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The variable clinical course of follicular lymphoma (FL) is determined by the molecular heterogeneity of tumor cells and complex interactions within the tumor microenvironment (TME). IL-4 producing follicular helper T cells (TFH) are critical components of the FL TME. Binding of IL-4 to IL-4R on FL cells activates JAK/STAT signaling. We identified STAT6 mutations (STAT6MUT) in 13% of FL (N = 33/258), all clustered within the DNA binding domain. Gene expression data and immunohistochemistry showed upregulation of IL-4/STAT6 target genes in STAT6MUT FL, including CCL17, CCL22, and FCER2 (CD23). Functionally, STAT6MUT was gain-of-function by serial replating phenotype in pre-B CFU assays. Expression of STAT6MUT enhanced IL-4 induced FCER2/CD23, CCL17 and CCL22 expression and was associated with nuclear accumulation of pSTAT6. RNA sequencing identified PARP14 -a transcriptional switch and co-activator of STAT6- among the top differentially upregulated genes in IL-4 stimulated STAT6MUT lymphoma cells and in STAT6MUT primary FL cells. Quantitative chromatin immunoprecipitation (qChIP) demonstrated binding of STAT6MUT but not STAT6WT to the PARP14 promotor. Reporter assays showed increased IL-4 induced transactivation activity of STAT6MUT at the PARP14 promotor, suggesting a self-reinforcing regulatory circuit. Knock-down of PARP14 or PARP-inhibition abrogated the STAT6MUT gain-of-function phenotype. Thus, our results identify PARP14 as a novel therapeutic target in STAT6MUT FL.

Background Fine-needle aspiration (FNA) is used to diagnose malignancies, recurrences, and metastases. The procedure is quick and well tolerated and can be facilitated by ultrasound guidance. Methods This article describes the authors' experience in using serial FNA to harvest cellular material during 4 clinical trials of immunotherapy by in situ vaccination in patients with low-grade lymphoma. Results Two hundred ninety-six FNA samples were collected from 44 patients over a span of approximately 6 weeks for each patient. Samples were sufficient in quantity and quality to be analyzed by flow cytometry and/or single-cell messenger RNA sequencing. FNA samples yielded an average of 12 × 106 cells with a mean cellular viability of 86%. Material collected from the tumor lymph nodes differed significantly in the proportions and phenotypes of cellular populations in comparison with matched peripheral blood samples. A comparison of flow cytometry results obtained by FNA directly from the patient and by FNA performed ex vivo and a dissociation of the same lymph node after surgical excision confirmed that FNA sampling of the patient accurately represented the tumor and the microenvironment. An analysis of the FNA samples from immunotherapy-treated target lymph nodes versus nodes from nontreated tumor sites provided insight into the impact of specific immunotherapy regimens. Conclusions This is the largest study describing the use of serial FNA sampling to harvest cellular material during immunotherapy clinical trials. The success of this technique opens the door for FNA sampling to expand significantly future investigations of the dynamic effects of investigational agents, be they immunotherapies or targeted therapies.

In this proof-of-concept study, we developed a single cell method that identifies somatic alterations found in coding regions of mRNAs and integrates these mutation genotypes with their matching cell transcriptomes. We used nanopore adaptive sampling on single cell cDNA libraries, generated long read sequences from target gene transcripts and identified coding variants among individual cells. Short-read single cell transcriptomes characterized the cell types with mutations. We delineated CRISPR edits from a cancer cell line. From primary cancer samples, we targeted hundreds of cancer genes, identified somatic coding mutations and a gene rearrangement among individual tumor cells.

Tumor heterogeneity complicates biomarker development and fosters drug resistance in solid malignancies. In lymphoma, our knowledge of site-to-site heterogeneity and its clinical implications is still limited. Here, we profiled 2 nodal, synchronously acquired tumor samples from 10 patients with follicular lymphoma (FL) using single-cell RNA, B-cell receptor (BCR) and T-cell receptor sequencing, and flow cytometry. By following the rapidly mutating tumor immunoglobulin genes, we discovered that BCR subclones were shared between the 2 tumor sites in some patients, but in many patients, the disease had evolved separately with limited tumor cell migration between the sites. Patients exhibiting divergent BCR evolution also exhibited divergent tumor gene-expression and cell-surface protein profiles. While the overall composition of the tumor microenvironment did not differ significantly between sites, we did detect a specific correlation between site-to-site tumor heterogeneity and T follicular helper (Tfh) cell abundance. We further observed enrichment of particular ligand-receptor pairs between tumor and Tfh cells, including CD40 and CD40LG, and a significant correlation between tumor CD40 expression and Tfh proliferation. Our study may explain discordant responses to systemic therapies, underscores the difficulty of capturing a patient’s disease with a single biopsy, and furthers our understanding of tumor-immune networks in FL.

High-dose therapy and autologous stem cell transplantation (HDT/ASCT) is an effective salvage treatment for eligible patients with follicular lymphoma (FL) and early progression of disease (POD). Since the introduction of rituximab, HDT/ASCT is no longer recommended in first remission. We here explored whether consolidative HDT/ASCT improved survival in defined subgroups of previously untreated patients. We report survival analyses of 431 patients who received frontline rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) for advanced FL, and were randomized to receive consolidative HDT/ASCT. We performed targeted genotyping of 157 diagnostic biopsies, and calculated genotype-based risk scores. HDT/ASCT improved failure-free survival (FFS; hazard ratio [HR], 0.8, P = .07; as-treated: HR, 0.7, P = .04), but not overall survival (OS; HR, 1.3, P = .27; as-treated: HR, 1.4, P = .13). High-risk cohorts identified by FL International Prognostic Index (FLIPI), and the clinicogenetic risk models m7-FLIPI and POD within 24 months–prognostic index (POD24-PI) comprised 27%, 18%, and 22% of patients. HDT/ASCT did not significantly prolong FFS in high-risk patients as defined by FLIPI (HR, 0.9; P = .56), m7-FLIPI (HR, 0.9; P = .91), and POD24-PI (HR, 0.8; P = .60). Similarly, OS was not significantly improved. Finally, we used a machine-learning approach to predict benefit from HDT/ASCT by genotypes. Patients predicted to benefit from HDT/ASCT had longer FFS with HDT/ASCT (HR, 0.4; P = .03), but OS did not reach statistical significance. Thus, consolidative HDT/ASCT after frontline R-CHOP did not improve OS in unselected FL patients and subgroups selected by genotype-based risk models.

The unprecedented benefits of immunotherapy in advanced malignancies have resulted in increased interests in exploiting immune stimulatory agents in earlier-stage solid tumors in the neoadjuvant setting. However, systemic delivery of immunotherapies may cause severe immune-related side-effects and hamper the development of combination treatments. Intratumoral delivery of neoadjuvant immunotherapy provides a promising strategy in harnessing the power of immunotherapy while minimizing off-target toxicities. The direct injection of immune stimulating agents into the tumor primes the local tumor-specific immunity to generate a systemic, durable clinical response. Intratumoral immunotherapy is a highly active area of investigation resulting in a plethora of agents, for example, immune receptor agonists, non-oncolytic and oncolytic viral therapies, being tested in preclinical and clinical settings. Currently, more than 20 neoadjuvant clinical trials exploring distinct intratumoral immune stimulatory agents and their combinations are ongoing. Practical considerations, including appropriate timing and optimal local delivery of immune stimulatory agents play an important role in safety and efficacy of this approach. Here, we discuss promising approaches in drug delivery technologies and opportunity for combining intratumoral immunotherapy with other cancer treatments and summarize the recent preclinical and clinical evidences that highlighted its promise as a part of routine oncologic care.

PURPOSE Understanding the immunobiology of the 15% to 30% of patients with follicular lymphoma (FL) who experience progression of disease within 24 months (POD24) remains a priority. Solid tumors with low levels of intratumoral immune infiltration have inferior outcomes. It is unknown whether a similar relationship exists between POD24 in FL. PATIENTS AND METHODS Digital gene expression using a custom code set—five immune effector, six immune checkpoint, one macrophage molecules—was applied to a discovery cohort of patients with early- and advanced-stage FL (n = 132). T-cell receptor repertoire analysis, flow cytometry, multispectral immunofluorescence, and next-generation sequencing were performed. The immune infiltration profile was validated in two independent cohorts of patients with advanced-stage FL requiring systemic treatment (n = 138, rituximab plus cyclophosphamide, vincristine, prednisone; n = 45, rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone), with the latter selected to permit comparison of patients experiencing a POD24 event with those having no progression at 5 years or more. RESULTS Immune molecules showed distinct clustering, characterized by either high or low expression regardless of categorization as an immune effector, immune checkpoint, or macrophage molecule. Low programmed death-ligand 2 (PD-L2) was the most sensitive/specific marker to segregate patients with adverse outcomes; therefore, PD-L2 expression was chosen to distinguish immune infiltrationHI (ie, high PD-L2) FL biopsies from immune infiltrationLO (ie, low PD-L2) tumors. Immune infiltrationHI tissues were highly infiltrated with macrophages and expanded populations of T-cell clones. Of note, the immune infiltrationLO subset of patients with FL was enriched for POD24 events (odds ratio [OR], 4.32; c-statistic, 0.81; P = .001), validated in the independent cohorts (rituximab plus cyclophosphamide, vincristine, prednisone: OR, 2.95; c-statistic, 0.75; P = .011; and rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone: OR, 7.09; c-statistic, 0.88; P = .011). Mutations were equally proportioned across tissues, which indicated that degree of immune infiltration is capturing aspects of FL biology distinct from its mutational profile. CONCLUSION Assessment of immune-infiltration by PD-L2 expression is a promising tool with which to help identify patients who are at risk for POD24.

The Follicular Lymphoma (FL) International Prognostic Index (FLIPI) and FLIPI-2 are well-described clinical risk models. Age >60 years at diagnosis is a risk factor in both scores. Recently, we showed that older age is not associated with higher risk of disease progression or inferior treatment efficacy. Instead, shorter survival of older patients results mainly from an increased risk of nonrelapse deaths. This questions the value of age as a meaningful component of scores intended to predict disease-specific survival. The newly proposed PRIMA-prognostic index (PRIMA-PI) only includes β2-microglobulin levels and bone marrow infiltration as risk factors. Here, we independently validate the PRIMA-PI in a clinical trial cohort of 475 patients with advanced FL who uniformly received cyclophosphamide, doxorubicin hydrochloride, vincristine sulfate, prednisone, and rituximab (R-CHOP) as frontline therapy. The PRIMA-PI separated 3 similar sized risk cohorts with 5-year progression-free survival (PFS) rates of 74%, 59%, and 39%, respectively (P < .0001). Furthermore, we compare the PRIMA-PI with the FLIPI and FLIPI-2. We demonstrate that the PRIMA-PI has the highest specificity to identify high-risk patients (80% for 5-year PFS) because of its superior risk stratification in patients >60 years (73% vs 33% [FLIPI] and 47% [FLIPI-2] for 5-year PFS). Thus, the PRIMA-PI is a promising clinical tool to stringently identify patients at highest risk of poor outcome after frontline R-CHOP for advanced FL, and is particularly useful in patients with older age. Further validation in non–R-CHOP treated cohorts is needed.

Relapsed follicular lymphoma (FL) can arise from common progenitor cells (CPCs). Conceptually, CPC-defining mutations are somatic alterations shared by the initial and relapsed tumours, mostly B-cell leukaemia/lymphoma 2 (BCL2)/immunoglobulin heavy locus (IGH) translocations and other recurrent gene mutations. Through complementary approaches for highly sensitive mutation detection, we do not find CPC-defining mutations in highly purified BCL2/IGH-negative haematopoietic progenitor cells in clinical remission samples from three patients with relapsed FL. Instead, we find cells harbouring the same BCL2/IGH translocation but lacking CREB binding protein (CREBBP), lysine methyltransferase 2D (KMT2D) and other recurrent gene mutations. Thus, (i) the BCL2/IGH translocation can precede CPC-defining mutations in human FL, and (ii) BCL2/IGH-translocated cells can persist in clinical remission.

Summary Tumor cells orchestrate their microenvironment. Here, we provide biochemical, structural, functional, and clinical evidence that Cathepsin S (CTSS) alterations induce a tumor-promoting immune microenvironment in follicular lymphoma (FL). We found CTSS mutations at Y132 in 6% of FL (19/305). Another 13% (37/286) had CTSS amplification, which was associated with higher CTSS expression. CTSS Y132 mutations lead to accelerated autocatalytic conversion from an enzymatically inactive profrom to active CTSS and increased substrate cleavage, including CD74, which regulates major histocompatibility complex class II (MHC class II)-restricted antigen presentation. Lymphoma cells with hyperactive CTSS more efficiently activated antigen-specific CD4+ T cells in vitro. Tumors with hyperactive CTSS showed increased CD4+ T cell infiltration and proinflammatory cytokine perturbation in a mouse model and in human FLs. In mice, this CTSS-induced immune microenvironment promoted tumor growth. Clinically, patients with CTSS-hyperactive FL had better treatment outcomes with standard immunochemotherapies, indicating that these immunosuppressive regimens target both the lymphoma cells and the tumor-promoting immune microenvironment.

Duodenal-type follicular lymphoma (DTFL) is a rare and highly indolent follicular lymphoma (FL) variant. It is morphologically and immunophenotypically indistinguishable from typical FL, characterized by restricted involvement of intestinal mucosa, and lacks extraintestinal manifestations. The molecular determinants of this distinct clinical behavior are largely unknown. Thirty-eight diagnostic biopsies from patients with DTFL were evaluated. The 10-year overall survival rate was 100% in clinically evaluable patients (n = 19). We compared the targeted mutation profile of DTFL (n = 31), limited-stage typical FL (LSTFL; n = 17), and advanced-stage typical FL (ASTFL; n = 241). The mutation frequencies of recurrently mutated genes, including CREBBP, TNFRSF14/HVEM, and EZH2 were not significantly different. However, KMT2D was less commonly mutated in DTFL (52%) and LSTFL (24%) as compared with ASTFL (79%). In ASTFL, 41% of KMT2D-mutated cases harbored multiple mutations in KMT2D, as compared with only 12% in LSTFL (P = .019) and 0% in DTFL (P < .0001). Whole exome and targeted sequencing of DTFL revealed high mutation frequencies of EEF1A1 (35%) and HVCN1 (22%). We compared the immune microenvironment gene expression signatures of DTFL (n = 8) and LSTFL (n = 7). DTFL clearly separated from LSTFL by unsupervised, hierarchical clustering of 147 chemokines and cytokines and was enriched for a chronic inflammation signature. In conclusion, the mutational landscape of DTFL is highly related to typical FL. The lower frequency of multiple mutations in KMT2D in DTFL and LSTFL indicates an increasing selection pressure for complete KMT2D loss in ASTFL pathogenesis. The highly dissimilar immune microenvironment of DTFL suggests a central role in the biology of this disease.

The efficacy of an induced anti-tumor immune response is determined by a dynamic interaction and co-evolution of tumor cells and their microenvironment, leading to continuous changes in cellular and molecular properties of the tumor. Therefore, longitudinal tracking of subclonal evolution and the interplay between tumor and immune cells is important to dissect anti-tumor immunity and develop novel immunotherapy strategies. In situ vaccination is an effective immunotherapeutic treatment in indolent lymphoma, prompting tumor regression in the treated tumor site as well as in the untreated tumor sites (Frank et al., Cancer Discov 2018, Hammerich et al., Nat Med 2019). Here, we investigate dynamic implications of in situ vaccination on follicular lymphoma (FL) tumor cells by performing single cell RNA sequencing (scRNA-seq) and single cell B cell receptor sequencing (scBCR-seq) on serial samples from a clinical trial. Tumor specimens from 12 patients with FL enrolled in an ongoing in situ vaccination trial (NCT02927964) were selected for this analysis. As study treatment, one lymphoma site is treated with low-dose radiation (2Gy d1, 2Gy d2) and intratumoral injection of a TLR9 agonist (CpG) weekly for 5 doses. In addition, after 2 CpG injections, the patients receive daily oral ibrutinib, used here to enhance the T cell dependent systemic anti-tumor response (Sagiv-Barfi et al., Blood 2015). To profile the locally and systemically induced changes in tumor cells, fine needle aspirates were obtained serially - prior to treatment and, when possible after 1 and 6 weeks of treatment - from the injected and a non-injected tumor site. These specimens were subjected to scRNA-seq and scBCR-seq using the 10x chromium platform. On average, we sequenced 7,903 cells per sample detecting an average of 1,344 median genes per cell. We were able to analyze 68 patient samples including samples from both tumor sites and all time points. In total, we identified 198,640 tumor cells based on clonal light chain expression and presence of inferred copy number alterations. Longitudinal examination of the tumor cells revealed transcriptional changes during therapy at both the injected and non-injected sites, some of which related to clinical regression in the non-injected sites reflecting the induced immune-mediated anti-tumor response. In the pre-treatment samples, we found that increased expression of inflammation related pathways by tumor cells significantly correlated with inferior clinical response. In addition, tumor cell expression of the "don't eat me" signal CD47 was associated with less abscopal tumor regression (Fig. 1A), implicating CD47 as a potential target of future combination therapy. Among all patients, we detected a strong interferon alpha response to treatment at the injected tumor sites (Fig. 1B), though this did not correlate with clinical response. In contrast, therapy-induced expression of the MHC II genes was associated with abscopal clinical regression. Using the scBCR-seq data, we inferred the putative original tumor V(D)J sequence in each case and identified its somatically mutated derivatives. Tumor BCR subclones were defined as tumor subpopulations that had identical mutated V(D)J sequences. Tracking BCR subclones that were comprised of at least 15 cells, we discovered notable subclonal shifts at both the locally injected and the non-injected tumor sites during therapy (Fig. 1C). While the BCR subclone composition was similar within the 1-2 week time frame, several pre-existing subclones become dominant by the week 6 time point, suggesting possible selection for resistance phenotypes. Our translational single cell study provides a deep analysis of the tumor cell response during in situ vaccination in lymphoma patients, demonstrating not only dynamic changes in tumor cell phenotypes, but also therapy-induced differences among patients that correlated with clinical response. By integrating scRNA-seq and scBCR-seq data, we also have the unique opportunity to characterize BCR subclones transcriptionally, to link their phenotypes to tumor regression or resistance and to discover new targets for combinational therapies. Figure 1 Figure 1. Disclosures Shree: Gilead: Other: Spouse's employment. Levy: GigaGen: Membership on an entity's Board of Directors or advisory committees; Teneobio: Membership on an entity's Board of Directors or advisory committees; Nurix: Membership on an entity's Board of Directors or advisory committees; Dragonfly: Membership on an entity's Board of Directors or advisory committees; Apexigen: Membership on an entity's Board of Directors or advisory committees; Viracta: Membership on an entity's Board of Directors or advisory committees; Spotlight: Membership on an entity's Board of Directors or advisory committees; Immunocore: Membership on an entity's Board of Directors or advisory committees; Walking Fish: Membership on an entity's Board of Directors or advisory committees; Kira: Membership on an entity's Board of Directors or advisory committees; Abintus Bio: Membership on an entity's Board of Directors or advisory committees; Khloris: Membership on an entity's Board of Directors or advisory committees; Virsti: Membership on an entity's Board of Directors or advisory committees; BiolineRx: Membership on an entity's Board of Directors or advisory committees; BeiGene: Membership on an entity's Board of Directors or advisory committees; Quadriga: Membership on an entity's Board of Directors or advisory committees.

Introduction: In situ vaccination aims to induce an immune response locally at one tumor site that propagates systemically to all tumor sites. This approach can be effective in indolent lymphoma (Brody et al., JCO 2010, Frank et al., Cancer Discov 2018, Hammerich et al., Nat Med 2019). We designed a novel clinical strategy combining in situ vaccination with systemic ibrutinib, a kinase inhibitor that modulates B and T cells. Our preclinical work had shown that combined intratumoral CpG injection and systemic ibrutinib administration was curative of systemic disease in a mouse lymphoma model, an effect that was T cell dependent (Sagiv-Barfi, Blood, 2015). Here we report the results and correlative data from the Phase I/II clinical trial testing this combination along with local low-dose radiation in adults with recurrent low-grade B cell lymphoma (NCT02927964). Methods: Enrolled patients received intratumoral injections of CpG (SD-101, 3 mg) weekly for 5 doses and local radiation (4Gy in two fractions) to the same site. Daily oral ibrutinib (560mg) began after the second intratumoral injection. Revised Lugano criteria (Cheson et al., JCO, 2014) were used to assess overall radiographic responses to therapy. Distal responses were assessed by excluding the injected site and measuring only non-injected sites. Fine needle aspirates (FNAs) were obtained from CpG-injected and non-injected nodal tumor sites pre- and post-treatment and analyzed by flow cytometry and droplet-based single-cell RNA sequencing (scRNAseq). Results: Among the twenty patients treated on study, median age was 64, 55% were male, and all but one had a diagnosis of follicular lymphoma. All patients were previously treated with an average of 2 lines of therapy, and half had previously received chemotherapy. Adverse events (AEs) were consistent with known effects of ibrutinib (including diarrhea and rash) and of CpG (including fever and flu-like reactions). No drug-related grade 4, serious, or unexpected AEs were observed. As anticipated, all patients experienced tumor reduction at the locally treated site (median 84% reduction). Remarkably, all patients experienced some tumor reduction at non-injected non-irradiated index lesions (median 45%, range 13-100%), suggesting the generation of systemic immune responses (Figure 1A). By Cheson criteria, ten patients achieved an objective response, including one complete response (ORR 50%). Despite an overall improvement in tumor burden, three patients had new or progressing non-index lesions and scored as progressive disease. Treatment induced an expansion of naïve and effector memory T cells and reductions in T follicular helper (Tfh) and activated regulatory T cells (Tregs) at the injected site. T cells with high expression of transcripts related to oxidative phosphorylation (Toxphos) increased preferentially in patients with subsequent clinical tumor reduction (Figure 1B), implicating T cell metabolism in successful generation of immune responses. Analysis of single cell T cell receptor (TCR) sequencing data revealed>300 clones that were comprised of at least 2 cells at each timepoint and which expanded or contracted at least two-fold during treatment. Expanding clones were more likely than contracting clones to be activated or memory T cells and less likely than contracting clones to be Tfh or Tregs (Figure 1C-D). Clone dynamics were often similar at the two sampled tumor sites, reflecting systemic immune responses. Finally, in vitro assays showed treatment-induced expansion of tumor-specific T cells in the peripheral blood of all 6 evaluable patients. Conclusion: The combination of oral ibrutinib, intratumoral CpG, and local low-dose radiation is safe and can generate systemic antitumor immune responses and systemic tumor shrinkage in low-grade B cell lymphoma. Figure 1 Figure 1. Disclosures Shree: Gilead: Other: Spouse's employment. Khodadoust: CRISPR Therapeutics, Nutcracker Therapeutics: Research Funding; Myeloid Therapeutics: Membership on an entity's Board of Directors or advisory committees; Alexion, AstraZeneca Rare Disease: Other: Study investigator. Frank: Kite-Gilead: Membership on an entity's Board of Directors or advisory committees; Adaptive Biotechnologies: Research Funding; Allogene Therapeutics: Research Funding. Beygi: Kite/Gilead: Current Employment. Levy: GigaGen: Membership on an entity's Board of Directors or advisory committees; Teneobio: Membership on an entity's Board of Directors or advisory committees; Nurix: Membership on an entity's Board of Directors or advisory committees; Dragonfly: Membership on an entity's Board of Directors or advisory committees; Apexigen: Membership on an entity's Board of Directors or advisory committees; Viracta: Membership on an entity's Board of Directors or advisory committees; Spotlight: Membership on an entity's Board of Directors or advisory committees; Immunocore: Membership on an entity's Board of Directors or advisory committees; Walking Fish: Membership on an entity's Board of Directors or advisory committees; Kira: Membership on an entity's Board of Directors or advisory committees; Abintus Bio: Membership on an entity's Board of Directors or advisory committees; Khloris: Membership on an entity's Board of Directors or advisory committees; Virsti: Membership on an entity's Board of Directors or advisory committees; BiolineRx: Membership on an entity's Board of Directors or advisory committees; BeiGene: Membership on an entity's Board of Directors or advisory committees; Quadriga: Membership on an entity's Board of Directors or advisory committees.

Introduction: In situ vaccination aims to induce an immune response locally at one tumor site, that propagates systemically to all tumor sites. Prior clinical studies have demonstrated that this strategy can be effective in indolent lymphoma (Brody et al., JCO 2010, Frank et al., Cancer Discov 2018, Hammerich et al., Nat Med 2019). The underlying mechanisms, however, remain unclear, as immune recognition and destruction of cancer cells occurs at the level of the tumor microenvironment (TME), and the human TME has been difficult to study due to challenges in acquiring adequate tissue samples. Here, we directly investigate changes induced in the TME by in situ vaccination, applying single cell methods to serial samples from patients on a clinical trial, and relate these changes to clinical tumor response. Methods: We profiled serial specimens from 2 sites of disease in 10 indolent lymphoma patients enrolled in an in situ vaccination trial (NCT02927964). Motivated by compelling preclinical data demonstrating the efficacy of intratumoral CpG, a TLR9 agonist, and systemic ibrutinib, a BTK inhibitor (Sagiv-Barfi et al., Blood 2015), patients receive local low-dose radiation and CpG intratumorally to one site of disease and begin oral ibrutinib in the second week of treatment. Tumor fine needle aspirates (FNAs) from the injected and a distant uninjected tumor site as well as peripheral blood samples are obtained prior to, and at 1 and 6 weeks after treatment start. Single cells from the FNAs and blood samples are then subject to droplet-based single cell RNA sequencing, with approximately 3,000-10,000 cells sequenced per sample. Results: In total, we analyzed 314,827 cells from 52 tumor samples and 30 peripheral blood samples (Fig. 1A). At both the local injected and the distant uninjected tumor sites, we found significant changes in proportions and transcriptional phenotypes of tumor and immune cells, several of which tracked with clinical response. Upon treatment, the proportions of tumor cells decreased significantly at the treated site, even within the 6-week time frame (p=0.003). Increased expression of inflammation related genes at both the injected and uninjected sites (Fig. 1B) and of TGFb pathway genes at the uninjected site (Fig. 1C) were negatively associated with clinical response. Conversely, high expression of antigen presentation genes by week 6 at the injected site correlated with greater shrinkage of distant uninjected tumors (Fig. 1D). Among T and NK cells (Fig. 1E), we observed treatment-induced increases in naïve and cytotoxic CD4 and CD8 T cells, and reductions in T follicular helper and exhausted T cells (Fig. 1F). While all patients exhibited strong interferon responses in their T and NK cells, the degree of interferon response was not associated with overall clinical response (Fig. 1G). Instead, higher cytotoxic CD4 T cells at the injected site and fewer exhausted T cells at the uninjected site after treatment correlated with clinical response. Conclusions: By sampling multiple tumors over time in patients undergoing in situ vaccination, we identify significant changes in tumor and microenvironmental cells at both the injected and uninjected sites, several of which associate with clinical tumor regression. Our approach represents successful application of single-cell genomics to a clinical trial, illuminating treatment-induced cellular dynamics, and implicating tumor cell antigen presentation and CD4 T cell responses as possible determinants of clinical response. Disclosures Levy: Immunocore: Membership on an entity's Board of Directors or advisory committees; Walking Fish: Membership on an entity's Board of Directors or advisory committees; Viracta: Membership on an entity's Board of Directors or advisory committees; Quadriga: Membership on an entity's Board of Directors or advisory committees; Beigene: Membership on an entity's Board of Directors or advisory committees; GigaGen: Membership on an entity's Board of Directors or advisory committees; Teneobio: Membership on an entity's Board of Directors or advisory committees; Sutro: Membership on an entity's Board of Directors or advisory committees; Checkmate: Membership on an entity's Board of Directors or advisory committees; Nurix: Membership on an entity's Board of Directors or advisory committees; Dragonfly: Membership on an entity's Board of Directors or advisory committees; Abpro: Membership on an entity's Board of Directors or advisory committees; Apexigen: Membership on an entity's Board of Directors or advisory committees; Spotlight: Membership on an entity's Board of Directors or advisory committees; 47 Inc.: Membership on an entity's Board of Directors or advisory committees; XCella: Membership on an entity's Board of Directors or advisory committees.

Haploidentical hematopoietic stem cell transplantation (haplo-HSCT) using T-cell-replete grafts and post-transplantation cyclophosphamide (PTCY) provides a popular curative approach for older patients (pts) with high-risk (HR) MDS/AML. The sequential therapeutic concept herein, is used to optimize disease control and gain time, especially in patients suffering from active disease at time of haplo-HSCT. Yet, sequential conditioning regimens prior to haplo-HSCT are often associated with a considerable risk of severe adverse events especially in older comorbid patients. Previous studies in the HLA-matched setting have demonstrated feasibility and safety of treosulfan-based reduced intensity conditioning (RIC) by stable engraftment and low non-relapse mortality (NRM). However, data for treosulfan-based conditioning in the unmanipulated HLA-haplo-HSCT setting in HR AML/MDS pts are rare, especially in the context of sequential conditioning. Here we report on a matched-pair analysis of 26 patients treated with either a treosulfan- or melphalan-based sequential conditioning for haplo-HSCT using PTCY as GvHD prophylaxis in HR MDS/AML. We retrospectively analyzed the outcome and toxicity profile of 26 patients undergoing sequential haplo-HSCT at our center between January 2009 and June 2019. Thirteen patients with HR AML/MDS and >54 years old who underwent sequential haplo-HSCT using treosulfan (3x10g/m2) for RIC were considered for potential matching with recipients (n=30) of a sequential melphalan-based RIC regimen. Matching criteria comprised (1) disease activity (blast yes or no), (2) disease status (relapse, refractory, high-risk cytogenetics), (3) HCT-CI and (4) age (+/- 5 years). Post-grafting immunosuppression consisted of cyclophosphamide, tacrolimus and MMF. Thirteen patients undergoing treosulfan-haplo-HSCT were successfully pair-matched with thirteen recipients of melphalan-based haplo-HSCT, respectively ((1) p=1.0; (2) p=1.0; (3) p=1.0; (4) p=0,76). Median age of the entire cohort was 63 years (54-71). Each group consisted of two MDS patients and eleven AML patients. All recipients treated with treosulfan showed neutrophil engraftment with a median of 20 days while only 69% of the melphalan treated patients engrafted (median=19 days, p= 0.9). In the melphalan group one graft rejection occurred, three patients died in early aplasia. Acute GvHD °II-IV occurred in 23% and 44% of the patients treated with treosulfan or melphalan, respectively. Severe (°III-IV) non-hematologic regimen-related toxicities were seen in 2/13 pts of the treosulfan and 7/13 pts of the melphalan group, predominately affecting the GI-tract in both. NRM at day +100 was 0% and 31% (p=0.06) for the treosulfan and melphalan group, respectively. Thereby, infections made up for most NRM events. Conversely, CI of relapse at one year was 23% vs 0 % (p=0.004) for treosulfan vs melphalan. OS at 1-year (treosulfan group: 69% vs melphalan gropup: 62%) and PFS at 1-year (treosulfan group: 69% vs melphalan group: 62%) did not differ significantly between the groups (p=0.72) Sequential haplo-HSCT using treosulfan and PTCY in older advanced MDS/AML patients is safe, resulting in lower NRM at the expense of higher relapse incidence compared to the melphalan-based sequential conditioning approach. Treosulfan-based RIC in haplo-HSCT though might be an alternative in older pts with low leukemic burden. However for disease control its intensity should be reconsidered and all available post-grafting mantainance strategies applied. Disclosures Fraccaroli: Medac: Other: Travel Grant. Buecklein:Celgene: Research Funding; Amgen: Consultancy; Pfizer: Consultancy; Gilead: Consultancy, Research Funding; Novartis: Research Funding.

This study evaluates the role of sequential therapy in HLA-haploidentical transplantation (haplo-HSCT) of high-risk, relapsed/refractory AML/MDS. We analyzed the course of 33 adults with active disease at time of transplantation (AML n = 30; MDS n = 3; median age 58 years, range: 32-71). Sequential therapy consisted of cytoreductive chemotherapy (FLAMSA n = 21; clofarabine n = 12) applied shortly prior to reduced intensity conditioning for T-cell-replete haplo-HSCT using post-transplantation cyclophosphamide as GvHD prophylaxis. No graft rejection was observed. Complete remission at day +30 was achieved in 97% of patients. CI of acute GvHD grade II-IV and chronic GvHD was 24% (no grade IV) and 23%, respectively. NRM at 1 and 3 years was 15%, each. Severe regimen-related toxicities (grade III-IV) were observed in 58%, predominantly involving the gastrointestinal tract (diarrhea 48%, mucositis 15%, transient elevation of transaminases 18%). Probability of relapse at 1 and 3 years was 28% and 35%. At a median follow-up of 36 months, the estimated 1- and 3-year overall survival was 56% and 48%. Disease-free survival was 49% and 40%, respectively. At 3 years, GvHD and relapse-free survival (GRFS) was 24% while chronic GvHD and relapse-free survival (CRFS) was 29%. Thus, our results indicate that sequential haplo-HSCT is an effective salvage treatment providing high anti-leukemic activity, favorable tolerance, and acceptable toxicity in patients suffering from advanced AML/MDS.

Chronic lymphocytic leukemia (CLL) cells fail to enter apoptosis in vivo as opposed to their non-malignant B-lymphocyte counterparts. The ability of CLL cells to escape apoptosis is highly dependent on their microenvironment. Compared to non-malignant B cells, CLL cells are more responsive to complex stimuli that can be reproduced in vitro by the addition of cytokines. To understand the molecular mechanism of the environment-dependent anti-apoptotic signaling circuitry of CLL cells, we quantified the effect of the SDF-1, BAFF, APRIL, anti-IgM, interleukin-4 (IL4) and secreted CD40L (sCD40L) on the survival of in vitro cultured CLL cells and found IL4 and sCD40L to be most efficient in rescuing CLL cells from apoptosis. In quantitative dose-response experiments using cell survival as readout, the binding affinity of IL4 to its receptor was similar between malignant and non-malignant cells. However, the downstream signaling in terms of the amount of STAT6 and its degree of phosphorylation was highly stimulated in CLL cells. In contrast, the response to sCD40L showed a loss of cooperative binding in CLL cells but displayed a largely increased ligand binding affinity. Although a high-throughput microscopy analysis did not reveal a significant difference in the spatial CD40 receptor organization, the downstream signaling showed an enhanced activation of the NF-kB pathway in the malignant cells. Thus, we propose that the anti-apoptotic phenotype of CLL involves a sensitized response for IL4 dependent STAT6 phosphorylation, and an activation of NF-kB signaling due to an increased affinity of sCD40L to its receptor.

It is increasingly evident that the composition of the tumor microenvironment (TME) and the interplay between malignant and immune cells determine the efficacy of antitumor immune responses, whether pre-existing or induced by therapy. To profile the complexity and plasticity of the TME and track antitumor immunity, we performed single cell RNA sequencing on tumor fine needle aspirates and peripheral blood of lymphoma patients undergoing immunotherapy on a clinical trial (NCT02927964). In this in situ vaccination study motivated by compelling preclinical data (Sagiv-Barfi et al., Blood 2015), patients with low-grade lymphoma receive local low-dose radiation and a TLR9 agonist (CpG) intratumorally to one site of disease. In the second week, after the second of 5 intratumoral CpG injections, they begin taking oral ibrutinib. Tumor fine needle aspirates (FNAs)and peripheral blood samples are obtained prior to treatment, and at 1 week and 6 weeks after treatment start. Single cell preparations of FNA and blood samples are processed using the 10X Genomics platform (based on Zheng et al., Nat Commun 2017). Libraries are sequenced to an average targeted depth of 50,000 reads/cell. Identification of variable genes, principal component and graph-based clustering, and differential expression analysis of single-cell gene expression data is performed using the Seurat algorithm (Butler et al., Nat Biotech, 2018). We have prepared sequencing libraries from 58 tumor FNA and peripheral blood samples from 7 patients thus far. For the first 6 patients, approximately 3,000-10,000 cells per sample have been sequenced, with excellent sequencing quality metrics. Evaluating treatment-induced changes at the CpG-injected site across patients, we found a loss of tumor B cells and T follicular helper cells (Tfh) along with increases in CD8 and CD4 effector cells. Genes associated with cell death, DNA damage response, interferon response, and antigen presentation were induced in tumor B cells after treatment, while genes associated with several signaling pathways, including Myc, Wnt/beta-catenin, and MTOR were down-regulated. In contrast, treatment-induced changes in the tumor-resident T-cells were dominated by a strong interferon response (to both interferon-alpha and -gamma), strongest in CD4 effector and memory populations and weakest in T follicular helper cells and exhausted T cells. T-cells also showed induction of genes associated with TNF-alpha signaling, IL6 signaling, and inflammatory chemokines and cytokines. Interestingly, at the distal, non-injected site, similar changes occurred with smaller magnitude and more so at the week 6 timepoint. Further expression analysis, sequencing and analysis of single cell TCR clonotypes, and relation of results to clinical data is ongoing. Deep profiling of serial biopsies offers a comprehensive view of the evolving immune microenvironment during immunotherapy. By sampling multiple tumors over time in patients undergoing in situ vaccination, we identify significant and distinct transcriptional shifts in different tumor microenvironmental subpopulations at both the injected and un-injected sites, including activation of T-cells both sites with different dynamics. Our approach represents successful application of single-cell genomics to a clinical trial, illuminating cellular dynamics induced by treatment. Disclosures Levy: Apexigen: Membership on an entity's Board of Directors or advisory committees; Nohla: Membership on an entity's Board of Directors or advisory committees; Spotlight: Membership on an entity's Board of Directors or advisory committees; 47 Inc: Membership on an entity's Board of Directors or advisory committees; XCella: Membership on an entity's Board of Directors or advisory committees; Immunocore: Membership on an entity's Board of Directors or advisory committees; Walking Fish: Membership on an entity's Board of Directors or advisory committees; Five Prime: Membership on an entity's Board of Directors or advisory committees; Corvus: Membership on an entity's Board of Directors or advisory committees; Quadriga: Membership on an entity's Board of Directors or advisory committees; BeiGene: Membership on an entity's Board of Directors or advisory committees; GigaGen: Membership on an entity's Board of Directors or advisory committees; Teneobio: Membership on an entity's Board of Directors or advisory committees; Sutro: Membership on an entity's Board of Directors or advisory committees; Checkmate: Membership on an entity's Board of Directors or advisory committees; Nurix: Membership on an entity's Board of Directors or advisory committees; Dragonfly: Membership on an entity's Board of Directors or advisory committees; Innate Pharma: Membership on an entity's Board of Directors or advisory committees; Abpro: Membership on an entity's Board of Directors or advisory committees.

Transplant-associated microangiopathy (TAM) is a life-threatening complication after allogeneic transplantation, related to endothelial toxicity caused by chemoradiotherapy, infections, immunosuppressive drugs and GvHD. Clinical manifestations include severe thrombocytopenia, microangiopathic hemolysis and organ dysfunction (e.g. renal, neurological) in the absence of disseminated intravascular coagulation. The reported incidence of TAM after allogeneic hematopoietic stem cell transplantation (HSCT) varies between 0,5 to 70%. Data for TAM occurrence and outcome in the context of HLA-haploidentical transplantation (haplo-HSCT) are rare. Here, we report our experience on TAM incidence, disease manifestation, treatment and outcome in T-cell-replete haplo-HSCT using PTCY as GvHD prophylaxis. We retrospectively analyzed the treatment course of 148 adult patients undergoing haplo-HSCT with regard to the incidence of TAM at our center from January 2012 to April 2019. The diagnosis of TAM required the fulfillment of the criteria as defined by Ruutu et al., Haematologica 2007. Median age of the entire cohort was 54 years (23-74). The majority of patients was transplanted for myeloid disease (60%). Postgrafting immunosuppression consisted of PTCY, CNI and MMF in all patients. Median follow-up time upon survivors was 3 years (4 months - 7 years). Twenty of 148 patients developed TAM, with a cumulative incidence of 10% at day 100. Median interval from haplo-HSCT to TAM onset was 63 days (23-295 days), with seven patients showing TAM after day +100. Median platelet count at diagnosis was 20 x 109/L (range: 6-116), predominantly de novo or worsening thrombocytopenia. Median LDH level was 437 IU/L (305-1445 IU/L). Serum haptoglobin levels were decreased in 85% of the TAM patients. 12/20 patients had active infection at the time of TAM diagnosis, most commonly viral (10/12). All but three patients presented with concurrent active acute GvHD requiring systemic steroid treatment in 16 patients Renal function abnormalities were diagnosed in 55% of the patients affected by TAM, with 4 patients requiring hemodialysis. Nine patients developed grade III hypertension and three patients showed neurologic dysfunction. Upon diagnosis of TAM, CNI dose was reduced (7 patients) or temporarily discontinued (7 patients). No switch to another CNI was performed. FFPs were transfused in nine patients, three patients underwent plasma exchange therapy without any effect. In four patients rituximab was applied. With a CI of 18% vs 2% (p0.002) using a PBSC graft was a risk factor for TAM development when compared to BM. Neither origin of disease (myeloid/lymphoid) nor sex of patient/donor or conditioning intensity (RIC/MAC) influenced the incidence significantly. Estimated one-year and three-year overall survival did not differ between the TAM and the non-TAM cohort (61% vs 61% and 46% vs 47%, p=0.9). Only one patient died because of TAM. With an incidence of 10% at day +100 at our center TAM is a serious but not rare complication after haplo-HSCT using PTCY, CNI and MMF for GvHD prophylaxis. However, in our cohort disease course was moderate with low TAM-associated mortality. The use of a PBSC graft was the only factor influencing TAM incidence. Disclosures Hiddemann: F. Hoffmann-La Roche: Research Funding.

Follicular lymphoma (FL) originates from a single B cell that has rearranged one copy of its BCL2 gene on chromosome 18 to the Ig locus on chromosome 14 and in addition has acquired a mutation in a histone modifying gene such as CREBBP or KMTD2. By the time the disease is diagnosed the progeny of this original cell harbors additional mutations and is usually found at multiple lymphoid sites throughout the body. At each of these sites the malignant cells are accompanied by a rich network of follicular dendritic cells, T cells and other immune cells. This tumor microenvironment (TME) is clearly an important feature of the biology of FL and can impact the clinical behavior of the disease (Dave et al., NEJM, 2004). It remains unknown whether tumor clonal heterogeneity and the composition of the TME differ between various lymphoma sites within the same patient. Single cell RNA sequencing facilitates a detailed and unbiased view of both the tumor clone and the complex TME. To profile the TME and explore FL tumor evolution, we obtained fine needle aspirates (FNAs) at 2 different sites in the body and peripheral blood specimens all on the same day and subjected these samples to single cell RNA sequencing and immune repertoire analysis. These biopsies were taken prior to therapy from patients entering immunotherapy clinical trials (NCT02927964, NCT03410901). Single cell RNA sequencing of FNA and blood samples was performed using the 10X Genomics platform to an average targeted depth of 50,000 reads/cell. We have prepared sequencing libraries from 15 tumor FNA and peripheral blood samples from 5 patients thus far. Typically, 3,000-10,000 cells have been sequenced per sample, with excellent sequencing quality metrics. By applying Uniform Manifold Approximation and Projection (UMAP), a dimensionality reduction algorithm, we found the TME of these FL patients to be richly populated by many phenotypically discrete non-malignant cells, including many subpopulations of T cells, B-cells, myeloid cells, NK cells and dendritic cells. Evaluating the combined dataset containing all tumor samples for all 5 patients, we found that malignant B cells from different patients clearly clustered apart from each other, a feature not dependent on immunoglobulin clonality or HLA type. Each patient's tumor population contained 3-5 distinct subpopulations, presumably a result of multiclonal tumor evolution. Nonetheless, we were able to define several malignant B-cell sub-phenotypes common to all patients. Intriguingly, compared to malignant B cells, infiltrating non-malignant B cells showed higher MHC I expression, activation markers, and an enrichment in interferon-induced genes. Of note, we could also detect circulating tumor cells in peripheral blood samples of several patients, and these exhibited a distinct gene expression profile compared to their counterparts within lymph nodes. Analysis of the diverse T cell subpopulations within tumors revealed distinct functional states. For example, in regulatory and T follicular helper cells, we identified activated clusters (CD27, BATF, TNFRSF4) and putative resting clusters (SELL, KLF2, IL7R), while effector T cells resided in separate cytotoxic (GZMA, GZMB, GNLY) and exhausted (TIGIT, CXCL13, LAG3) clusters. Tumor B cell gene expression and composition of the TME from site to site within the same patient were similar in some cases and remarkably divergent in others. For example, we detected a significant upregulation of interferon signaling pathways in the tumor B cells and an enrichment of effector T cells in only one of the two sites within one patient. Analysis of B cell and T cell antigen receptor sequences to evaluate tumor subclonality and TCR clonotype diversity are ongoing. To the best of our knowledge, this is the first study to compare different sites of FL in the same patients at the single cell level. Our analyses characterize inter- and intra-patient heterogeneity in malignant and immune cell subsets and provide a baseline for eventual comparison of alterations occurring over time as these patients receive experimental immunotherapy interventions. Disclosures Levy: XCella: Membership on an entity's Board of Directors or advisory committees; Immunocore: Membership on an entity's Board of Directors or advisory committees; Walking Fish: Membership on an entity's Board of Directors or advisory committees; Five Prime: Membership on an entity's Board of Directors or advisory committees; Corvus: Membership on an entity's Board of Directors or advisory committees; Quadriga: Membership on an entity's Board of Directors or advisory committees; BeiGene: Membership on an entity's Board of Directors or advisory committees; GigaGen: Membership on an entity's Board of Directors or advisory committees; Teneobio: Membership on an entity's Board of Directors or advisory committees; Sutro: Membership on an entity's Board of Directors or advisory committees; Checkmate: Membership on an entity's Board of Directors or advisory committees; Nurix: Membership on an entity's Board of Directors or advisory committees; Dragonfly: Membership on an entity's Board of Directors or advisory committees; Innate Pharma: Membership on an entity's Board of Directors or advisory committees; Abpro: Membership on an entity's Board of Directors or advisory committees; Apexigen: Membership on an entity's Board of Directors or advisory committees; Nohla: Membership on an entity's Board of Directors or advisory committees; Spotlight: Membership on an entity's Board of Directors or advisory committees; 47 Inc: Membership on an entity's Board of Directors or advisory committees.

The highly variable clinical course of follicular lymphoma (FL) is determined by the molecular heterogeneity of the tumor cells and complex interactions with the microenvironment. Here, we provide biochemical, structural, functional and clinical evidence that aberrant Cathepsin S (CTSS) activity induces a supportive immune microenvironment in FL. By targeted DNA sequencing of 305 diagnostic FL biopsies, we identified somatic mutations of CTSS in 8% of cases (24/305), mostly clustered at Y132 (19/24) converting Y to D (16/19). A subset of CTSS Y132 mutations (N=5) occurred at lower variant allele frequencies (5-10%), indicating subclonality. Another 13% of FL had CTSS amplifications (37/286). CTSS Y132 mutations and CTSS amplifications were mutually exclusive. In a cohort of 51 FL, CTSS amplifications were associated with higher CTSS expression (P=0.05). Of note, a subset of FL without CTSS amplifications also had higher CTSS expression, suggesting additional mechanisms of transcriptional dysregulation. CTSS is a cysteine protease that is highly expressed in endolysosomes of antigen presenting cells and malignant B-cells. CTSS is involved in proteolytical processing of antigenic peptides for presentation on MHC-II to be recognized by antigen specific CD4+ T-cells. CTSS is synthesized as an inactive zymogen, which is converted to its active form by autocatalytic cleavage of the autoinhibitory propeptide (pro-CTSS). We used CRISPR/Cas9 to introduce CTSS Y132D into Karpas422, a B-cell lymphoma cell line that harbors the FL hallmark translocation t(14;18). Single-cell derived Y132D mutant clones showed >3-fold higher ratios of active CTSS to pro-CTSS (N=4, P=0.0003). Immunoprecipitated CTSS Y132D had >3-fold higher in vitro substrate cleavage activity compared to CTSS wild type (WT) (N=6, P=0.001). We purified pro-CTSS WT and Y132D and assayed their in vitro autocatalytic cleavage over time. The time required to convert 50% of pro-CTSS decreased from 17 minutes for WT to 11 minutes for Y132D (N=3, P=0.04). In contrast, purified active CTSS WT and Y132 had similar in vitro cleavage activities. Molecular dynamics simulations showed that the Y132D mutation shortens the distances by ~2Å between the catalytic triad of active CTSS (C139, H278, N298) and a stretch of amino acids from the proform (L80, G81, D82, S94), which may facilitate intramolecular cleavage. By mass spectrometry we could indeed detect novel intermediate-sized CTSS fragments. Thus, Y132D does not increase the activity of the mature enzyme but is a gain-of-function mutation by accelerating the conversion from pro-CTSS to catalytically active CTSS. CD74 (invariant chain) is a physiologic CTSS substrate that plays critical roles in the assembly, trafficking and stabilization of peptide-free MHC-II. CTSS cleaves CD74, thereby allowing binding and presentation of antigens on MHC-II to antigen specific CD4+ T-cells. We could show that CTSS Y132D enhanced CD74 cleavage in Karpas422 cells. We then tested the impact of CTSS on antigen specific CD4+ T-cell activation in co-culture assays. CTSS knock-out lymphoma cells were broadly incapable of activating CD4+ T-cells. Overexpression of CTSS WT activated CD4+ T-cells more efficiently compared to empty vector control. CTSS Y132 had the highest capacity to stimulate antigen specific CD4+ T-cell responses. Furthermore, in primary FL biopsies (N=51) CTSS Y132 mutations had gene expression profiles linked with antigen-processing and chemokine perturbation, including CXCL13, a B-cell chemoattractant produced by activated CD4+ T-follicular helper cells. Lastly, we aimed to correlate CTSS aberrations with clinical outcome in patients who received standard immunochemotherapy (R-CHOP) for advanced FL (N=51 with available CTSS mutation and gene expression data). Compared to all other patients (N=34), patients with CTSS Y132 mutations or CTSS overexpression (N=17) had longer failure free survival (P=0.012) and overall survival (P=0.041). In summary, we propose that aberrant CTSS activity - even if only present in a FL subclone - can elicit a CD4+ T-cell driven tumor-promoting immune response, which could be amplified within the microenvironment via pro-inflammatory and chemotactic cytokines and substantially impact the biology and clinical course of the disease. Thus, aberrant CTSS activity is a promising biomarker and therapeutic target in FL and potentially also other tumors. Disclosures Klapper: Roche, Takeda, Amgen, Regeneron: Honoraria, Research Funding. Hiddemann:Bayer: Research Funding; Roche: Consultancy, Honoraria, Research Funding; Gilead: Consultancy, Honoraria; Janssen: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria; Vector Therapeutics: Consultancy, Honoraria. Steidl:Juno Therapeutics: Consultancy; Bristol-Myers Squibb: Research Funding; Nanostring: Patents & Royalties: Filed patent on behalf of BC Cancer; Roche: Consultancy; Tioma: Research Funding; Seattle Genetics: Consultancy; Bayer: Consultancy. Kridel:Gilead Sciences: Research Funding. Weinstock:Celgene: Research Funding; Verastem Oncology: Research Funding. Weigert:Novartis: Research Funding; Roche: Research Funding.

A fundamental challenge in the era of next-generation sequencing (NGS) is to design effective treatments tailored to the mutational profiles of tumors. Many newly discovered cancer mutations are difficult to target pharmacologically; however, T-cell-based therapies may provide a valuable alternative owing to the exquisite sensitivity and specificity of antigen recognition. To explore this concept, we assessed the immunogenicity of a panel of genes that are common sites of driver mutations in follicular lymphoma, an immunologically sensitive yet currently incurable disease.Exon capture and NGS were used to interrogate tumor samples from 53 patients with follicular lymphoma for mutations in 10 frequently mutated genes. For 13 patients, predicted mutant peptides and proteins were evaluated for recognition by autologous peripheral blood T cells after in vitro priming.Mutations were identified in 1-5 genes in 81% (43/53) of tumor samples. Autologous, mutation-specific CD8(+) T cells were identified in 23% (3/13) of evaluated cases. T-cell responses were directed toward putative driver mutations in CREBBP and MEF2B. Responding T cells showed exquisite specificity for mutant versus wild-type proteins and recognized lymphoma cells expressing the appropriate mutations. Responding T cells appeared to be from the naïve repertoire, as they were found at low frequencies and only at single time points in each patient.Patients with follicular lymphoma harbor rare yet functionally competent CD8(+) T cells specific for recurrent mutations. Our results support the concept of using NGS to design individualized immunotherapies targeting common driver mutations in follicular lymphoma and other malignancies. Clin Cancer Res; 22(9); 2226-36. ©2015 AACR.

The Bruton tyrosine kinase (BTK) inhibitor ibrutinib induces responses in 70% of patients with relapsed and refractory mantle cell lymphoma (MCL). Intrinsic resistance can occur through activation of the nonclassical NF-κB pathway and acquired resistance may involve the BTK C481S mutation. Outcomes after ibrutinib failure are dismal, indicating an unmet medical need. We reasoned that newer heat shock protein 90 (HSP90) inhibitors could overcome ibrutinib resistance by targeting multiple oncogenic pathways in MCL. HSP90 inhibition induced the complete degradation of both BTK and IκB kinase α in MCL lines and CD40-dependent B cells, with downstream loss of MAPK and nonclassical NF-κB signaling. A proteome-wide analysis in MCL lines and an MCL patient-derived xenograft identified a restricted set of targets from HSP90 inhibition that were enriched for factors involved in B-cell receptor and JAK/STAT signaling, the nonclassical NF-κB pathway, cell-cycle regulation, and DNA repair. Finally, multiple HSP90 inhibitors potently killed MCL lines in vitro, and the clinical agent AUY922 was active in vivo against both patient-derived and cell-line xenografts. Together, these findings define the HSP90-dependent proteome in MCL. Considering the disappointing clinical activity of HSP90 inhibitors in other contexts, trials in patients with MCL will be essential for defining the efficacy of and mechanisms of resistance after ibrutinib failure.

Chronic lymphocytic leukemia (CLL) cells fail to enter apoptosis in vivo as opposed to their non-malignant B-lymphocyte counterparts. The ability of CLL cells to escape apoptosis is highly dependent on their microenvironment. Compared to non-malignant B cells, CLL cells are more responsive to complex stimuli that can be reproduced in vitro by the addition of cytokines. To understand the molecular mechanism of the environment-dependent anti-apoptotic signaling circuitry of CLL cells, we quantified the effect of the SDF-1, BAFF, APRIL, anti-IgM, interleukin-4 (IL4) and secreted CD40L (sCD40L) on the survival of in vitro cultured CLL cells and found IL4 and sCD40L to be most efficient in rescuing CLL cells from apoptosis. In quantitative dose-response experiments using cell survival as readout, the binding affinity of IL4 to its receptor was similar between malignant and non-malignant cells. However, the downstream signaling in terms of the amount of STAT6 and its degree of phosphorylation was highly stimulated in CLL cells. In contrast, the response to sCD40L showed a loss of cooperative binding in CLL cells but displayed a largely increased ligand binding affinity. Although a high-throughput microscopy analysis did not reveal a significant difference in the spatial CD40 receptor organization, the downstream signaling showed an enhanced activation of the NF-kB pathway in the malignant cells. Thus, we propose that the anti-apoptotic phenotype of CLL involves a sensitized response for IL4 dependent STAT6 phosphorylation, and an activation of NF-kB signaling due to an increased affinity of sCD40L to its receptor.

Chronic lymphocytic leukemia is characterized by the accumulation of B cells that are resistant to apoptosis. This resistance is induced by pro-survival stimuli from the microenvironment. TCL1 and ATM are central to the pathogenesis of the disease and associated with more aggressive disease. Their protein products have recently been shown to physically interact in leukemic cells and to impact on NF-κB signaling, which is a key regulator of apoptosis. In the present study we show that TCL1 and ATM are significantly co-expressed and up-regulated in malignant cells compared to non-malignant B cells, and that expression of TCL1 is partially deregulated by aberrant DNA-methylation. In addition, complex external stimuli induce essentially similar TCL1 and ATM time-course kinetics. In line with a coordinative regulation of NF-κB signaling by TCL1, its knockdown induced apoptosis in primary leukemia cells. These findings suggest that both genes functionally cooperate to modulate similar apoptosis-related cellular pathways.

Mantle cell lymphoma (MCL) makes up approximately 6% of non-Hodgkin’s lymphoma cases and has an aggressive disease course with a particularly poor outcome. To date there is no standard treatment and despite good initial response to chemotherapy, most patients relapse with long-term survival achieved in less than 40%. In almost all cases, MCL is distinguished by overexpression of Cyclin D1 (CCND1) usually caused by a translocation between chromosomes 11 and 14. Both CCND1 and BTK are known clients of heat shock protein 90 (HSP90). In previous studies, we demonstrated potent cytotoxic activity of second- (NVP-AUY922, PU-H71) and third-generation (NVP-HSP990) HSP90 inhibitors against the MCL cell lines Granta519, JeKo1, MAVER1, Rec1, and Z-138 (IC50s for AUY922, 3-11nM; HSP990, 5-24nM; PU-H71, 40-287 nM). Immunobloting of MCL cell lines exposed to 50nM AUY922 demonstrated reduced expression of client proteins CCND1, CDK4 and AKT and induction of G0/G1 cell cycle arrest within 6-8h followed by apoptosis within 27h. We now demonstrate that combining Ibrutinib with AU922 results in synergistic or additive effects in all lines except for the highly Ibrutinib- sensitive JEKO-1. In fact, AUY922 overcame ibrutinib-resistance due to activation of non B-cell receptor (BCR)-driven alternative NFkB signaling in Granta519 and Z-138 cells. Due to the promising results of AUY922 we conducted two in vivo studies. Current mouse MCL models are generated by injecting MCL cell lines in matrigel subcutaneously. The MCL grows as a solid tumor and treatment is typically initiated when mean tumor volume is approximately 200 mm3. First, we xenografted luciferized MAVER1 (ibrutinib-sensitive) and Z-138 (ibrutinib-resistant) cells into SCID beige mice (10 million cells per mouse). Mice were randomized to receive either AUY922 (50 mg/kg by tail vein injection thrice weekly) or vehicle. Tumors analyzed from mice sacrificed after 5 days of treatment showed complete loss of cyclin D1 and Ki67 staining by immunohistochemistry in those receiving AUY922. Tumor growth was significantly slowed in AUY922 treated animals in both lines, which translated into a survival advantage (p Disclosures Weinstock: Novartis: Consultancy, Research Funding.