Biology subjects

Izraeli, S.

Publications and source records attributed to Izraeli, S..

5 recordsLinked to original sources

bioRxiv2026

Context-dependent determinants of CRISPR-Cas9 editing efficiency revealed through cross-species endogenous editing analysis

Accurate prediction of CRISPR-Cas9 guide RNA (gRNA) editing efficiency remains limited, particularly outside human systems, where models trained on exogenous human datasets show poor generalization. We analyzed Cas9 efficiency and repair outcomes using novel endogenous editing data from four human cell types, two tomato cell types, and cells from giant river prawn and black soldier fly. While integrating publicly available predictors via ensemble frameworks improved performance, our analysis revealed hundreds of novel features affecting activity. Crucially, dominant features related to sites competition for gRNA, and local geometric properties varied across systems, highlighting the strong context dependence of Cas9 efficiency and arguing against a universal model. Interestingly, codon usage bias-based features also emerged as informative predictors, as they are proxies for chromatin accessibility. In contrast, trends in repair outcomes remained conserved. This work provides essential resources for more generalizable CRISPR guide design.

synthetic biology↗

bioRxiv2026

Epigenetic Liquid Biopsy Enables Universal Mutation-Agnostic Molecular Surveillance for High-Risk Neuroblastoma

Pediatric solid tumors present a challenge for precision oncology as most tumors harbor low mutational burden, limiting the applicability of standard mutation-based liquid biopsy approaches for molecular monitoring. To overcome this, we developed a mutation-independent liquid biopsy framework based on Oxford Nanopore Technology sequencing, utilizing robust DNA methylation-based biomarkers for detection and surveillance of high-risk neuroblastoma (HR-NBL), a common pediatric solid tumor. Comparative analysis of tumor-derived DNA methylation profiles against a comprehensive atlas of normal human cell types identified 72 NBL-specific differentially methylated regions (termed meNBLs). Integration of 25 selected meNBLs into the methylation atlas enabled quantitative deconvolution of NBL-derived cfDNA, outperforming copy number and mutation-based estimates. NBL-specific blood plasma-derived cfDNA was detected at diagnosis but not in healthy controls, absent during remission, and markedly elevated at relapse, even before clinical detection of disease recurrence. These findings establish methylation-based deconvolution as a robust, mutation-independent approach for cfDNA monitoring in HR-NBL.

cancer biology↗

bioRxiv2025

CAR T-cells dysfunction in the central nervous system is mediated by BBB-induced activation-induced cell death

Chimeric Antigen Receptor (CAR) T-cells can eliminate leukemia and lymphoma within the central nervous system (CNS). Following a case with CD19+ relapse in the CNS in the presence of persisting Tisagenlecleucel, we generated several models to study CAR T-cells in the CNS. In both immunocompetent and humanized leukemia-bearing mice, CNS-residing CAR T-cells were shown to have inferior ex-vivo killing capacities compared to CAR T-cells harvested from the spleen or bone marrow of receptive mice. In a mechanistic work-up, we identified two contributing factors: First, CAR T-cells cultured in cerebrospinal fluid showed impaired cytotoxic and proliferative function compared to those in serum or other media. Second, using a unique in vitro human blood-brain barrier (BBB) model composed of endothelial cells and brain pericytes, we demonstrated that CAR T-cells that crossed the BBB exhibited antigen-independent activation and diminished cytolytic capacity. This led to increased activation-induced cell death of the BBB-migrating CAR T-cells and was confirmed to be independent of the CAR target and the costimulatory domain. Our findings add possible mechanisms of CAR T-cell resistance in the CNS, relevant for CNS hematologic and non-hematologic tumors.

cancer biology↗

bioRxiv2020

Signaling input from divergent pathways subverts malignant B-cell transformation

Malignant transformation typically involves multiple genetic lesions whose combined activity gives rise to cancer1. Our analysis of 1,148 patient-derived B-cell leukemia (B-ALL) samples revealed that individual mutations did not promote leukemogenesis unless they converged on one single oncogenic pathway characteristic for the differentiation status of these transformed B cells. Specifically, we show here the JAK/STAT5 signaling pathway supports the developmental stage-specific expansion of pro-B ALL whereas the ERK-pathway that of pre-B ALL. Mutations that were not aligned with the central oncogenic driver would activate divergent pathways and subvert malignant transformation. Oncogenic lesions in B-ALL frequently mimic survival and proliferation signals downstream of cytokine receptors (through activation of STAT5)2-7 or the pre-B cell receptor (through activation of ERK)8-13. STAT5- (372 cases) and ERK- (386 cases) activating lesions were frequently found but only co-occurred in [~]3% (37) of cases (P=2.2E-16). Single-cell mutation and phosphoprotein analyses revealed that even in these rare cases, oncogenic STAT5- or ERK-activation were mutually exclusive and segregated to competing clones. STAT5 and ERK engaged opposing biochemical and transcriptional programs orchestrated by MYC and BCL6, respectively. Genetic reactivation of the divergent (suppressed) pathway came at the expense of the principal oncogenic driver and reversed malignant transformation. Conversely, Cre-mediated deletion of divergent pathway components triggered leukemia-initiation and accelerated development of fatal disease. Thus, persistence of divergent signaling pathways represents a powerful barrier to malignant transformation while convergence on one principal driver defines a key event during leukemia-initiation. Proof-of-concept studies in patient-derived B-ALL cells revealed that pharmacological reactivation of suppressed divergent circuits strongly synergized with direct inhibition of the principal oncogenic driver. Hence, pharmacological reactivation of divergent pathways can be leveraged as a previously unrecognized strategy to deepen treatment responses and to overcome drug-resistance. Current treatment approaches for drug-resistant cancer are focused on drug-combinations to suppress the central oncogenic driver and multiple alternative pathways14-17. Here, we introduce a concept based on inhibition of the principal driver combined with pharmacological reactivation of divergent pathways.

cancer biology↗

bioRxiv2020

An instructive role for IL7RA in the development of human B-cell precursor leukemia.

B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is preceded by a clinically silent pre-leukemia. Experimental models that authentically re-capitulate disease initiation and progression in human cells are lacking. We previously described activating mutations in interleukin 7 receptor alpha (IL7RA) that are associated with the poor-prognosis Philadelphia-like (Ph-like) subtype of BCP-ALL. Whether IL7RA signaling has a role in initiation of human BCP-ALL is unknown. IL7RA is essential for mouse B-cell development; however, patients with truncating IL7RA germline mutations develop normal mature B-cell populations. Herein, we explore the consequences of aberrant IL7RA signaling activation in human hematopoietic progenitors on malignant B-cell development. Transplantation of human cord-blood hematopoietic progenitors transduced with activated mutant IL7RA into NOD/LtSz-scid IL2R{gamma}null mice resulted in B-cell differentiation arrest with aberrant expression of CD34+ and persistence of pro-B cells that survive despite failing to achieve productive rearrangement of immunoglobulin V(D)J gene segments. Activation of IL7RA signaling enhanced self-renewal and facilitated the development of a BCP-ALL in secondary transplanted mice. The development of leukemia was associated with spontaneous acquired deletions in CDKN2A/B and IKZF1 similar to what is observed in Ph-like BCP-ALL in humans. Single cell gene expression analysis suggested that pre-leukemic cells resided within a subpopulation of early B-cell precursors with CD34+CD10highCD19low immunophenotype. The development of a bona fide BCP-ALL from IL7RA transduced cells supports the hypothesis that aberrant activation of the IL7RA pathway in human B-cell lineage progenitors has an instructive role by creating a pre-leukemic state which is vulnerable to transformation. These are the first demonstrations of a role for IL7RA in human B-cell differentiation and of a de-novo Ph-like BCP-ALL development from normal human hematopoietic progenitors in vivo.

cancer biology↗