Citations

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.

AbstractPurposeOverall there is a lack of evidence on the accuracy and precision of phase‐contrast (PC) MRI in patients with cardiac implantable electronic devices (CIEDs). The purpose of this study is to determine whether aortic velocity measurements are influenced by a CIED.MethodsWe scanned 21 adult patients and 8 pediatric volunteers using clinical standard PC and real‐time PC (rt‐PC) sequences with and without a CIED generator taped on human subjects (below the left clavicle for adults and children; also on the abdomen for children) to mimic image artifacts. Peak and mean velocities above the aortic valve were calculated.ResultsThe Bland–Altman analyses on peak velocity measurements in pediatric subjects showed that both the accuracy and precision worsen as the distance between the CIED and aortic valve decreases (i.e., from abdomen to below the left clavicle). Specifically, both the bias and the coefficient of variation (CV) for both clinical PC and rt‐PC increased from the abdominal position (clinical: bias = −1.1%, CV = 4.3%; rt‐PC: bias = −0.3%, CV = 3.4%) to the clavicle position (clinical: bias = −4.0%, CV = 8.1%; rt‐PC: bias = 8.2%, CV = 7.3%). A similar trend was observed for mean velocity. The mean difference in peak and mean velocity measurements between rt‐PC with CIED (either position) and clinical standard PC with no CIED was within 7.5%. In adult patients, the mean difference between rt‐PC with CIED and clinical standard PC with CIED in peak velocity was 6.9%, and the CV was 7.9%.ConclusionThis study demonstrates that aortic velocity measurements are influenced by CIED in both adult and pediatric subjects.

Abstract Idiopathic pulmonary fibrosis (IPF) is characterized by the sustained activation of interstitial fibroblasts leading to excessive collagen deposition and progressive organ failure. Epigenetic and metabolic abnormalities have been shown to contribute to the persistent activated state of scar-forming fibroblasts. However, how epigenetic changes regulate fibroblast metabolic responses to promote fibroblast activation and progressive fibrosis remains largely unknown. Here, we show that the epigenetic regulator CBX5 (chromobox protein homolog 5) is critical to the transition of quiescent fibroblasts to activated collagen-producing fibroblasts in response to bleomycin-induced lung injury. Loss of mesenchymal CBX5 attenuated fibrosis development, and this effect was accompanied by the downregulation of pathogenic fibroblast genes, including Cthrc1, Col1a1, and Spp1, and by the upregulation of metabolic genes with antifibrotic activity such as Ppara and Pparg. Single-cell RNA sequencing and immunohistochemistry analyses revealed that CBX5 expression was enriched in pathogenic fibroblasts and fibroblastic foci of IPF lungs. Bulk RNA-sequencing analysis combined with metabolic assessments demonstrated that CBX5 silencing in IPF fibroblasts potently inhibited transforming growth factor–stimulated glycolysis while enhancing AMPK signaling and mitochondrial metabolism. Finally, interruption of the CBX5 pathway in IPF fibroblasts in vitro and in IPF lung explants ex vivo synergistically potentiated the activation of metformin-induced AMP-activated protein kinase activation and inhibited collagen secretion. Collectively, our findings identify CBX5 as an epigenetic regulator linking metabolic maladaptation to the persistent activated state of lung fibroblasts during IPF progression.

BACKGROUND ELRA is a humanized, BCMA/CD3 bispecific antibody. In the phase 2 registrational MagnetisMM-3 (MM-3) trial, SC ELRA given as 2 step-up priming doses (12 mg on day 1 and 32 mg on day 4 of cycle 1) followed by 76 mg QW in patients (pts) with RRMM naive to BCMA-directed therapy resulted in an ORR of 61.0%. With a median follow-up of 28.4 mos, the median DOR, PFS, and OS were not reached (NR; 2-year rate, 66.9%), 17.2, and 24.6 mos, respectively. Overall, 56.3% of pts had CRS (grade 2, 14.3%; no grade ≥3). Most events occurred after doses 1 (44.5%), 2 (20.2%), and 3 (5.9%); 0.8% (1 pt) had CRS with doses ≥4. Recurrent CRS occurred in 15.1% of pts. The phase 1/2 MagnetisMM-9 (MM-9; NCT05014412) study is examining an alternative priming regimen and longer dosing intervals of ELRA. Here, we present updated MM-9 results. METHODS In MM-9, pts with RRMM and disease refractory to ≥1 IMiD drug, ≥1 PI, and ≥1 anti-CD38 antibody were given SC ELRA as step-up priming doses of 4 and 20 mg on Day 1 and Day 4 of Cycle 1, respectively. After the priming doses, ELRA 76 mg was given QW for the next 6 cycles (Part 1) or for 1 cycle followed by 116 (dose level 1 [DL1]) or 152 (dose level 2 [DL2]) mg Q2W for the next 5 cycles (Part 2A). After 6 cycles, the dosing frequency was decreased from QW to Q2W (Part 1) or from Q2W to Q4W (Part 2) in pts who achieved ≥PR lasting ≥2 months. The recommended phase 2 dose from Part 2A (152 mg, DL2) was evaluated in Part 2B (dose expansion). The primary endpoint for both parts is grade ≥2 CRS rate per ASTCT criteria during Cycle 1. Secondary endpoints include evaluation of efficacy and adverse events. Data cutoff: February 13, 2024. RESULTS Overall, 85 pts (median age, 64.0 y) were treated with ELRA. The majority (72.9%) of pts had R-ISS stage I/II disease (23.5% with R-ISS stage III); 31.8% had high-risk cytogenetics. Median number of prior lines of therapy was 5.0 (range, 1-12). The median treatment duration was 8.6, 2.9, 1.4, and 3.3 mos, in Part 1, Part 2A DL1, Part 2A DL2, and Part 2B, respectively. Median follow-up for pts overall (n=85), in Part 1 (n=33), Part 2A DL1 (n=12), Part 2A DL2 (n=11), and Part 2B (n=29) was 10.4, 23.3, 16.5, 15.2, and 9.3 mos, respectively. Overall, the ORR was 58.8%. For pts in Part 1, Part 2A DL1, Part 2A DL2, or Part 2B, ORR was 66.7%, 58.3%, 36.4%, and 58.6%, respectively; median DOR was NR (9-mo rate: 86.4%), 10.8 mos (9-mo rate: 80.0%), NR (9-mo rate: 100.0%), and NR (9-mo rate: 84.8%); median PFS was 17.1 (9-mo rate: 62.8%), 11.6 (9-mo rate: 50.9%), 1.6 mos (9-mo rate: 40.0%), and NR (9-mo rate: 57.1%); median OS was NR (9-mo rate: 75.8%), 17.4 mos (9-mo rate: 66.7%), NR (9-mo rate: 60.0%), and NR (9-mo rate: 72.4%), respectively. For pts in Part 1, Part 2A DL1, Part 2A DL2, and Part 2B, grade ≥2 CRS rates during Cycle 1 were 15.2%, 16.7%, 27.3%, and 6.9%, respectively. For pts in Part 1, Part 2A DL1, Part 2A DL2, and Part 2B, CRS rates were 30.3%, 33.3%, 36.4%, and 24.1% after dose 1, 27.3%, 25.0%, 36.4%, and 24.1% after dose 2, 15.2%, 33.3%, 27.3%, and 20.7% after dose 3, 6.1%, 8.3%, 0%, and 3.4% after dose 4, and 6.1%, 16.7%, 9.1%, and 0% after doses ≥5. Recurrent CRS occurred in 18.2%, 33.3%, 18.2%, and 17.2% of pts in Part 1, Part 2A DL1, Part 2A DL2, and Part 2B. The most common (>60%) TEAEs (any grade/grade ≥3) were hematologic TEAEs (Part 1, 75.8%/75.8%; Part 2A DL1, 83.3%/83.3%; Part 2A DL2, 81.8%/81.8%; Part 2B, 79.3%/69.0%), infections (Part 1, 78.8%/48.5%; Part 2A DL1, 83.3%/66.7%; Part 2A DL2, 72.7%/63.6%; Part 2B, 62.1%/37.9%), and CRS (Part 1, 60.6%/0%; Part 2A DL1, 83.3%/0%; Part 2A DL2, 90.9%/9.1%; Part 2B, 48.3%/0%). Grade 5 TEAEs not including PD were infection (n=4), fall (n=1), subdural hematoma (n=1), and food poisoning (n=1). CONCLUSIONS The 4/20 mg step-up priming regimen and alternative dosing schedules in MM-9 resulted in similar efficacy vs the step-up regimen used in the registrational MM-3 study (12/32 mg). Responses were durable with encouraging PFS and OS with the alternative step up and longer dosing schedule. While the overall safety signals with the alternative step up regimen are similar to those seen with MM-3, the CRS profile differed with more CRS events after each subsequent dose and a higher prevalence of recurrent CRS. Thus, the optimal ELRA step-up regimen remains 12/32 mg from the original regimen in the MM-3 study. In addition, these early results suggest that reducing the dose frequency of ELRA may not compromise efficacy.

Despite the high initial responses to chimeric antigen receptor T (CART) cell therapy, most patients relapse within the first 1-2 years. T cell quality influences the success of CART cell therapies greatly, and T cells from cancer patients are prone to transition into dysfunctional states, such as exhaustion or senescence. The role of exhaustion in CART cell failures has been studied extensively; however, the role of T cell senescence has remained mostly unexplored. In this study, we aimed to determine the development of CART cell senescence and its impact on CART therapeutic efficacy. First, we studied the development of CART cell senescence using an in vitro model to induce CART cell dysfunction. Here, we cyclically activated CD19-directed chimeric antigen receptor T (CART19) cells (either costimulated via 4-1BB (BBζ) or CD28 (28ζ)). Activation cycles are designed to mimic recurrent activation of CART cells to study the impact of T cell activation on CART cell fates throughout treatment. We added a rest time in between activation cycles to focus on senesced CART cell populations since, unlike exhaustion, senescence is irreversible even after rest. We examined CART immunophenotype, cell cycle regulators, transcriptomic profile, senescence marker gene expressions and T cell effector functions on days 0 (D0-T cell), 8 (D8-baseline CART), and 15 (D15-CART cell after one activation/rest cycles). Following an activation/rest cycle, T cell exhaustion markers CTLA4, LAG3, and PD1 returned to basal levels after an initial increase due to activation, while only TIM-3 levels remained elevated (BBζ: p=0.0090, 28ζ: p=0.0394). Increased TIM-3 expression is associated with T cell senescence, which prompted us to further investigate the development of a senescence phenotype. We found a prominent T cell senescence phenotype in BBζ compared to 28ζ, as evident by increased expression of p53 (BBζ: p=0.0248), p21 (BBζ: p=0.0483), CD27 (BBζ: p=0.0080), CD28 (BBζ: p=0.0327), uPAR (BBζ vs. 28ζ: p<0.0001), and KLRG1 (BBζ vs. 28ζ: p=0.0029) in recurrently activated-rested CART cells. Next, we evaluated the transcriptomic signature of recurrently activated-rested CART cells. Gene set enrichment analysis (GSEA) indicated enrichment of gene sets related to senescent T cells as well as senMayo, a novel gene set which is reported to be selectively enriched in senescing cells or tissues, in BBζ, but not in 28ζ, compared to T cell D0 or in BBζ D15 compared to 28ζ D15 (p=0.00014 and p=0.089, respectively). MYC-related gene sets were found to be significantly enriched in recurrently activated/rested BBζ and depleted in 28ζ (p<0.1). MYC expression is increased in BBζ (p= 0.0010) while decreased in 28ζ (p=0.0036) upon recurrent activation and is higher in BBζ (D8: p=0.0018, D15: p= 0.0022) compared to 28ζ at indicated time points by qPCR. Given these results, we induced senescence in CART cells using two alternative strategies: MYC-T58A activation (oncogene-induced senescence) and irradiation. Senescence induced by MYC-T58A overexpression ameliorated only BBζ killing (p=0.0057), whereas senescence induced by irradiation improved 28ζ killing (p= 0.0086), indicating versatile impact of senescence on treatment outcome diverse CART cell therapies. Finally, analysis with two independent patient data sets correlated the emergence of senescence with contradicting clinical outcomes to BBζ and 28ζ treatments. The presence of senescent 28ζ cells in the peripheral blood of 28ζ-treated patients was reported to be associated with complete response in the clinic in an independent analysis. In another cohort, 28ζ-treated patients with higher senescence score were correlated with longer disease-free survival (p=0.0029), while senMayo gene set enrichment in BBζ-treated patients was associated with non-response in the clinic (p=0.014). In the same cohort, MYC-related gene sets-the same genes sets enriched in our recurrently activated/rested BBζ-are also enriched in nonresponsive BBζ-treated patients. In summary, our study indicates that (i) CART cells are susceptible to a state of senescence, as demonstrated using three independent approaches (repeated activation/rest, irradiation, and MYC modulation), (ii) CART senescence is more prominent in BBζ than 28ζ, and (iii) senescence is associated with worse outcomes following BBζ but not 28ζ treatment.

Chimeric antigen receptor (CAR) T-cell therapy has revolutionized the treatment of hematological malignancies. However, CAR T-cell therapy still has low durable response rates and common associated toxicities such as cytokine release syndrome (CRS). We recently reported that sequential therapy with the CD19 monoclonal antibody tafasitamab and CD19-directed CAR T (CART19, 41BBζ costimulated) cells significantly ameliorated CAR T-cell apoptosis and tumor cell pyroptosis, improving CAR T safety and efficacy (PMID: 37879074). Building on these findings, we hypothesized that controlling massive initial CAR T-cell stimulation by diminishing extensive tumor cell pyroptosis is critical to improve CAR T safety and durability. To test this hypothesis, we evaluated several caspase (Casp) inhibitors, including Casp1, Casp3, Casp7, and Casp11, in combination with CAR T cells. We found that the Casp1 inhibitor VX765 did not inhibit CAR T antigen-specific cytotoxicity and thus focused on VX765 in subsequent assays. We first assessed CAR T proliferation upon stimulation with the CD19+ JeKo-1 mantle cell lymphoma cell line in the presence of VX765. CAR T with vehicle control showed greater proliferation at day 3, but CAR T with VX765 showed higher proliferation at day 5 (p=0.03, absolute CD3+ counts by flow cytometry). We then co-cultured CAR T and JeKo-1 for 24 hours and observed a significant reduction in apoptotic CAR T (Annexin V+ and 7-AAD- via flow cytometry) in VX765-treated conditions (p=0.05). Additionally, there was significantly reduced pyroptosis (Annexin V+ 7-AAD+) (p=0.02) but higher apoptosis (Annexin V+ 7-AAD-) in JeKo-1 in VX765-treated conditions (p=0.04). VX765-treated CAR T showed higher Bcl2 expression via flow cytometry (p=0.03). We also studied tumor cell pyroptosis by measuring the level of HMGB-1. CART19, JeKo-1, and VX765 or vehicle control were co-cultured for 24 hours, and the level of HMGB-1 was found to be significantly reduced in VX765-treated conditions, indicating reduced tumor pyroptosis (p=0.006). We then assessed the impact of Casp1 inhibition in our in vitro model of CAR T exhaustion. We stimulated CAR T with CD19+ JeKo-1 every other day for 2 weeks and then assessed CCR7 and CD45RA expression on CAR T. VX765-treated CAR T showed higher central memory (p=0.08) and naïve (p=0.02) and lower terminally differentiated effector memory phenotypes (p=0.03). We next studied the effect of Casp1 inhibition with VX765 in vivo. To recapitulate CAR T-cell toxicities, including CRS, we utilized an immunocompetent mouse model. First, we generated murine CART19 (mCART19, CD28ζ costimulated) cells. Recipient mice were then engrafted with luciferase+ murine CD19+ TBL12 cells, a murine lymphoma cell line. Mice were treated 12 days later with cyclophosphamide (300 mg/kg, ip) and 24 hours after mice were imaged and randomized to receive 1 x 107, 1) untransduced T cell control (UTD), 2) mCART19 + vehicle control, or 3) mCART19 + VX765 (25 mg/kg). VX765 was given immediately before the CART19 injection and on day 2 post-CAR T injection. Mice were serially monitored and weighed to assess CAR T-cell toxicity. Tumor burden was assessed via weekly bioluminescent imaging. Mice treated with vehicle control showed a significant reduction in weight compared to the UTD control (p=0.02), while mice treated with VX765 maintained their weight and remained active without signs of CRS, including motor weakness and hunched body. UTD mice reached humane endpoints within 3 weeks after T-cell injection. Three satellite mice from each group were euthanized and spleens were harvested. Flow cytometric analysis showed a significant reduction in apoptotic CAR T (p=) and pyroptotic tumor cells in mice treated with VX765 (p=0.03). Western blot showed lower cleaved GSDME and GSDMD in mice treated with VX765. VX765-treated mice demonstrated prolonged CAR T persistence with durable anti-tumor activity. In summary, Casp1 inhibition with VX765 significantly reduced CAR T apoptosis, improved memory phenotype, and increased delayed CAR T proliferation. VX765 also reduced tumor cell pyroptosis and CRS incidence without impacting CAR T anti-tumor activity in vivo. Given the favorable preclinical outcomes and existing clinical data on VX765, this approach holds substantial translational potential for enhancing the safety and efficacy of CAR T-cell therapy in patients with large B-cell lymphoma.

Brexucabtagene autoleucel (brexu-cel), a CD28-costimulated CD19-targeted chimeric antigen receptor T cell (CART19) product, was FDA-approved in 2020 after demonstrating remarkable efficacy in the pivotal ZUMA-2 trial of patients with mantle cell lymphoma (MCL). However, despite the impressive initial activity of CART19 cell therapy in MCL, most patients relapse within the first 3 years following treatment. Myeloid cells, such as monocytes and macrophages, have been demonstrated to be major inhibitors of other immune cells, including T cells. Growing evidence shows that monocytes and macrophages contribute to CART cell failure, although the exact mechanisms are not fully understood. To better understand the mechanisms contributing to CART treatment resistance in MCL, we first utilized brexu-cel products from patients with MCL on the ZUMA-2 trial to uncover their transcriptomic features by single cell RNA sequencing (scRNAseq) analysis. To understand if myeloid cells had negative impacts on clinical outcomes, we then analyzed autologous baseline peripheral blood mononuclear cell (PBMC) samples by scRNAseq. Our analyses of the brexu-cel samples revealed reduced response to IL-1β and its downstream signaling pathway as well as impaired T cell functions in non-responders. Transcriptomic analyses of the autologous baseline monocyte populations showed downregulation of IL-1β production and its associated pathways as well as upregulation of M2 phenotype-associated genes and IL-1 receptor antagonist (IL-1ra) in non-responder monocytes, implying a potential role of myeloid cells in CART resistance through impairment of IL-1 signaling in brexu-cel products. To validate our findings from the ZUMA-2 samples, we further studied the interactions between macrophages, MCL cells, and CART19 cells in preclinical models. First, CD28-costimulated CART19 cells generated from healthy donors were cocultured with JeKo-1, a CD19+ MCL cell line, and freshly isolated monocytes or ex vivo differentiated M2-like macrophages. M2-like macrophages were generated by incubating fresh monocytes with rhGM-CSF followed by coculturing with JeKo-1. CART19 antigen-specific proliferation was significantly inhibited by M2-like macrophages but not fresh monocytes (JeKo-1+CART19 vs JeKo-1+M2+CART19, p=0.00503). Transwell assays indicated that suppression by M2-like macrophages was contact-independent. Cytokine profile analysis of coculture supernatants showed significant elevation of IL-1ra in M2-like macrophage cocultures (JeKo-1+Mono+CART19 vs JeKo-1+M2+CART19, p=0.0292). This led us to hypothesize that M2-like macrophages inhibit CART19 by secreting IL-1ra to block IL-1 signaling in CART19. To test this hypothesis, we interrogated the role of IL-1ra in CART19. CART19 + JeKo-1 cocultures were supplemented with IL-1β + IL-1ra or IL-1β + IL-1ra + IL-1ra neutralizing antibody (neuAb). CART19 proliferation was improved by IL-1β (vehicle control vs IL-1β, p<0.0001). IL-1ra inhibited IL-1β-dependent CART19 proliferation (IL-1β vs IL-1β+IL1ra, p=0.0006), which was restored by IL-1ra neutralization (IL-1β+IL-1ra vs IL-1β+IL-1ra+IL-1ra neuAb, p=0.0215). Next, we assessed the impact of IL-1ra on CART functions in mouse MCL xenografts in the presence of M2-like macrophages. NOD-SCID-γ-/- (NSG) mice were subcutaneously injected with 0.5 million of human macrophages and 1 million of luciferase+ JeKo-1. Mice were then randomized once tumor engraftment was confirmed by bioluminescence imaging (BLI), followed by treatment with 2 million CART19 with 10 mg/kg IL-1ra neuAb or control IgG for 3 weeks. Combination of CART19 cells and IL-1ra neuAb led to improved antitumor activity based on BLI measurements compared to control IgG (IL-1ra neuAb vs control IgG, p=0.0058). Additionally, expression of IL-1RI, receptor of IL-1β and IL-1ra, was measured on T cells after coculturing CART19, JeKo-1, and M2-like macrophages. M2-like macrophages downregulated IL-1RI expression on CART cells, which might potentially desensitize CART response to IL-1β, resulting in further suppression in CART proliferation (JeKo-1+M2+CART19 vs JeKo-1+CART19, p=0.001). Overall, our study elucidates a potential mechanism of IL-1 pathway modulation mediated by myeloid cells in contributing to CART19 failure in MCL.

CD19-targeted chimeric antigen receptor T (CART19) cell therapy has shown outstanding clinical success. However, patients can develop CART-induced toxicities, including cytokine release syndrome (CRS) and neurotoxicity. Studies have found that activation of myeloid cells by granulocyte monocyte-colony stimulating factor (GM-CSF) can contribute to toxicity development. GM-CSF depletion leads to reduced myeloid activation, prevention of CART-induced toxicities, and improved CART efficacy. CART cells upregulate cytokine receptors upon activation, and our results indicate that CART19 cells significantly upregulate GMCSFR upon antigen-specific stimulation (<10% vs >30%, p<0.01). This led us to hypothesize that GMCSFR signaling contributes to CART cell activity. To understand the role of GM-CSFR upregulation on CART cell functions, we compared the impacts of neutralizing GM-CSF or blocking GM-CSF receptor alpha (GM-CSFRα) on CART19. First, 4-1BB-costimulated CART19 cells generated from healthy donors were stimulated with CD3/CD28 beads at a 1:3 ratio for 6 days. CART cells were maintained at 1 x 106/mL throughout the culture and supplemented with IgG isotype control, GM-CSF neutralizing antibody, or GM-CSFRα blockade at 10 μg/mL, 20 μg/mL, or 100 μg/mL. On day 6, cells were debeaded and rested for 2 days. Then, CART cells were cocultured with NALM6, a CD19+ acute lymphoblastic leukemia cell line, at a ratio of 1:1 for 3 days. The cocultures were supplemented with the same doses of antibodies listed above. Antigen-specific proliferation of CART cells was measured by flow cytometry. Our data suggested that CART19 proliferated is not impacted by GM-CSF neutralization but is inhibited by GM-CSFRα blockade (IgG isotype vs 10 μg/mL GM-CSFRα blockade, p<0.0001; IgG isotype vs 20 μg/mL GM-CSFRα blockade, p<0.0001; IgG isotype vs 100 μg/mL GM-CSFRα blockade, p=0.009). CART cells were assessed in a cytotoxicity assay with NALM6 luciferase+ cells as well, which did not show significant impacts from GM-CSF neutralization or GM-CSFRα blockade. To evaluate the impacts of GM-CSF neutralization and GM-CSFRα blockade in a mouse model, we engrafted NSG mice with 1 million NALM6 luciferase+ cells intravenously. Mice were then treated with 1.4 million CART19 plus 10 mg/kg IgG isotype control, GM-CSF neutralizing antibody, or GM-CSFRα blockade intraperitoneally. GM-CSFRα blockade drastically suppressed antitumor activities of CART (CART19+GM-CSFRα blockade vs CART19+IgG isotype control, p<0.0001; CART19+GM-CSFRα blockade vs CART19+GM-CSF neutralizing antibody, p<0.0001; CART19+ GM-CSFRα blockade vs untransduced T cell, n.s.). Serum cytokines were analyzed 2 days after CART treatment, showing that mice with GM-CSFRα blockade had significantly lower levels of human IFNγ (p=0.0189) and IL-2 (p=0.0121) compared to IgG isotype control group, while GM-CSF neutralization did not show significant impacts. Mice treated with CART plus IgG isotype control or GM-CSF neutralizing antibody showed prolonged survival compared to mice treated with GM-CSFRα blockade or untransduced T cells (p=0.0285). To unravel the mechanisms behind functional differences between GM-CSFRα blockade and GM-CSF neutralization, CART cells (n = 3 biological replicates) were cocultured with NALM6 at a 1:1 ratio supplemented with 10 μg/mL GM-CSF neutralizing antibody, GM-CSFRα blockade, or IgG isotype control overnight, followed by T cell isolation, bulk RNA isolation, and RNA sequencing (RNAseq) analysis. Our RNAseq data indicated significant upregulation (Log2FC>0.5, padj. <0.05) of T cell exhaustion- and dysfunction-associated genes (RGS16, PDCD1, CTLA4, NR4A3, CD101, LAG3) as well as negative regulators of T cell functions (G0S2, PIK3IP1, LGALS3) in the GM-CSFRα blockade group compared to GM-CSF neutralizing antibody or IgG isotype control groups. T cell activation-associated pathways were enriched in the GM-CSFRα blockade group. Overall, our data show that GM-CSFRα blockade impacts CART functions differently from GM-CSF neutralization. Specifically, GM-CSFRα blockade inhibits CART proliferation in vitro and antitumor activity in vivo. Interestingly, GM-CSFRα blockade leads to enrichment of T cell exhaustion- and dysfunction-associated genes in CART19, which is worth further investigation. These findings may be applicable to other cytokine receptors upregulated on activated CART cells.

Abstract Waldenstrom macroglobulinemia (WM) is a lymphoplasmacytic lymphoma associated with an increase in serum immunoglobulin M (IgM) monoclonal protein. The underlying causes of the disease are still not fully understood, but cells in the bone marrow (BM) microenvironment (TME) are anticipated to play a significant role in disease progression. We previously reported that myeloid-derived suppressor cells (MDSCs), a phenotypically heterogeneous group of cells known for their ability to suppress immune responses, are expanded in the bone marrow of patients with WM and that the expansion of MDSCs is particularly notable for increased numbers of polymorphonuclear MDSCs (PMN-MDSCs). In the present study, we evaluated the ability of WM cells to attract MDSCs to the tumor microenvironment (TME). We also evaluated whether PMN-MDSCs suppress the cytotoxic function of T-cells and thereby promote the survival of WM cells. Our study confirms the expansion of MDSCs, notably PMN-MDSCs in BM of WM patients as compared to normals. We also found that PMN-MDSCs expressing CD66b was a predominant population in WM patients. To determine the phenotype and transcriptome of both PMN-MDSCs and monocytic MDSCs (M-MDSCS) in WM, we compared BM aspirates from WM patients to normal bone marrow (NBM) and performed cellular indexing of transcriptomes and epitopes by sequencing (CITEseq) analysis (WM=3, NBM=2) followed by qPCR validation. We found that MDSCs in WM express significantly higher levels of HIF1-α overall (p<0.02) compared to NBM. Furthermore, PMN-MDSCs are more abundant in WM bone marrow than M-MDSCs and express significantly higher levels of CXCR4 (p<0.001), myeloperoxidase (MPO; p<0.0003), and azuricidin (AZU1; p<0.0004), suggesting an activated phenotype. To determine whether WM cells attract MDSCs to the BM, we performed a transwell assay and showed that WM cells (BCWM.1 cell line) attracted MDSCs, particularly PMN-MDSCs, to a greater extent than M-MDSCs (n=3; p<0.001). We next evaluated whether MDSCs prevent cytotoxic T-cells from lysing WM cells. In-vitro co-culture studies with BCWM.1 cells and T-cytotoxic cells (B:CD8-T) showed that T-cytotoxic cells were able to lyse the WM cell line by 46.4% , (median range 46.4 - 47.8%, p=0.001). However, when BCWM.1 cells and T-cytotoxic cells were co-cultured in the presence of MDSCs (i.e B:CD8-T:M), the specific lysis of BCWM.1 cells was reduced by 12.6% respectively (range 2.2- 12.6%, p<0.001). Furthermore, we observed that B:CD8-T:M co-culture significantly reduced CD8-T cell activation as compared to activated T cells alone (17.9%) (median range 17.8- 18%, p<0.001). In contrast, no affect was observed with B: CD8-T coculture by 91% (range 90.6- 91.4% p<.001) confirming that MDSCs suppress CD8-T cell activation. Our study therefore provides evidence that MDSCs in WM have an activated phenotype and that PMN-MDSCs in WM are attracted by malignant cells in the bone marrow. Furthermore, we find that the increased presence of PMN-MDSCs in the WM bone marrow environment suppresses T-cell lysis of malignant cells and may thereby contribute to disease progression. These findings provide a strong rationale for targeting MDSCs as a potential therapeutic strategy in WM.

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 >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.