.5 × 109/L cells with the expression of CD3+CD8+CD16+/−CD57+/− and a T-cell receptor gamma gene rearrangement as T-cell LGL leukemia, and CD3-CD16+CD56+ as NK-cell LGL leukemia. If the LGL cell count was <0.5 × 109/L by peripheral blood flow cytometry, then this was deemed to be precursor state. Transformation was defined as an aggressive progression of disease with lymphocytosis. Descriptive data summarized patient and disease characteristics. Treatments were categorized as methotrexate-based, cyclophosphamide-based, cyclosporine A-based, growth factors, or other immunosuppression, which included steroids and mycophenolate. Response rates were evaluated by blood counts and organ response after four 28-day cycles of therapy. A complete response (CR) was defined as improvement of hemoglobin >11 g/dL, platelets >100 × 109/L, ANC >1.5 × 109/L, and lymphocyte count <4 × 109/L; a partial response defined as improvement in counts without meeting CR, stable disease as no response within 4 months, and progressive disease (PD) as worsening cytopenias or organomegaly.4 Multivariate hazard ratios were calculating with the Cox proportional hazard model. Overall survival (OS) was defined as the time from date of diagnosis to death from any cause. Disease specific survival (DSS) was defined as the time from date of diagnosis to death from hematologic malignancy. Patients who were alive were censored at the date of last contact (data cutoff December 31, 2020). Kaplan–Meier curves were used to estimate survival and compared by log-rank tests. Causes and dates of death were confirmed by using data from the National Death Index through December 31, 2020.5 p-values were reported for two-sided tests. This study was approved by the Institutional Review Boards at the VA Long Beach Healthcare System and the University of California, Irvine and was conducted in accordance with the principles of the Declaration of Helsinki. From 1998 through 2020, 280 patients were identified with LGL leukemia. Seventeen were identified to have a precursor LGL leukemia. Almost half were diagnosed by peripheral blood flow cytometry (n = 139), the other half diagnosed by bone marrow biopsy (n = 138) precluding calculation of absolute circulating LGL cell count. The method of diagnosis was unknown for seven patients. Median time from diagnosis to initiation of treatment was 0.8 months (range, 0–100 months). A minority of patients underwent next generation sequencing, and eight patients were found to have a STAT3 mutation. Supplementary Table 1 summarizes patient characteristics. Notably, 28% of patients had at least one military exposure, almost 20% of patients were exposed to Agent Orange (AO), 10% to combat, very few were exposed to Southwest Asia theater of conflict, Camp Lejeune, and none to ionizing radiation. Supplementary Table 2 summarizes patient management with the time to treatment within 1 month, 1–6 months, 6–12 months, and over 1 year calculated as 90 (32%), 50 (18%), 6 (2%), and 20 (7%) patients, respectively. In AO exposed patients, the median OS and DSS were 8.7 years (95% confidence interval [CI], 6.2-not reached [NR]) and NR (95% CI, NR-NR) compared to 7.0 years (95% CI, 6.1–9.0) and NR (95% CI, NR-NR) for AO unexposed patients, respectively (Figure 1A,B). For the overall cohort, the median OS and DSS were 7.4 years (95% CI, 6.5–9.1) and NR (95% CI, NR-NR), respectively (Supplementary Figure 1A,B). Notably, patients with LGL leukemia were more likely to die from other causes (67%) than their hematologic malignancies (33%); causes of death are summarized in Supplementary Table 3. On univariate analysis, anemia with hemoglobin (HGB) <11 g/dL, having another cancer, and increasing age were statistically significantly associated with worse survival, but race, branch of military, tobacco use, ANC <1.5 × 109/L, thrombocytopenia with platelet (PLT) less than 100 × 109/L, autoimmune disease, AO exposure, combat exposure, and viral infections were not. On multivariate analysis, anemia with HGB <11 g/dL (HR 1.776, 95% CI 1.179–2.674), having another cancer (HR 1.43, 95% CI 1.002–2.052), and increasing age at diagnosis (HR 1.052, 95% CI 1.028–1.077) remained statistically significantly associated with worse survival. Median OS of patients who presented with ANC <1.5 × 109/L, HGB <11 g/dL, or PLT <100 × 109/L compared to patients who had higher blood counts were 7.1 years (6.3–17.5) versus 7.4 years (95% CI, 6.1–9.2), p = .412, 4.9 years (95% CI, 4.3–6.8) versus 8.7 years (95% CI, 7.1–17.5), p < .0001, and 6.2 years (95% CI, 4.2–9.2) versus 7.4 years (95% CI, 6.5–9.4), p = .364, respectively (Supplementary Figure 2A–C). Median DSS of patients with ANC <1.5 × 109/L, HGB <11 g/dL, or PLT <100 × 109/L compared to patients with higher blood counts were NR (95% CI, NR-NR) in both, p = .058, 11.2 (95% CI 11.2-NR) versus NR (95% CI, NR-NR), p < .0001, NR (95% CI, NR-NR) in both, p = .999, respectively (Supplementary Figure 2D–F). Our data are consistent with several large retrospective cohorts of similar size in that patients with LGL leukemia have an excellent median DSS.6 Our population was predominantly male and older with the median age of diagnosis of 70 years compared to the other reports where the median age of diagnosis was 65 (range, 17–90) and there was more equal distribution between genders.6 About half of veterans had enlisted in the army, 2/3 had a history of tobacco use, and 1/3 had known military exposures. Even with our mostly male cohort, our data support the association of autoimmune disease with LGL disorders.6 A small proportion of patients were exposed to specific military exposures, limiting analysis on their impact on outcomes. Over half of patients were monitored as first line of therapy. Since many underwent diagnostic work up for cytopenias, about a third of patients started treatment within 1 month of diagnosis in the VA system. In our veteran population and consistent with the literature, anemia (HGB <11 g/dL) has been shown to be associated with worse survival6 whereas neutropenia and thrombocytopenia did not seem to impact survival. Our data show that 40% of veterans with LGL disorders also have a second malignancy, which is consistent with published data.6 There are case reports of patients with T-cell LGL leukemia who present with transformation based on an acute onset of systemic B symptoms, organomegaly, cytopenias, and lymphoadenopathy.7 Our study had two patients who had a similar course. This entity may be underreported and warrants further investigation. Limitations of this secondary analysis of a national VA medical record system include systemic error, selection bias, incomplete data, inconsistent documentation, and heterogeneous data quality. The national VA electronic medical record was established in 1999, and there may be different clinical outcomes in patients diagnosed prior to consistent electronic health documentation. There may be unknown confounding variables that bias the analysis. The classification of lymphoid malignancies has also changed several times in the past 20 years, potentially changing how diagnoses were categorized. In conclusion, exposure to AO did not seem to adversely impact survival. Even with a predominantly male population, the incidence of autoimmune disease was similar to reports of civilian patients with balanced gender distributions. Because of the severity of cytopenias at diagnosis, half of patients required treatment within 6 months. This historical cohort did not have routine next generation sequencing, which may be beneficial to better understand the biology and inform future treatment strategies. Veterans with LGL leukemia, managed at the VA have excellent outcomes, consistent with published reports. Helen Ma conceived the idea, collected the data, performed statistical analysis, wrote, and edited the manuscript. Thomas P. Loughran and Pankaj Gupta contributed clinical expertise and critically edited the manuscript. Helen Ma is a Lymphoma Research Foundation Lymphoma Scientific Research Mentoring Program scholar and recipient of a VA Career Development Award (1-IK2 CX002437-01A1). Helen Ma and Pankaj Gupta have no competing interests to report. Thomas P. Loughran is a member of Scientific Advisory Board and consultant for Keystone Nano, Dren Bio, Kymera Therapeutics, Recludix Pharma, and Prime Genomics. This study was approved by the Institutional Review Boards at the VA Long Beach Healthcare System and the University of California, Irvine and was conducted in accordance with the principles of the Declaration of Helsinki. Data S1. Supporting Information. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

<p>The full names of components in the EMT network corresponding to the abbreviated node labels used in Figure 3 and Figure 5A (S1); Evidence for interactions among nodes in the EMT network (S2); Boolean update rules and initial state of the 68 node EMT network (S3); Key experimental outcomes reproduced by the EMT network model (S4); Boolean rules and initial state for the 19 node reduced EMT network (S5).</p>

Introduction: Peripheral T-cell lymphomas (PTCL) are a rare and heterogeneous group of malignancies that share a unifying feature of epigenetic dysregulation. Recent evidence suggests that PTCL, unlike other forms of cancer or even lymphoma, exhibits a marked vulnerability to hypomethylating agents (HMAs) alone and especially in combination with HDAC inhibitors. HMAs like azacitidine (AZA) and decitabine (DAC) have been shown to reverse transcriptional repression secondary to hypermethylation. Cladribine (CLAD) is FDA-approved for the treatment of hairy cell leukemia and is postulated to inhibit both DNA and histone methylation. Here, we sought to define the mechanistic differences between different DNA HMAs in order to inform a rationale on the optimal combinations that might exploit the epigenetic vulnerabilities of PTCL. Methods: Cell viability, caspase activity assay, and western blotting (WB) were performed on a panel of T-cell lymphoma cell lines to identify the effects of AZA/DAC/CLAD on cell survival, apoptosis, and DNA methyltransferase (DNMT) levels. Liquid chromatography-based mass spectrometry (LC-MS) was done to quantify 5-methyl cytosine (5-mC) levels. Results: Cell viability analysis confirmed that the dose and time-dependent sensitivity of the six PTCL cell lines differed following exposure to AZA/DAC/CLAD, where CLAD showed the lowest IC50 value (0.1–1 µM) across all cell lines, followed by AZA (IC50: 1–10 µM), and DAC had the least effect on cell viability (IC50: >100 µM, except T-ALL). A differential threshold of caspase activation was observed across the PTCL cell lines where CLAD showed the most superior caspase activity leading to the highest apoptotic potential. However, WB analysis showed that after 24 hours of treatment, DNMT1 and DNMT3A protein levels were significantly depleted at low concentrations of DAC (<0.01 µM) compared to AZA whereas CLAD did not affect the DNMT1 and DNMT3A levels. LC-MS-based quantification of 5-mC showed a similar relationship in methylation, with initial changes observed at doses >0.01 μM of DAC and >0.1 μM of AZA/CLAD. Taking the short half-life of AZA/DAC into account, cell viability assays with daily addition of AZA/DAC showed increased cell cytotoxicity for AZA/DAC treated samples, which was comparable to CLAD. Ongoing analyses of gene expression and metabolism of the universal methyl donor S-adenosylmethionine (SAM) will help to understand the mechanistic difference between these HMAs. Conclusions: These data suggest that the HMAs have a distinct mechanism of action for hypomethylation. While AZA/DAC induces hypomethylation by depletion of DNMTs, CLAD acts in a DNMT depletion-independent pathway. A mechanistic understanding of AZA/DAC/CLAD will inform how best to use them in clinic as well as assist in the strategic development of biological correlates to further support their therapeutic application. The research was funded by: Translational Orphan Blood Cancer Research Initiative Fund and RO1 # FD-R-006814-01. Keywords: Genomics, Epigenomics, and Other -Omics, Molecular Targeted Therapies No conflicts of interests pertinent to the abstract.