Ding, Wei

Abstract Introduction: A subset of patients with chronic lymphocytic leukemia (CLL) experiences disease progression from CLL to Richter transformation (RT), characterized by the occurrence of a high-grade lymphoma. The outcomes of patients with RT are typically dismal and identifying better therapeutic strategies remains critically important for these patients. To discern the biologic underpinnings driving this transformation, we studied immune changes and genetic evolution in samples from CLL patients who developed RT. Methods: We identified 18 patients with CLL who developed RT; and performed single cell (sc) RNA-sequencing(seq) on sorted B and T cells from peripheral blood mononuclear cells (PBMCs) at the time of RT (n=18) and at the earlier time of CLL diagnosis (n=11). The median time between the CLL sample and the one closest to RT was 4.3 years (range, 0.2-7.3); and patients received a median of 1 CLL directed treatment (range, 0 – 7). A total of 749,906 cells and 36,601 genes were captured during scRNAseq and 720,580 cells and 21,892 genes were retained for downstream analysis, respectively. Analysis was performed using the immunopipe (https://github.com/pwwang/immunopipe) that wraps around Seurat (v5.1.0) and identified enriched pathways using Enrichr service. The sc-T cell receptor (TCR)-repertoire(R)-seq data was analyzed and visualized using scplotter (). The whole exome sequencing (WES) analysis with tumor B-cells from same patients of CLL & RT stages were done using the Agilent sureselect Human all exon v5 + UTR capture kit. Reads from paired end sequencing were processed with the sarek pipeline. Results: Analysis of 720,580 cells from 11 CLL and 18 RT samples showed 16 distinct cell types- 3 B and 13 T cell subtypes. We observed an increasing trend of CD8 TEM [mean 0.548 vs. 0.384, p = 0.12 (Wilcoxon test)] but a decreasing trend of CD4 TCM (mean 0.236 vs. 0.337, p = 0.08) and B-memory (mean 0.0085 vs. 0.0195, p = 0.51) subsets in RT compared to their CLL stage. When comparing transcriptional changes, we found that among the top 18 highly variable genes, the expression of FP236383.3 (lncRNA) and TCL1A was significantly higher (p<0.0001) in the B cell subsets of patients with RT vs. CLL stage. Additionally, in T cell subsets—primarily dnT, γδT, and CD8/CD4 naïve cells—the expression of FP236383.3, NKG7, GNLY, and CCL5 was significantly higher (p<0.0001), while the expression of LDHB, GZMK, and IL32 was significantly lower (p<0.0001) in RT vs. CLL stage samples. Comparison of specific gene set enrichment analysis showed significantly increased expression of GZMB in gdT (p<0.001) and decreased expression of GZMA, GZMK, TIGIT and TCF7 in dnT and CD8 Naïve cells (p<0.001) for RT vs. CLL stage. The top 10 differentially expressed pathways in RT included oxidative phosphorylation, allograft rejection, IFN-α/-γ responses, TNF-α signaling via NF-κβ, complement, Myc targets V1, mTORC1, hypoxia, and p53 signaling across various B and T cell subsets compared to the CLL stage. Initial analysis of TCR-R data showed that patients with RT stage have lower number of unique clones (p<0.5) and reduced clonal diversity (p<0.5), and a higher number of large and hyperexpanded clones compared to their CLL stage. Additionally, WES data indicated that the most frequently mutated gene is TP53 in tumor B cells of both CLL and RT stages. However, a higher percentage of RT-stage samples carry mutations in MGA, ATM, and IRF2BP2 genes compared to their CLL-stage. WES data also showed a trend toward differing frequencies of copy number amplification at 19q12 (p=0.10) and 4q13.1 (p=0.52) between RT and CLL stages. Conclusions: The main findings of our study are as follows:The transcriptional landscape showed significant changes in multiple genes and pathway enrichment related to cell growth, differentiation and immune response in RT vs. CLL stage.A decreased fraction of CD4 TCM cells and reduced TCR clonal diversity were observed in samples at the RT stage and may indicate a poor prognosis for the patients at this stage. WES data of tumor B cells also indicated possible genetic alterations in the RT vs. CLL stage. Data from in-depth analyses on understanding of the dynamics of T cell response and additional experiments on these patients are expected to provide valuable insights into tumor genetic heterogeneity, transcriptional and immune regulation in blood-based immune subsets.

Abstract CD19-targeted chimeric antigen receptor T cell (CART19) therapy has been remarkably successful in treating a subset of patients with hematological malignancies. However, it is associated with significant toxicities, including cytokine release syndrome (CRS) and neurotoxicity (NT). Furthermore, the rate of durable responses after CART19 therapy is low, and most patients develop resistance to the therapy. One of the predominant mechanisms for CART cell resistance is intrinsic T cell dysfunction which leads to a suboptimal CART product. The Bruton's tyrosine kinase (BTK) inhibitor ibrutinib has been shown to favorably modulate CART phenotype and function through downregulation of inhibitory receptors and enhancement of CART cell efficacy in preclinical models and early clinical studies. However, ibrutinib is an irreversible receptor tyrosine kinase (RTK) inhibitor, and thus there are concerns that it inhibits CART cell proliferation and expansion. In contrast to ibrutinib and other BTK inhibitors, vecabrutinib has recently emerged as a potent, reversible, non-covalent BTK inhibitor that can block the activity of both wild type and C481 mutant BTK as well as interleukin-2-inducible T-cell kinase (ITK). We hypothesized that treatment with vecabrutinib improves CART19 antitumor efficacy through the reversible inhibition of BTK/ITK, independent of its antitumor effect. To test this hypothesis, we assessed whether vecabrutinib potentiates CART19 cytotoxicity against CD19 + tumor cells. Killing of the CD19 + mantle cell lymphoma cell line, JeKo-1, was significantly increased when CART19 were combined with vecabrutinib (Fig. 1A). Of note, vecabrutinib did not induce antitumor activity in this model as a single agent (Fig. 1A). In addition, vecabrutinib (10 µM) treatment of CART19 resulted in enhanced antigen-specific proliferation (Fig. 1B). Next, we aimed to study the direct impact of vecabrutinib on CART19 cytokine production. We measured the levels of multiple pro-inflammatory cytokines in the supernatant of CART19 co-cultured for 3 days with JeKo-1 cells and vecabrutinib. Vecabrutinib did not impair CART19 degranulation, as measured by flow cytometric assessment of CD107a expression (Fig. 1C). Cytokines known to play a crucial part in the development of CRS, such as IL-6, IL-10, and MIP-1β were significantly downregulated in cocultures with vecabrutinib (Fig. 1D-F). We then investigated whether the addition of vecabrutinib to CART19 caused a synergistic antitumor effect in vivo. We used our established JeKo-1 lymphoma xenograft models. Here NSG mice were engrafted with CD19 + luciferase + JeKo-1 cells. Mice were then imaged for engraftment and randomized to treatment with 1) untransduced control T cells, 2) CART19 with vehicle, or 3) CART19 with vecabrutinib 50 mg/kg BID administered via oral gavage over a period of 4 weeks. Vecabrutinib combination with CART19 treatment led to sustained antitumor activity (Fig.1G) and increased CART19 proliferation (Fig.1H). Encouragingly, mice treated with vecabrutinib better maintained their body weight following CART19 infusion, suggesting possibly dampened toxicity (Fig.1I). We also measured serum cytokine levels from patients on a phase 1 clinical trial (NCT03037645) testing vecabrutinib in B cell malignancies at baseline and four weeks after treatment. We found that vecabrutinib significantly reduces the levels of multiple pro-inflammatory cytokines linked to CART cell toxicity, including MIP-1β, IP-10, and TNF-a (Fig. 1J-L), further validating our preclinical findings. Finally, we interrogated the transcriptome of CART19 co-cultured with JeKo-1 with or without vecabrutinib. Total RNA sequencing of activated CART19 highlighted a significant enhanced expression of multiple genes involved in the PI3K/AKT and Th1 pathways compared to antigen stimulated CART19 alone (Fig.1M, N). These results could explain the enhanced proliferation and cytotoxicity induced by vecabrutinib. In summary, we demonstrate for the first time that using the reversible BTK inhibitor, vecabrutinib, is a potent and a novel strategy to favorably modulate CART19 function by increasing their efficacy and decreasing toxicity. Further studies are currently underway to compare the effect of reversible versus irreversible BTK/ITK inhibition on CART functions and to further validate the mechanisms responsible for the observed effects. Figure 1 Figure 1. Disclosures Sakemura: Humanigen: Patents & Royalties. Cox: Humanigen: Patents & Royalties. Fox: Sunesis Pharmaceuticals: Current Employment. Ding: Merck: Membership on an entity's Board of Directors or advisory committees, Research Funding; Octapharma: Membership on an entity's Board of Directors or advisory committees; DTRM: Research Funding. Parikh: Pharmacyclics, MorphoSys, Janssen, AstraZeneca, TG Therapeutics, Bristol Myers Squibb, Merck, AbbVie, and Ascentage Pharma: Research Funding; Pharmacyclics, AstraZeneca, Genentech, Gilead, GlaxoSmithKline, Verastem Oncology, and AbbVie: Membership on an entity's Board of Directors or advisory committees. Kay: MEI Pharma: Research Funding; Sunesis: Research Funding; Rigel: Membership on an entity's Board of Directors or advisory committees; AstraZeneca: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; CytomX Therapeutics: Membership on an entity's Board of Directors or advisory committees; TG Therapeutics: Research Funding; Juno Therapeutics: Membership on an entity's Board of Directors or advisory committees; Bristol Meyer Squib: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Behring: Membership on an entity's Board of Directors or advisory committees; Genentech: Research Funding; Morpho-sys: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees, Research Funding; Targeted Oncology: Membership on an entity's Board of Directors or advisory committees; Tolero Pharmaceuticals: Research Funding; Dava Oncology: Membership on an entity's Board of Directors or advisory committees; Acerta Pharma: Research Funding; Agios Pharm: Membership on an entity's Board of Directors or advisory committees; Pharmacyclics: Membership on an entity's Board of Directors or advisory committees, Research Funding; Oncotracker: Membership on an entity's Board of Directors or advisory committees. Kenderian: Humanigen, Inc.: Consultancy, Honoraria, Research Funding.

Abstract Clinical practice guidelines recommend that individuals with HC MBL are evaluated annually for evidence of progression as it has been shown that they progress to develop CLL requiring therapy at a rate of 1-5%/year. Next-generation sequencing identified 59 genes recurrently mutated in CLL, and we previously showed that the tumor mutational load (TML), i.e., the total number of these genes mutated, is associated with a shorter time to first treatment (TTT) among 112 HC MBLs independent of the CLL international prognostic index (CLL-IPI), an established prognostic score. Herein, we continue to support our finding in additional HC MBLs and report the pooled results across the two cohorts. From the Mayo Clinic CLL Resource, we sequenced a total 167 HC MBL (112 from the initial round and 55 from additional sequencing). We extracted DNA from CD5+/CD19+ B-cells and sequenced the coding regions of 59 driver genes. Somatic mutations were called using MuTect2 in tumor-only mode. Germline variants were eliminated based on minor allele frequencies >0.01% and by those identified in public databases, unless present in known CLL mutation hotspots. After filtering, we computed the TML based on the number of genes with high impact (nonsense, frameshift and splicing) and hotspot mutations. Cox regression was used to estimate hazard ratios (HR) and 95% confidence intervals (CI), adjusted for sex and CLL-IPI. Stratified analyses were conducted by low/intermediate risk and high/very high CLL-IPI. Of the 167 HC MBL, low risk CLL-IPI comprised 60%, intermediate risk 28%, high risk 12%; and none were very-high risk. The most commonly mutated genes were SF3B1 (11%), NOTCH1 (9%), TP53 (7%), BIRC3 (7%), and MYD88 (6%); and 52 (31%) individuals had mutations in at least one gene. The median follow-up was 4.4 years, and 26 of the 167 individuals progressed to CLL requiring therapy. HC MBL with ≥2 mutated genes had a 28% 5-year risk of needing therapy compared to 6% among those with no mutated genes. Similar to our initial finding (HR=1.53, CI:1.12-2.07; P=0.007), we found a shorter TTT in the additional HC MBLs (HR=4.63, CI:1.57-13.7, P=0.006), and in the pooled cohort (HR=1.72; CI:1.29-2.28, P=0.0002). When we stratified by CLL-IPI risk, TML remained associated with TTT among individuals with low/intermediate CLL-IPI risk in the additional HC MBLs (HR=3.52, CI:1.11-11.2, P=0.03) and in the pooled cohort (HR=2.25, CI:1.34-3.77, P=0.002). A non-significant 2.8 fold association was observed with high risk CLL-IPI in the pooled cohort. In conclusion, the TML along with the CLL-IPI provide clinicians with a more accurate prognostic information regarding disease progression requiring therapy, especially for those MBLs with low to intermediate risk based on CLL-IPI. If validated, these findings may modify current practice guidelines for individuals with HC MBL. Citation Format: Geffen Kleinstern, Cecilia Bonolo de Campos, Nicholas J. Boddicker, Daniel R. O'Brien, Shulan Tian, Chantel Barney, Kari G. Rabe, Cristine Allmer, Laura Bruins, Aaron D. Norman, Timothy G. Call, Sameer A. Parikh, Jose F. Leis, Wei Ding, Huihuang Yan, James R. Cerhan, Neil E. Kay, Celine Vachon, Esteban Braggio, Susan L. Slager. Tumor mutational load derived from recurrently mutated genes in chronic lymphocytic leukemia (CLL) predicts time-to-first treatment in high-count monoclonal B-cell lymphocytosis (HC MBL) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 884.

Abstract Background:Recurrent mutations in ATM, JAK1/3 and STAT5B genes have been identified in T-cell prolymphocytic leukemia (T-PLL), a mature T cell leukemia with poor survival. However, much remains to be understood regarding the dysregulated pathways involved in the pathogenesis of this aggressive disease. Here, we integrated the analyses of whole exome sequencing (WES) and transcriptomes of a cohort of 12 T-PLL samples to gain further insights into molecular mechanisms of this malignancy. Methods: Leukemic cells were isolated from peripheral blood or bone marrow samples of T-PLL patients. Tumor DNA and RNA, and germline DNA were extracted from purified leukemic T cells and bone marrow derived stromal cells, respectively. WES (n=12) and transcriptome analysis (n=10) were performed and data analyzed with published standard methods (Robinson et al. 2010 and DePristo et al. 2011) Results: 7 paired tumor and germline DNA and 5 tumor-only DNA samples were used for WES analysis. Mutations in ATM and TET2 were detected in 4 (33%) and 1 (8%) patients, respectively. JAK3 (p.M511I, p.Q501H and p.Q503H) or STAT5B (2 p.T628S and 1 p.N642H) mutations each occurred in 3 (25%) cases and were mutually exclusive, consistent with prior reports. Importantly, we found several novel mutations in genes with regulatory roles in the NOTCH signaling pathway. Specifically, 2 somatic mutations p.A3V and p.A3S in NOTCH2 and 2 other mutations (p.S244L and p.A1414V) in NOTCH4 were identified in 4 (33%) patients. One mutation was in the EGF- like and another one in the NODP domain critical for NOTCH-mediated cellular differentiation. Two (16.7%) novel missense mutations (p.G174D and p.V836I) were found in MAML2. Three missense mutations (2 p.S583N and 1 p.R190H) occurred in MAML1. Both MAML2 and MAML1 are essential cofactors of the NOTCH signaling pathway. In addition, a somatic mutation in the NOTCH signal regulator DTX2 (p.G268D) was detected. Altogether 7 (58.3%) patients harbored mutations in genes with a regulatory role in the NOTCH pathway. Among the epigenetic modifiers, we found deletions and point mutations in KDM6B and KDM6A in 4 (30%) patients including 2 codon deletions in KDM6B (p.X751Val) and 1 missense mutation each in KDM6B (p.R1016Q) and KDM6A (p.V510G). KDM6A and KDM6B are histone H3 lysine 27 demethylases known to be involved in regulation of DNA repair and play an important role in embryonic differentiation. Transcriptome analyses of 10 T-PLL cases versus normal CD3+ T cells from 5 healthy donors revealed 706 up-regulated and 655 down-regulated genes. Consistent with prior data, TCL1A and TCL1B were significantly overexpressed (23.7 and 13.1 fold, respectively). Using Ingenuity Pathway Analysis, we found PTEN Signaling, glutamate receptor, and axonal guidance signaling to be among the top 3 upregulated pathways. The top upstream regulators implicated for the up-regulated signals were FGF, Wnt/β-catenin and TNF. The top 3 down-regulated pathways were granulocyte adhesion and diapedesis, IL-17A in psoriasis and IL-10 signaling. The top regulators for the down-regulated pathways were LPS, TNF and IFNg. Wnt/β-catenin and Human embryonic stem cell pluripotency signaling were among the top 20 up-regulated pathways. Many genes involved in the regulation of Wnt signal pathway were included in the above pathways, including Wnt ligands (Wnt9A, Wnt4), transmembrane receptors (CDH1, LRP5, FZD6, FZD7, SMO), cytoplasmic factor (AXIN2), and nuclear factors (MYC, SOX12, SOX8, SOX18, CCND1). Summary: Our study identified recurrent mutations in the NOTCH signaling pathway as well as dysregulated embryonic developmental pathway, e.g. Wnt/NOTCH as newly implicated molecular mechanisms in T-PLL pathogenesis for further functional studies. Additionally, novel (KDM6A and KDM6B) and known mutations (ATM, TET2) in chromatin regulatory genes underscore the importance of epigenetic dysregulation in the tumorigenesis of T-PLL. Disclosures Parikh: Pharmacyclics: Honoraria, Research Funding. Mustjoki:Ariad: Research Funding; Bristol-Myers Squibb: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; Novartis: Honoraria, Research Funding. Ding:Merck: Research Funding.