Mehdi Borji
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View article: Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation
Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation Open
Programmable control of gene expression in specific cell types is essential for both basic discovery and therapeutic intervention, yet current strategies lack scalability across diverse cellular contexts. Here, we introduce SPICE (Splicing…
View article: A clonally expanded nodal T-cell population diagnosed as T-cell lymphoma after CAR-T therapy
A clonally expanded nodal T-cell population diagnosed as T-cell lymphoma after CAR-T therapy Open
Reports of secondary malignancies after chimeric antigen receptor (CAR)-T and possible CAR-T derived malignant transformation necessitate caution. Here we describe a patient with diffuse large B-cell lymphoma who developed new lymphadenopa…
View article: Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors
Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors Open
A key challenge in cancer research is to identify the secreted factors that contribute to tumor cell survival. Nowhere is this more evident than in Hodgkin lymphoma, where malignant Hodgkin Reed Sternberg (HRS) cells comprise only 1-5% of …
View article: Scalable imaging-free spatial genomics through computational reconstruction
Scalable imaging-free spatial genomics through computational reconstruction Open
Tissue organization arises from the coordinated molecular programs of cells. Spatial genomics maps cells and their molecular programs within the spatial context of tissues. However, current methods measure spatial information through imagi…
View article: Human Airway and Alveolar Organoids from BAL Fluid
Human Airway and Alveolar Organoids from BAL Fluid Open
"Human Airway and Alveolar Organoids from Bronchoalveolar Lavage Fluid." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
View article: Coordinated Immune Cell Networks in the Bone Marrow Microenvironment Define the Graft versus Leukemia Response with Adoptive Cellular Therapy
Coordinated Immune Cell Networks in the Bone Marrow Microenvironment Define the Graft versus Leukemia Response with Adoptive Cellular Therapy Open
Summary Understanding how intra-tumoral immune populations coordinate to generate anti-tumor responses following therapy can guide precise treatment prioritization. We performed systematic dissection of an established adoptive cellular the…
View article: Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes
Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes Open
A major challenge in human genomics is to decipher the context specific relationship of sequence to function. However, existing tools for locus specific hypermutation and evolution in the native genome context are limited. Here we present …
View article: Integrative genotyping of cancer and immune phenotypes by long-read sequencing
Integrative genotyping of cancer and immune phenotypes by long-read sequencing Open
Single-cell transcriptomics has become the definitive method for classifying cell types and states, and can be augmented with genotype information to improve cell lineage identification. Due to constraints of short-read sequencing, current…
View article: 115 Spatial dissection of T cell clonotype identity, transcriptional profiles, and cell-cell interactions in the tumor microenvironment and tertiary lymphoid structures
115 Spatial dissection of T cell clonotype identity, transcriptional profiles, and cell-cell interactions in the tumor microenvironment and tertiary lymphoid structures Open
Background Determining the spatial interactions of T cell clonotypes in tumor microenvironments and tertiary lymphoid structures (TLSs) is essential to understanding adaptive anti-tumoral immune responses, but existing spatial sequencing m…
View article: Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response
Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response Open
View article: 76 Spatial mapping of T cell receptors and transcriptomes in renal cell carcinoma following immune checkpoint inhibitor therapy
76 Spatial mapping of T cell receptors and transcriptomes in renal cell carcinoma following immune checkpoint inhibitor therapy Open
Background Because conventional single-cell strategies rely on dissociating tissues into suspensions that lose spatial context, 1 we developed Slide-TCR-seq to sequence both whole transcriptomes and TCRs with 10µm-spatial resolution, & app…