Inhibition of Human Dendritic Cell ER Stress Response Reduces T Cell Alloreactivity Yet Spares Donor Anti-tumor Immunity

Acute graft- vs. -host disease (GVHD) is an important cause of morbidity and death after allogeneic hematopoietic cell transplantation (HCT). We identify a new approach to prevent GVHD that impairs monocyte-derived dendritic cell (moDC) alloactivation of T cells, yet preserves graft- vs.-leukemia (GVL). Exceeding endoplasmic reticulum (ER) capacity results in a spliced form of X-box binding protein-1 (XBP-1s). XBP-1s mediates ER stress and inflammatory responses. We demonstrate that siRNA targeting XBP-1 in moDCs abrogates their stimulation of allogeneic T cells. B-I09, an inositol-requiring enzyme-1α (IRE1α) inhibitor that prevents XBP-1 splicing, reduces human moDC migration, allo-stimulatory potency, and curtails moDC IL-1β, TGFβ, and p40 cytokines, suppressing Th1 and Th17 cell priming. B-I09-treated moDCs reduce responder T cell activation via calcium flux without interfering with regulatory T cell (Treg) function or GVL effects by cytotoxic T lymphocytes (CTL) and NK cells. In a human T cell mediated xenogeneic GVHD model, B-I09 inhibition of XBP-1s reduced target-organ damage and pathogenic Th1 and Th17 cells without impacting donor Tregs or anti-tumor CTL. DC XBP-1s inhibition provides an innovative strategy to prevent GVHD and retain GVL

Inhibition of Human Dendritic Cell ER Stress Response Reduces T Cell Alloreactivity Yet Spares Donor Anti-tumor Immunity

Acute graft- vs. -host disease (GVHD) is an important cause of morbidity and death after allogeneic hematopoietic cell transplantation (HCT). We identify a new approach to prevent GVHD that impairs monocyte-derived dendritic cell (moDC) alloactivation of T cells, yet preserves graft- vs.-leukemia (GVL). Exceeding endoplasmic reticulum (ER) capacity results in a spliced form of X-box binding protein-1 (XBP-1s). XBP-1s mediates ER stress and inflammatory responses. We demonstrate that siRNA targeting XBP-1 in moDCs abrogates their stimulation of allogeneic T cells. B-I09, an inositol-requiring enzyme-1α (IRE1α) inhibitor that prevents XBP-1 splicing, reduces human moDC migration, allo-stimulatory potency, and curtails moDC IL-1β, TGFβ, and p40 cytokines, suppressing Th1 and Th17 cell priming. B-I09-treated moDCs reduce responder T cell activation via calcium flux without interfering with regulatory T cell (Treg) function or GVL effects by cytotoxic T lymphocytes (CTL) and NK cells. In a human T cell mediated xenogeneic GVHD model, B-I09 inhibition of XBP-1s reduced target-organ damage and pathogenic Th1 and Th17 cells without impacting donor Tregs or anti-tumor CTL. DC XBP-1s inhibition provides an innovative strategy to prevent GVHD and retain GVL

Clinical Impact of Neoantigen Burden and HLA Loss in Aggressive B-Cell Lymphomas Treated with CD19 CAR T-Cell

INTRODUCTION: CD19-directed chimeric antigen receptor (CAR-19) T cells have revolutionized clinical outcomes in heavily pretreated patients with aggressive B-cell lymphoma. Notably, emerging evidence suggests that the efficacy of CAR-19 therapy extends beyond direct tumor killing and includes its ability to stimulate and guide the host immune system in the fight against tumor cells. To delve deeper into this crucial aspect, our study utilized whole-genome sequencing (WGS) data to explore the impact of neoantigen burden and HLA loss in patients with aggressive large B-cell lymphoma (rrLBCL) who received CAR-19 therapy (WGS; Jain et al. Blood 2022). METHODS: To characterize the importance of genomic immunogenicity in rrLBCL, we conducted a comprehensive analysis of 61 whole-genome sequencing (WGS) and 54 RNA sequencing samples from 54 rrLBCL patients who underwent CAR-19 therapy. Among these samples, 39 were collected at baseline and 15 at relapse, with samples from 7 patients obtained both before and after treatment. Our analytical workflow defined HLA class I mono- or biallelic loss by integrating copy number variants, structural variants, single nucleotide variants, and small insertion-deletion data with allele-specific HLA loss information obtained from LOHHLA software. pVACseq algorithm was used to predict the number of clonal neoantigens in each sample, along with the corresponding HLA allele presenting each of them. RESULTS: HLA class I loss was detected in 38.9% of the patients, with no impact on progression free survival (PFS). Interestingly 7 patients had biallelic loss of HLA-B, and all of them experienced progression within the first year (p=0.03). To expand our analysis, we explored B2M an essential component of HLA class I complexes. B2M was lost in 33.3% of the patients without showing any association with shorter PFS. However, restricting the analysis to patients with B2M biallelic loss (defined as presence of deletions of both alleles, or deletion and mutation with high impact in the structure and function of the B2M protein) 4/4 patients progressed. Overall, all 11 patients with genomic events leading to biallelic loss of HLA class I progressed (p=0.007). Notably, in one patient (CAR_39), biallelic inactivation of HLA class I was not detected at baseline but emerged with the dominant clone at disease progression. HLA class I biallelic loss was associated with genomic drivers previously identified in our study as significantly associated with CAR-19 failure: APOBEC (3/11) and SBS18 (oxygen radical stress; 2/11) mutational signatures, chromothripsis (4/11), RHOA deletions (6/11), and double minutes (4/11). Next, we analyzed the impact of the neoantigen burden corrected for their HLA affinity and allelic status on the outcome of CAR-19 treatment. Patients with high number of neoantigens had shorter PFS (p=0.0095) and were enriched for genomic drivers associated with poor response after CAR-19 (e.g., APOBEC and SBS18). Interestingly, the neoantigen burden had a bimodal distribution across patients that progressed with two distinct groups: one with high neoantigen burden, biallelic loss of HLA, and high genomic complexity and the other with low genomic complexity and low neoantigen burden. Restricting the analysis to patients with retained HLA and low genomic complexity, high neoantigen burden associated with prolonged and favorable response to CAR-T therapy (p=0.04). CONCLUSION: This study offers evidence that there is a critical relationship between CAR-19 efficacy, LBCL immunogenicity, and the endogenous immune response

DataSheet_1_CAR-T manufactured from frozen PBMC yield efficient function with prolonged in vitro production.docx

Chimeric antigen receptor (CAR)-T cells are engineered to identify and eliminate cells expressing a target antigen. Current manufacturing protocols vary between commercial CAR-T cell products warranting an assessment of these methods to determine which approach optimally balances successful manufacturing capacity and product efficacy. One difference between commercial product manufacturing methods is whether T cell engineering begins with fresh (unfrozen) patient cells or cells that have been cryopreserved prior to manufacture. Starting with frozen PBMC material allows for greater manufacturing flexibility, and the possibility of collecting and storing blood from patients prior to multiple lines of therapy. We prospectively analyzed if second generation anti-CD19 CAR-T cells with either CD28 or 4-1BB co-stimulatory domains have different phenotype or function when prepared side-by-side using fresh or cryopreserved PBMCs. We found that cryopreserved PBMC starting material is associated with slower CAR-T cell expansion during manufacture but does not affect phenotype. We also demonstrate that CAR-T cell activation, cytokine production and in vitro anti-tumor cytotoxicity were not different when CAR-T cells were manufactured from fresh or cryopreserved PBMC. As CAR-T cell therapy expands globally, the need for greater flexibility around the timing of manufacture will continue to grow. This study helps support the concept that cryopreservation of PBMCs could be the solution to these issues without compromising the quality of the final CAR-T product.</p

Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma

CD19-directed chimeric antigen receptor (CAR-19)-T cells are groundbreaking immunotherapies approved for use against large B-cell lymphomas. While host inflammatory and tumor microenvironmental markers associate with efficacy and resistance, the tumor-intrinsic alterations underlying these phenomena remain undefined. CD19 mutations associate with resistance but are uncommon, and most patients who relapse retain expression of the wild-type receptor, implicating other genomic mechanisms. We therefore leveraged the comprehensive resolution of whole-genome sequencing to assess 51 tumor samples from 49 CAR-19-treated large B-cell lymphoma patients. We find that pre-treatment presence of complex structural variants, APOBEC mutational signatures, and genomic damage from reactive oxygen species predict CAR-19 resistance. In addition, the recurrent 3p21.31 chromosomal deletion containing the RHOA tumor suppressor was strongly enriched in patients failed by CAR-T therapy. Pretreatment reduced expression or mono-allelic loss of CD19 did not affect responses, suggesting CAR-19 therapy success and resistance are due to multiple mechanisms. Our study shows tumor-intrinsic genomic alterations are key among the complex interplay of factors that underly CAR-19 efficacy and resistance for large B-cell lymphomas

Figure S3 from Baseline Serum Inflammatory Proteins Predict Poor CAR T Outcomes in Diffuse Large B-cell Lymphoma

Figure S3 shows that prophylactic steroids do not improve efficacy outcomes in high risk patients</p

Table S1 from Baseline Serum Inflammatory Proteins Predict Poor CAR T Outcomes in Diffuse Large B-cell Lymphoma

Table S1 shows a multivariable analysis of grade >2 ICANS using baseline CRP and Ferritin as continuous variables.</p

Table S4 from Baseline Serum Inflammatory Proteins Predict Poor CAR T Outcomes in Diffuse Large B-cell Lymphoma

Table S4: Baseline patient and tumor characteristics in the validation cohorts</p