Biology subjects

Schuschel, K.

Publications and source records attributed to Schuschel, K..

5 recordsLinked to original sources

bioRxiv2026

Integrative enhancer discovery identifies functional enhancer dependencies in pediatric acute myeloid leukemia

Pediatric acute myeloid leukemia (AML) is driven by aberrant transcriptional programs sustained by poorly defined cis-regulatory mechanisms. To systematically identify functional enhancer dependencies, we developed an integrative enhancer discovery strategy that combines H3K27ac CUT&Tag profiling, enhancer-associated transcription, and CRISPR interference (CRISPRi) screening. By leveraging enhancer-associated transcription to prioritize candidate regulatory elements, we identified 321 leukemia-associated enhancers for functional interrogation. This approach uncovered the hematopoietic MYB enhancer (H-ME) within the HBS1L-MYB-AHI1 locus as a critical regulator of leukemic growth. H-ME repression reduced chromatin accessibility and active histone marks at the MYB promoter, suppressed MYB expression, and induced differentiation-associated transcriptional programs. In contrast, selective depletion of the enhancer-associated transcript had no effect on MYB expression or leukemic proliferation, demonstrating that enhancer activity resides within the underlying regulatory DNA element rather than its mature RNA product. H-ME exhibited preferential activity in megakaryocytic leukemia, and its perturbation impaired leukemic growth in primary patient-derived models in vitro and in vivo. Together, our findings establish an integrative framework for the systematic discovery of functional enhancer dependencies and identified H-ME as an RNA-independent regulator of MYB in pediatric AML.

cancer biology↗

bioRxiv2025

The activation of TP53 pathway is a therapeutic vulnerability in NUP98::KDM5A+ pediatric AML

NUP98::KDM5A-rearranged pediatric acute myeloid leukemia (AML) is a rare, infancy-predominant entity with dismal outcome and no targeted therapeutic options. Given its suspected fetal origin, we hypothesized that leukemic maintenance depends on developmentally restricted vulnerabilities embedded within fetal hematopoietic programs. Using matched fetal and adult hematopoietic stem and progenitor cell models, we integrated transcriptomic and proteomic profiling with CRISPR-Cas9 screenings to define ontogeny-specific dependencies in NUP98::KDM5A leukemia. Fetal-derived NUP98::KDM5A leukemias exhibited greater in vivo aggressiveness, and retained fetal transcriptional signatures compared with adult counterparts. A comparative CRISPR-Cas9 screen using a library targeting fetal gene programs, conducted in both fetal- and adult-derived NUP98::KDM5A leukemias, identified the AAA ATPase TRIP13 as a selective and essential dependency in the fetal context. Mechanistically, TRIP13 physically interacted with the TP53 phosphatase PPM1D/WIP1, resulting in suppression of TP53 activation. Genetic ablation of Trip13, or pharmacologic inhibition using DCZ0415, a small-molecule inhibitor targeting TRIP13, reactivated TP53, induced G2/M arrest and mitochondrial apoptosis, and depleted leukemic cells in vitro; these effects were fully rescued by TP53 loss. In competitive transplantation assays, Trip13 ablation significantly impaired leukemic fitness in vivo. Together, these findings define a developmentally restricted TRIP13-PPM1D-TP53 survival axis in NUP98::KDM5A AML and provide mechanistic proof-of-concept that reactivation of the TP53 signaling pathway via TRIP13 inhibition represents a therapeutically targetable vulnerability in this high-risk pediatric leukemia. Visual abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/675580v4_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@143d103org.highwire.dtl.DTLVardef@14f3225org.highwire.dtl.DTLVardef@655541org.highwire.dtl.DTLVardef@c021ae_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Single cell transcriptional evolution of myeloid leukaemia of Down syndrome

Children with Down syndrome have a 150-fold increased risk of developing myeloid leukaemia (ML-DS). Unusually for a childhood leukaemia, ML-DS arises from a preleukaemic state, termed transient abnormal myelopoiesis (TAM), via a conserved sequence of mutations. Here, we examined the relationship between the genetic and transcriptional evolution of ML-DS from natural variation; a rich collection of primary patient samples and fetal tissues with a range of constitutional karyotypes. We distilled transcriptional consequences of each genetic step in ML-DS evolution, utilising single cell mRNA sequencing, complemented by phylogenetic analyses in progressive disease. We found that transcriptional changes induced by the TAM-defining GATA1 mutations are retained in, and account for most of the ML-DS transcriptome. The GATA1 transcriptome pervaded all stages of ML-DS, including progressive disease that had undergone genetic evolution. Our approach delineates the transcriptional evolution of ML-DS and provides an analytical blueprint for distilling consequences of mutations within their pathophysiological context.

cancer biology↗

bioRxiv2022

Nanoparticle-mediated Targeting of the Fusion Gene RUNX1/ETO in t(8;21)-positive Acute Myeloid Leukaemia

A hallmark of acute myeloid leukaemias (AMLs) are chromosomal rearrangements that give rise to novel leukaemia-specific fusion genes. Most of these fusion genes are both initiating and driving events in AML and therefore constitute ideal therapeutic targets but are challenging to target by conventional drug development. siRNAs are frequently used for the specific suppression of fusion gene expression but require special formulations for efficient in vivo delivery. Here we describe the use of siRNA-loaded lipid nanoparticles for the specific therapeutic targeting of the leukaemic fusion gene RUNX1/ETO. Transient knockdown of RUNX1/ETO reduces its binding to its target genes and alters the binding of RUNX1 and its co-factor CBF{beta}. Transcriptomic changes in vivo were associated with substantially increased median survival of a t(8;21)-AML mouse model. Importantly, transient knockdown in vivo causes long-lasting inhibition of leukaemic proliferation and clonogenicity, induction of myeloid differentiation and a markedly impaired re-engraftment potential in vivo. These data strongly suggest that temporary inhibition of RUNX1/ETO results in long-term restriction of leukaemic self-renewal. Our results provide proof for the feasibility of targeting RUNX1/ETO in a pre-clinical setting and support the further development of siRNA-LNPs for the treatment of fusion gene-driven malignancies.

cancer biology↗

bioRxiv2021

The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis

Given the plasticity of hematopoietic stem/progenitor cells, multiple routes of differentiation must be blocked during acute myeloid leukemia pathogenesis - the molecular basis of which is incompletely understood. Here we report that post-transcriptional repression of transcription factor ARID3A by miR-125b is a key event in megakaryoblastic leukemia (AMKL) pathogenesis. AMKL is frequently associated with trisomy 21 and GATA1 mutations (GATA1s), and children with Down syndrome are at a high risk of developing this disease. We show that chromosome 21-encoded miR-125b synergizes with Gata1s to drive leukemogenesis in this context. Leveraging forward and reverse genetics, we uncover Arid3a as the main miR-125b target underlying this synergy. We demonstrate that during normal hematopoiesis this transcription factor promotes megakaryocytic differentiation in concert with GATA1 and mediates TGF{beta}-induced apoptosis and cell cycle arrest in complex with SMAD2/3. While Gata1s mutations perturb erythroid differentiation and induce hyperproliferation of megakaryocytic progenitors, intact ARID3A expression assures their megakaryocytic differentiation and growth restriction. Upon knockdown, these tumor suppressive functions are revoked, causing a dual megakaryocytic/erythroid differentiation blockade and subsequently AMKL. Inversely, restoring ARID3A expression relieves the megakaryocytic differentiation arrest in AMKL patient-derived xenografts. This work illustrates how mutations in lineage-determining transcription factors and perturbation of post-transcriptional gene regulation interplay to block multiple routes of hematopoietic differentiation and cause leukemia. Surmounting this differentiation blockade in megakaryoblastic leukemia by restoring the tumor suppressor ARID3A represents a promising strategy for treating this lethal pediatric disease. Key pointsO_LIRepression of megakaryocytic transcription factor ARID3A by miR-125b synergizes with GATA1s to induce leukemia C_LIO_LIRestoring ARID3A expression relieves megakaryocytic differentiation arrest in megakaryoblastic leukemia C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/440795v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@146c2a7org.highwire.dtl.DTLVardef@9599fdorg.highwire.dtl.DTLVardef@1b0d22borg.highwire.dtl.DTLVardef@1b61447_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗