Kristmann, B. | Search bioRxiv

bioRxiv2026

Pan-B-Lineage Targeting with Adapter CAR-T Cells Controls Antigen-Heterogeneous Lymphoma

Antigen heterogeneity and antigen-negative relapse represent major limitations to durable CAR-T cell efficacy in B-lineage malignancies. We previously developed the Adapter CAR-T cell (AdCAR-T) platform, which enables flexible redirection of engineered T cells to distinct surface antigens through biotinylated adapter molecules (AMs). In this study, AMs generated from an in-house-produced tafasitamab biosimilar (anti-CD19), commercial rituximab (anti-CD20), and an in-house-produced daratumumab biosimilar (anti-CD38) mediated potent, antigen-specific AdCAR-T cell cytotoxicity. While single-antigen targeting resulted in the selection of antigen-negative tumor populations, simultaneous targeting of CD19, CD20, and CD38 effectively controlled a defined heterogeneous Burkitt lymphoma model in vitro and induced sustained tumor control in vivo. Selective loss of the CD38+ AdCAR-T cell population after CD38-directed AM exposure was consistent with fratricide; however, the surviving CD38low population retained cytotoxic activity. These findings establish combinatorial AdCAR-T cell targeting as a flexible pan-B-lineage strategy for addressing pre-existing antigen heterogeneity and support further development of antibody-derived AM combinations for B-cell malignancies.

immunology↗

bioRxiv2026

Single-Platform Nanopore Sequencing Enables Diploid Telomere-to-Telomere Genome Assembly and Haplotype-Resolved 3D Chromatin Maps

Telomere-to-telomere (T2T) genome assembly has transformed human genomics by resolving centromeres, segmental duplications, and other previously inaccessible regions. However, most diploid T2T assemblies rely on the combination of multi-platform sequencing strategies including short read genome sequencing, PacBio HiFi, Oxford Nanopore ultra-long reads, and chromatin conformation capture data (Hi-C), limiting both scalability and accessibility. Here, we present a streamlined Nanopore-only workflow for diploid human T2T assembly using three ultra-long and one Pore-C PromethION flow cell per individual. Across 23 genetically diverse individuals, we generated 360 gapless chromosomes and 446 near-complete T2T scaffolds, achieving median consensus accuracy of QV50 without Duplex sequencing or hybrid polishing. Assembly continuity, gene completeness, and structural variant detection were comparable to multi-platform Human Pangenome Reference Consortium assemblies. Pore-C data enabled chromosome-scale haplotype phasing without parental information and supported generation of haplotype-resolved chromatin contact maps. Integrated methylation and 3D genome analyses revealed allele-specific chromatin organization at imprinted loci and clear signatures of X-chromosome inactivation. Our openly accessible dataset expands public T2T resources and demonstrates that reference-grade diploid assemblies, phased methylomes, and 3D genome maps can be derived from a single sequencing platform. This approach reduces technical barriers and supports scalable population and functional genomics in the T2T era.

genomics↗