Impact of BEAM-101 Treatment on Red Blood Cell Hemoglobin Expression, Rheology and Sickling Properties: Initial Data from the BEACON Phase 1/2 Study of Autologous CD34⁺ Base Edited Hematopoietic Stem Cells in Sickle Cell Disease

BEAM-101 is an investigational cell therapy comprised of autologous CD34+ hematopoietic stem cells that are base edited to introduce A-to-G substitutions into the HBG1/2 gene promoters to disrupt BCL11A binding, leading to increased HbF production. The BEACON Phase 1/2 clinical trial is an open-label, single-arm, multicenter study evaluating the safety and efficacy of BEAM-101 in patients (pts) with sickle cell disease (SCD) and severe vaso-occlusive crisis (VOC).

Biomarkers of red blood cell (RBC) health and function including cellular expression of HbF and HbS, flow adhesion of whole blood to vascular cell adhesion molecule 1 (FA-WB-VCAM) and P-selectin (FA-WB-PSel), real-time sickling kinetics, hemorheology, and RBC morphology were measured before and after BEAM-101 treatment to assess the degree of resolution of SCD pathophysiology with this therapy.

Whole blood (WB) samples were collected from pts and double stained for HbF and HbS, followed by a duplex flow cytometry. For adhesion, WB samples were perfused through VCAM1- or PSel-coated microfluidic channels using pulsatile shear stress and images acquired and analyzed. Real-time sickling kinetics were captured using the dynamic sickling assay (DSA). Hemorheological assessments of blood such as oxygen affinity, deformability & RBC density were performed, as well as RBC count and cellular morphology.

Preliminary data as of July 2, 2024 includes exploratory biomarker assessments for ≥2 of the following visits: screening, Month (M) 1, 2, 3, and 6 for up to 3 pts (P1, P2, P3).

Duplex flow cytometry was performed at screening, M1, M2, and M6 (M6 for P1 only) for the first 3 pts and transfused cells were gated out in analysis. Total HbF⁺ cells in P1/2/3 increased from 34.1/20.8/48.5% at screening to >98% at M1 and >99% at M2; this further increased to 99.9% at M6 in P1. Total HbS⁺ cells in P1/2/3 decreased from 87.1/97.9/87.3% at screening to 34.6/26.2/19.1% at M2, respectively; this further decreased to 10.9% at M6 in P1. We observed >19 pg HbF/F-cell after treatment in all pts, above the protective threshold of 10pg to prevent sickling. Cells expressing HbS only for P1/2/3 were reduced to insignificant numbers after treatment from 65.9/79.1/51.4% at screening, to <2% at M1, and <0.4% at M2; this further reduced to 0.1% at M6 in P1.

Adherent cells as assessed by FA-WB-VCAM in P1/2 were reduced from 616/689 at screening to 68/179 cells/mm² at M3. Adherent cells in FA-WB-PSel in P1/2 were reduced from 52/118 at screening to 17.5/14 cells/mm² at M3. Adhesion indices after BEAM-101 treatment for VCAM1 and P-selectin (predictive biomarkers for VOCs in SCD) were well below the critical SCD index of 408 and 46 cells/mm², respectively. An increase in time under hypoxia for morphological point of sickling (mPoS), as well as a decrease in rate of sickling, maximum induced sickling and area under the curve (AUC) after BEAM-101 treatment were observed in P1/2 that were comparable to measurements observed in sickle cell trait (SCT) reference samples.

In P1, p50 decreased from 30.9 at screening to 22.7 mm Hg at M6 [normal reference range (ref): 23-28.5 mm Hg] indicating higher oxygen affinity post-treatment; PoS decreased from 41.8 at screening to 16.5 mm Hg at M6 (HbSS ref: 17-85.4 mmHg) supporting mPoS observed in DSA; % dense RBC decreased from 7.3% at screening to 3.7% at M6 (HbSS ref: 2-21.5%).

Abnormal morphology and sickle cells at screening resolved by M4/M6 in P1 and P2 along with an increase in RBC count.

Based on available data on exploratory biomarkers in up to 3 pts, we demonstrate 98-99% of RBCs expressing HbF as early as M1, with near complete elimination of RBCs expressing solely HbS post-BEAM-101. Flow adhesion showed reduction in cell adhesion from higher levels pretreatment to significantly below the critical threshold by M3 post-BEAM-101 indicating improvement in blood health and predicting reduced risk for VOC.

Reduced RBC sickling, comparable to SCT, was demonstrated post-BEAM-101 treatment. Oxygen affinity, RBC deformability and density showed improvements in hemorheological properties of blood post-BEAM-101. Finally, improvement in RBC cell number and resolution of abnormal RBC morphology were observed post-BEAM-101.

In summary, the initial RBC functional biomarker data support base editing of the HBG1/2 promoters as a potentially transformative therapeutic modality for the treatment of SCD and will continue to be investigated in the ongoing BEACON study.

Chockalingam:Beam Therapeutics: Current Employment, Current equity holder in publicly-traded company. Lin:Beam Therapeutics: Current Employment, Current equity holder in publicly-traded company. Chen:Beam Therapeutics: Current Employment, Current equity holder in publicly-traded company. Minella:Beam Therapeutics: Current Employment, Current equity holder in publicly-traded company. Chen:Beam Therapeutics: Current Employment, Current equity holder in publicly-traded company. Zhang:Frontage Laboratories, Inc: Current Employment, Current equity holder in publicly-traded company. Goyal:Beam Therapeutics: Current Employment, Current equity holder in publicly-traded company. Simon:Beam Therapeutics: Current Employment, Current equity holder in publicly-traded company.