ALBERT

Description: Successful hematopoietic stem cell transplantation (HSCT) requires vacating recipient hematopoietic stem cell (HSC) niches in the bone marrow to permit donor HSC engraftment that can provide life-long hematopoietic and immune function. Currently, HSCT in SCID relies on DNA damaging chemotherapy to eliminate recipient HSC and achieve niche clearance. We have pursued a non-toxic approach to target and deplete HSC using a humanized monoclonal antibody, JSP191, that binds human CD117 (c-Kit). We previously showed the safety and successful HSC engraftment in a Phase 1 trial of the first 6 patients with severe combined immunodeficiency (SCID), who underwent a second transplant because of HSC engraftment failure and poor immunity after their first transplantation. In these re-transplant patients even a low level of stringently measured myeloid chimerism resulted in significant and sustained generation of naive T cells and clinical improvement. Based on these results, the study of JSP191 (NCT#02963064)has opened a cohort of newly diagnosed infants with SCID. Here we report data from the first patient in this cohort, a SCIDX1 patient who received a primary HSCT with haploidentical CD34+ cells after conditioning with JSP 191. The patient had a c.270-15A〉G variant in the IL2RG gene, which is predicted to cause a null phenotype. Besides a T- B+ NK- phenotype typical of SCIDX1 including dysfunctional B cells, the patient had anemia and intermittent neutropenia and thrombocytopenia. Despite evidence of maternal T cell engraftment, the patient had no clinical graft-versus-host disease (GVHD). The patient was initially enrolled in a trial of lentiviral gene therapy, but harvested bone marrow cells died in vitro during transduction and culture. The patient also mobilized poorly with G-CSF/Plerixafor. Further investigation revealed heterozygosity for loss-of-function mutations in two genes involved in DNA repair, BRCA1 and RAD51; Diepoxybutane (DEB) breakage study showed greater than normal pathologic chromosomal breaks, but less than that seen in Fanconi anemia. Because of concern for possible hypersensitivity to alkylating agent-based conditioning, the patient was referred for transplant with JSP191 conditioning. The patient received a CD34+ peripheral blood HSCT from his father after conditioning with 0.3 mg/kg of JSP 191 antibody intravenously over an hour on Day -8 and rATG (Thymoglobulin) on Day -5, -4, -3 and -2 (3.5 mg/kg total) to prevent rejection by the maternal T cells. The cryopreserved donor CD34+ cells were administered after sufficient clearance of the JSP191 serum level. The antibody infusion was well tolerated without toxicity, and the post-transplant course was uneventful without acute toxicities or GVHD. As a surrogate marker for HSC engraftment, CD15+ myeloid cells from peripheral blood were stringently sorted by flow cytometry and donor levels were quantified by short-tandem repeat (STR) analysis. Progressive levels of myeloid engraftment were observed beginning at Week 4. The level of donor chimerism at 12 weeks was 8% in the sorted CD15+ blood cells, and a marrow aspirate showed 25% donor CD34+ cells. By 3 months pre-existing abnormal CD19-CD20+ host B lymphocytes were significantly reduced, and CD19+ donor-derived B lymphocytes were emerging. At 2 months, CD4+ recent thymic emigrant and naïve T lymphocytes were observed, and by 3 months, overall T and NK lymphocyte numbers were 390/uL and 117/uL, respectively. Normal blastogenic responses to the T cell mitogen PHA were observed at 3 months. These first-in-class results provide proof of concept of the safety and efficacy of the use of JSP191 antibody to clear host marrow niche space to enable sufficient donor HSC engraftment and immune reconstitution as primary therapy of SCID. Non-genotoxic conditioning with JSP191 may replace conventional conditioning for newly diagnosed infants with SCID, thereby avoiding toxicities of chemotherapy. Disclosures Kohn: Allogene Therapeutics: Consultancy, Membership on an entity's Board of Directors or advisory committees; Orchard Therapeutics: Consultancy, Patents & Royalties, Research Funding. De Oliveira:Orchard Therapeutics: Research Funding; bluebird bio, Inc.: Research Funding. Czechowicz:Rocket Pharmaceuticals, Inc.: Research Funding. Brown:Merck: Membership on an entity's Board of Directors or advisory committees; Ansun: Membership on an entity's Board of Directors or advisory committees; Cidara: Membership on an entity's Board of Directors or advisory committees; Allogene: Membership on an entity's Board of Directors or advisory committees; Cellerant Therapeutics: Membership on an entity's Board of Directors or advisory committees. Shizuru:Jasper Therapeutics, Inc: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees.

Description: The ability to accurately predict leukemic relapse post-HSCT would improve outcomes by allowing pre-emptive therapeutic strategies. Recent studies have identified post-transplant T- and CD34 cell chimerism as predictors of relapse in patients, who had undergone HSCT for hematologic malignancies (Preuner et al, 2016; Lee et al, 2015). However, these studies assess relapse risk looking at only a single threshold of chimerism using standard regression analysis, which permits only limited consideration of other patient variables. As the result, the findings of these analysis are frequently not applicable to patients generally. Machine learning methods offer the possibility to capture nonlinear relationships and simultaneous interactions between multiple variables, thus better recapitulate the dynamics and nuances of the relapse process in different patients. We use machine learning methods, specifically random forest classification (RF), to build a predictive model of post-transplant relapse and to analyze the data from a cohort of 46 pediatric patients, who received HSCT for acute lymphoblastic leukemia (ALL) and had serial lineage-specific chimerism testing post-transplant. Our model achieved 58 % sensitivity and 98% specificity at predicting relapses in cross validation compared to a baseline model (24% sensitivity, 76% specificity). Consistent with previous reports, our model implicates both peripheral blood (PB) donor CD34 and CD3 chimerism as important variables for relapse. More importantly, the RF showed how different variables interacted with each other, providing additional insights into how to best interpret post-transplant chimerism results. To our knowledge, this is the first study featuring RF machine learning methods in the clinical setting of relapse after HSCT. We use a dataset of patients with ALL undergoing HSCT at Lucile Packard Children's Hospital from 2012 to 2018. Variables collected are summarized in Table 1. The analytical sensitivity of STR-based chimerism testing is 1%. Chimerism results on the same day of relapse were excluded from the analysis. The RF model is based on a set of 500 individual decision trees, each based on a bootstrapped sample of the patient data. A 5-fold cross-validation was used to test predictive skill, with 20% of patients excluded from each fold. We compared results with a Monte Carlo baseline model in which relapse status was repeatedly assigned randomly to each patient with a probability based on the prevalence of relapse in our cohort. Patients, transplantation, and relapse characteristics are summarized in Table 2. Chimerism data are summarized in Table 3. The cross-validation results show a robust predictive skill of relapse within 2 years post-transplant. Our RF achieved 58% sensitivity and 98% specificity, greatly improving the predictive values from the base model (Table 4). Variable importance, the ability of a variable to decrease the error of the prediction model, was calculated for all variables used in our RF (Figure 1). Our analysis shows that the age at the time of transplant has the highest importance, followed by PB donor CD34 chimerism. Bone marrow chimerism generally has lower importance suggesting PB monitoring only is adequate in the clinical setting. We showcase the relationships of 1) age at transplant, 2) donor PB CD34, and 3) donor PB CD3 chimerism to the odds of relapse using a partial dependence plot. Younger patients relapse less often. Donor PB CD34 chimerism exhibits a threshold effect, in which the odds of relapse dramatically decreases when it is above 95% while donor PB CD3 chimerism has a more gradual linear profile (Figure 2). 2D dependence plot of donor PB CD34 and PB CD3 chimerism shows the interaction of the two variables (Figure 3) as continuous variables; relapse risk remaining low with even if donor PB CD3 chimerism is as low as 50% as long as donor PB CD34 chimerism is 〉 95%. Our study shows that machine learning methods such as RF can be very useful at making accurate predictive model of post-HSCT complications that incorporates multiple variables, allowing for more granular differentiation between different patients. Such analyses can enable more effective deployment of risk-adapted, personalized treatment. By building hundreds of independent decision trees, the RF is also able provide useful insights to the interaction between different variables in a clinically relevant manner. Disclosures No relevant conflicts of interest to declare.