Biology subjects

Jarocha, D.

Publications and source records attributed to Jarocha, D..

3 recordsLinked to original sources

bioRxiv2025

An integrated enzymatic and computational pipeline for quantifying off-target base-editing

DNA base editing is increasingly used for human genetic modification, but methods for monitoring off-target editing are nascent. Here we present a simple model-independent workflow for identifying sites of off-target base-editing in relevant cell types on a genome-wide level. We report that sites of off-target editing by the ABE8e editor could be identified using an ABE8e derivative with restored DSB cleavage activity. This allows marking of enzyme-generated double-stranded (ds) DNA breaks by incorporation of dsDNA oligonucleotides that are transfected into primary target cells. DNA sequencing at sites of oligonucleotide incorporation reported both the genomic location of off-target cleavage and the extent of base-editing nearby. We present a platform combining this cellular (BEiGUIDE-Seq) and computational workflow (CRISPRito) to generate optimized amplicon panels for convenient monitoring of off-target base editing. This work introduces a generalizable strategy to evaluate off-target edits in patient-derived cells, addressing a critical safety gap for clinical base editing.

molecular biology↗

bioRxiv2024

Studies of infused megakaryocytes into mice support a ''catch-and-release'' model of pulmonary-centric thrombopoiesis

Many aspects of thrombopoiesis, the release of platelets from megakaryocytes (Mks), remain under debate, including where this process occurs. Murine lung in situ-microscopy studies suggested that a significant fraction of circulating platelets was released from lung-entrapped, marrow-derived Mks. We now confirm these that endogenous murine (m) Mks are immobilized in the lungs. Intravenously infused in vitro-differentiated, mMks and human (h) Mks are similarly entrapped, followed by shedding of their cytoplasm over [~]30 minutes with a peak number of released platelets occurring 1.5-4 hours later. However, while infused Mks from both species shed large intrapulmonary cytoplasmic fragments that underwent further processing into platelet-sized fragments, the two differed: many mMks escaped from and then recycled back to the lungs, while most hMks were enucleated upon first intrapulmonary passage. Infused immature hMks, inflammatory hMks, umbilical cord-blood-derived hMks and immortalized Mk progenitor cell (imMKCL)-derived hMks were also immobilized in the lung of recipient mice, and released their cytoplasm, but did so to different degrees. Pharmacologically-treated hMks support that membrane stiffness was key to pulmonary thrombopoiesis. Intraarterial infused hMks resulted in few Mks being immobilized in tissues other than the lungs and was accompanied by a blunted and delayed rise in circulating human platelets. These studies demonstrate that the lung entraps and processes both circulating Mks and released large cytoplasmic fragments consistent with a prior lung/heart murine study and support a pulmonary-centric "catch-and-release" model of thrombopoiesis. Thrombopoiesis is a drawn-out process with the majority of cytoplasmic processing of Mks occurring in the pulmonary bed. Key PointsO_LIInfused in vitro-differentiated megakaryocytes synchronously release cytoplasmic fragments selectively in the pulmonary bed. C_LIO_LILarge, released megakaryocyte fragments recycle to the lungs, undergo further fission, terminally forming platelets. C_LI

cell biology↗

bioRxiv2020

RUNX1 haploinsufficiency causes a marked deficiency of megakaryocyte-biased hematopoietic progenitor cells: Mechanistic studies and drug correction

Patients with familial platelet disorder with a predisposition to myeloid malignancy (FPDMM) harbor germline monoallelic mutations in a key hematopoietic transcription factor RUNX1. Previous studies of FPDMM have focused on megakaryocyte (Mk) differentiation, and platelet production and signaling. However, the effects of RUNX1 haploinsufficiency on hematopoietic progenitor cells (HPCs) and subsequent megakaryopoiesis remains incomplete. To address this issue, we studied induced-pluripotent stem cell (iPSC)-derived HPCs (iHPCs) and Mks (iMks) from both patient-derived lines and a wildtype line modified to be RUNX1 haploinsufficient (RUNX1+/-), each compared to their isogenic wildtype control. All RUNX1+/- lines showed decreased iMk yield and depletion of a Mk-biased iHPC subpopulation. To investigate global and local gene expression changes underlying this iHPC shift, single-cell RNA sequencing was performed on sorted FPDMM and control iHPCs. We defined several cell subpopulations in FPDMM Mk-biased iHPCs. Analyses of gene sets upregulated in FPDMM iHPCs indicated enrichment for response to stress, regulation of signal transduction and response to cytokine gene sets. Immunoblotting studies in FPDMM iMks were consistent with these findings, but also identified augmented baseline c-Jun N-terminal kinase (JNK) phosphorylation, known to be activated by transforming growth factor {beta}1 and cellular stressors. J-IN8 and RepSox, small drugs targeting these pathways, corrected quantitative defects in FPDMM iHPC production. These findings were confirmed in adult human CD34+-derived stem and progenitor cells transduced with lentiviral RUNX1 short-hairpin (sh) RNA to mimic RUNX1+/-. These mechanistic studies of the defect in megakaryopoiesis in FPDMM suggest druggable pathways for clinical management of thrombocytopenia in affected patients. Key pointsO_LIRUNX1 haploinsufficiency results in a deficiency of megakaryocyte-biased hematopoietic progenitor cells (HPCs). C_LIO_LIRUNX1 haploinsufficiency elevates druggable proinflammatory and TGF{beta}R1-related pathways in HPCs. C_LI

molecular biology↗