Biology subjects

Jacobi, A. M.

Publications and source records attributed to Jacobi, A. M..

8 recordsLinked to original sources

bioRxiv2026

Sensitive Chromosomal Translocation Quantitation from Amplicon Sequencing Using Primer-Anchored Statistical Translocation Analysis (PASTA)

Chromosomal translocations are rare structural rearrangement outcomes of genome editing, requiring analytical frameworks that combine high quantitative accuracy with performant sensitivity and specificity. Amplicon sequencing offers a scalable means to detect rare rearrangements with ultra-deep targeted sequencing, but existing methods often rely on heuristic thresholds or ad hoc normalization steps that limit reproducibility and have unknown analytical performance. Here, we present a computational tool we call PASTA (Primer-Anchored Statistical Translocation Analysis), using a count-based differential-event statistical framework to quantify and statistically confirm translocation junctions from targeted amplicon sequencing data. Comparison of this method to ddPCR demonstrates that quantitation is highly accurate, and outperforms other NGS-based methods even when randomized adapter chemistry is not present in amplicon sequencing structures. To measure analytical performance, we create a benchmarking dataset for measuring chromosomal translocation analysis performance with frequencies ranging from 1% to sub-0.01%, and demonstrate that the method can detect frequencies down to 0.01% with >75% sensitivity when sufficient read depth is present. Taken together, this work demonstrates using amplicon sequencing with PASTA as a bioinformatics analysis tool is a solution for translocation detection in amplicon sequencing genotoxicity assessments, enabling identification of rare genome rearrangements in both research and preclinical applications

bioinformatics↗

bioRxiv2025

Clinical development of gene edited tacrolimus-resistant Treg (FKBP12KO-Treg) to enable simultaneous immunosuppression and support of immune regulation

Background: Unwanted immune responses play a central role in the pathogenesis of solid organ allograft rejection. These are managed by life-long immunosuppression with considerable burden for the patient and society. Adoptive therapy with regulatory T-cells (Treg) is a promising approach to restore sustainable immune balance and avoid long-term adverse effects of immunosuppression. While Treg effectively inhibit activation of unwanted immune responses, they are less effective in controlling pre-existing/activated memory effector T-cells (Teff). Thus, co-administration of Treg with immunosuppressants is required to achieve a sustainable organ acceptance. Calcineurin inhibitors (CNI) are powerful in controlling de novo generated and preformed Teff. However, CNI also dampen Treg immunoregulatory function. Thus, we hypothesize improved results of adoptive Treg therapy in immunosuppressed patients applying tacrolimus-resistant Treg. Methods: While retaining CNI modulation of Teff with tacrolimus, we knocked-out FKBP12 in Treg (FKBP12KO-Treg) by gene-editing using ribonucleoprotein-based CRISPR/Cas9 technology to generate tacrolimus-resistant Treg and characterised them using flow cytometry, functional assays and in-depth phenotyping. Results: This detailed in vitro analysis showed FKBP12KO-Treg were comparable to non-gene edited Treg and impervious to tacrolimus while maintaining immunoregulatory function and sensitivity to alternative CNIs raising no safety concerns. Furthermore, we aligned our methodology to achieve GMP compliance laying the basis for a manufacturing license in preparation of a clinical trial. Conclusion: Based on the presented preclinical dataset implying safety and efficacy of FKBP12KO-Treg, we are now seeking to undertake a proof-of-concept clinical trial to evaluate the co-administrationof FKBP12KO-Treg and tacrolimus to enhance the management of living donor kidney transplant recipients.

immunology↗

bioRxiv2025

UNCOVERseq Enables Sensitive and Controlled Gene Editing Off-Target Nomination Across CRISPR-Cas Modalities and Systems

The rapid development of CRISPR-Cas gene editing technologies has revolutionized genetic medicine, offering unprecedented precision and potential for treating a wide array of genetic disorders. However, assessing the risks of unintended gene editing effects remains critical, and is complicated by new editing modalities and unclear analytical guidelines. We present UNCOVERseq (Unbiased Nomination of CRISPR Off-target Variants using Enhanced RhPCR), an improved in cellulo off-target nomination workflow designed to sensitively nominate off-target sites (<0.01% editing) with defined input requirements and analytical process controls to provide empirical performance evidence across diverse circumstances. Using this workflow, we nominated off-targets across 192 guide RNAs (gRNAs) and demonstrated superior performance compared to existing methodologies. We identified a subset of six gRNAs with a dynamic range of specificity and confirmed the relevance and high true positive rate of our nomination method, providing relative risk assessments for multiple modalities (S.p. Cas9 and derived high-fidelity variants / base editors) in a translational system involving hematopoietic stem and progenitor cells (HSPCs). Additionally, we established that double-strand break (DSB) editing retains a strong, positive rank correlation to single-strand break (SSB)-mediated base editing, highlighting the importance of DSB nomination sites as candidate loci for base editing. Overall, UNCOVERseq improves informed risk assessment of gene editing in translational systems by enhancing the quality of off-target nomination.

molecular biology↗

bioRxiv2024

CCR2 silencing in sensory neurons blocks bone cancer progression

The peripheral nervous system contributes to cancer growth, in part by shaping the immunological niche of the tumor. How the nervous system influences bone cancer progression, and whether the underlying neuroimmune pathways can be targeted therapeutically, remain unclear. Here we demonstrate a profound influence of the peripheral nervous system on tumor progression that can be countered by silencing chemokine receptor signaling in sensory neurons. Axotomy of the tumor-innervating femoral nerve inhibits tumor progression in animals bearing bone cancer, whereas intrathecal delivery of the tumor-associated proinflammatory chemokine CCL2 promotes both tumor growth and allodynia. Silencing CCR2 in dorsal root ganglion (DRG) neurons with a newly developed lipid nanoparticle-formulated Dicer-substrate siRNA impedes tumor progression and pathological bone remodeling, and relieves bone cancer-associated pain. Mechanistically, bone cancer drives CCR2-dependent transport of substance P and CGRP along the tumor-innervating femoral nerve, and these neuropeptides expand the tumor-associated macrophage population; silencing CCR2 in DRG neurons normalizes the neuropeptide milieu and ameliorates altered bone remodeling. We thus define a targetable neuroimmune axis that contributes to cancer progression. HighlightsO_LICancer progression activates sensory neurons, driving pain hypersensitivity and neuropeptide release. C_LIO_LIAxotomy of the tumor-innervating femoral nerve impedes tumor progression. C_LIO_LICCL2-CCR2 signaling in DRG neurons promotes pain hypersensitivity and cancer growth. C_LIO_LISilencing CCR2 in the DRG reduces pain hypersensitivity, tumor-associated macrophage numbers and cancer growth. C_LI

neuroscience↗

bioRxiv2022

A versatile, high-efficiency platform for CRISPR-based gene activation

CRISPR-mediated transcriptional activation (CRISPRa) is a powerful technology for inducing gene expression from endogenous loci with exciting applications in high throughput gain-of-function genomic screens and the engineering of cell-based models. However, current strategies for generating potent, stable, CRISPRa-competent cell-lines present limitations for the broad utility of this approach. Here, we provide a high-efficiency, self-selecting CRISPRa enrichment strategy, which combined with piggyBac transposon technology enables rapid production of CRISPRa-ready cell populations compatible with a variety of downstream assays. We complement this with a new, optimized guide RNA scaffold that significantly enhances CRISPRa functionality. Finally, we describe a novel, synthetic guide RNA tool set that enables transient, population-wide gene activation when used with the self-selecting CRISPRa system. Taken together, this versatile platform greatly enhances the potential for CRISPRa across a wide variety of cellular contexts.

bioengineering↗

bioRxiv2021

Fast, efficient and virus-free generation of TRAC-replaced CAR T cells

Chimeric Antigen Receptor (CAR) redirected T cells are a potent treatment option for certain hematological malignancies. Recently, site-specific insertion of CARs into the T cell receptor (TCR) alpha constant (TRAC) locus using gene editing and adeno-associated viruses was shown to generate CAR T cells with improved functionality over their retrovirally transduced counterparts. However, the development of viruses for gene transfer is complex and associated with extensive costs at early clinical stages. Here, we provide an economical and virus-free method for efficient CAR insertion into the TRAC locus of primary human T cells via CRISPR-Cas mediated homology-directed repair (HDR). While the toxicity induced by transfected double-stranded template (donor) DNA was not fully prevented by pharmacological means, the combination of DNA-sensor inhibitors and HDR enhancers resulted in highly efficient gene editing with TCR-to-CAR replacement rates reaching up to 68%. The resulting TCR-deficient CAR T cells show antigen-specific cytotoxicity and cytokine production in vitro. Our GMP-compatible non-viral platform technology lays the foundation for clinical trials and fast-track generation of novel CAR T cells applicable for autologous or allogeneic off-the-shelf use.

immunology↗

bioRxiv2020

CRISPAltRations: a validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing

CRISPR systems enable targeted genome editing in a wide variety of organisms by introducing single- or double-strand DNA breaks, which are repaired using endogenous molecular pathways. Characterization of on- and off-target editing events from CRISPR proteins can be evaluated using targeted genome resequencing. We characterized DNA repair footprints that result from non-homologous end joining (NHEJ) after double stranded breaks (DSBs) were introduced by Cas9 or Cas12a for >500 paired treatment/control experiments. We found that building our understanding into a novel analysis tool (CRISPAltRations) improved results quality. We validated our software using simulated rhAmpSeq amplicon sequencing data (11 gRNAs and 603 on- and off-target locations) and demonstrate that CRISPAltRations outperforms other publicly available software tools in accurately annotating CRISPR-associated indels and homology directed repair (HDR) events. We enable non-bioinformaticians to use CRISPAltRations by developing a web-accessible, cloud-hosted deployment, which allows rapid batch processing of samples in a graphical user-interface (GUI) and complies with HIPAA security standards. By ensuring that our software is thoroughly tested, version controlled, and supported with a UI we enable resequencing analysis of CRISPR genome editing experiments to researchers no matter their skill in bioinformatics.

bioinformatics↗

bioRxiv2018

An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein

CRISPR/Cas9 can be used for precise genetic knock-in of epitope tags into endogenous genes, simplifying experimental analysis of protein function. However, Cas9-assisted epitope tagging in primary mammalian cell cultures is often inefficient and reliant on plasmid-based selection strategies. Here we demonstrate improved knock-in efficiencies of diverse tags (V5, 3XFLAG, Myc, HA) using co-delivery of Cas9 protein pre-complexed with two-part synthetic modified RNAs (annealed crRNA:tracrRNA) and single-stranded oligodeoxynucleotide (ssODN) repair templates. Knock-in efficiencies of ~5-30%, were achieved without selection in embryonic stem (ES) cells, neural stem (NS) cells, and brain tumour-derived stem cells. Biallelic-tagged clonal lines were readily derived and used to define Olig2 chromatin-bound interacting partners. Using our novel web-based design tool, we established a 96-well format pipeline that enabled V5-tagging of sixty different transcription factors. This efficient, selection-free and scalable epitope tagging pipeline enables systematic surveys of protein expression levels, subcellular localization, and interactors across diverse mammalian stem cells.

cell biology↗