Biology subjects

Zaugg, J. B.

Publications and source records attributed to Zaugg, J. B..

At least 19 recordsLinked to original sources

bioRxiv2026

Perturbation of the replication stress-ATR axis accelerates human erythroid differentiation but blocks terminal maturation

Replication stress (RS) can act as an input to differentiation: in erythroid and myeloid cells it is sufficient to accelerate commitment. Yet genotoxic chemotherapy, which imposes replication stress on the bone marrow can cause anemia; a frequent dose-limiting toxicity whose deficit of mature red cells is often attributed to progenitor depletion rather than to any effect on differentiation itself. Here, we ask how RS-induced accelerated commitment gives rise to impaired red cell output, using in vitro erythroid differentiation of cord-blood CD34+ progenitors perturbed with clinically relevant chemotherapy agents. We find that treated erythroblasts differentiate faster than controls but fail to mature, measured by lack of enucleated cells. Inhibition of ATR, but not ATM or DNA-PK, reproduces this phenotype. Mechanistically, single-cell profiling of drug-treated cells shows convergence on a transcriptional program, marked by loss of MYB and MYC activity. Treated cultures also accumulate aberrant late erythroblasts depleted for globin and heme programs and enriched for p53 and proteotoxic stress signatures. Together, these results propose that defective maturation is an alternative mechanism for chemotherapy-induced anemia, in addition to depletion of progenitors.

cell biology↗

bioRxiv2026

Multiscale biological interactions define clinical trajectories in acute myeloid leukemia

Cancer is characterized by complex interactions across genetic, cellular, and microenvironmental scales. However, a quantitative understanding of how these interactions shape clinical trajectories remains limited. Here, we present a multi-scale single-cell dataset from 184 treatment-naive acute myeloid leukemia (AML) patients spanning all major genetic subtypes, together with an analytical framework to dissect interactions across biological scales. We show that distinct clinical outcomes are encoded by specific cross-scale, cross-compartment interactions present at diagnosis: response to induction therapy is governed by interactions between genetic alterations and leukemic differentiation state; relapse following chemotherapy is associated with non-genetic programs linked to metabolism; and relapse after allogeneic stem cell transplantation is driven by interactions between the immune microenvironment and residual healthy hematopoiesis. Together, our study provides a framework to resolve intra- and inter-patient heterogeneity in cancer and supports a model in which clinical trajectories in AML emerge from defined interactions across biological scales.

cancer biology↗

bioRxiv2026

Leukemic Stem Cell Subtypes Drive Distinct Niche Remodeling in Acute Myeloid Leukemia

Leukemic stem cells (LSCs) sustain acute myeloid leukemia (AML) and are implicated in therapy resistance and relapse. Yet, it remains unknown how LSCs remodel the bone marrow niche. AML is known to alter stromal and vascular microenvironments, but these effects are difficult to separate from bulk leukemic burden and immune inflammation. Here, we use isogenic human AML xenografts with distinct LSC characteristics but comparable engraftment to define LSC-associated niche remodeling in vivo. Single-cell profiling revealed that LSC-high AML shifts the mesenchymal niche toward fibro-inflammatory states, expanding Fmod+ fibroblasts and Cd34+ perivascular fibroblast-like cells while suppressing osteolineage differentiation. The leukemic compartment remained heterogeneous, with a specific MEP-like LSC population expressing niche-remodeling ligands including TGFB1, IL1B, and ANGPT1. LSC-high AML activated a TGF{beta}-responsive, CREB3L1-controlled fibroblast trajectory, and perturbing TGF{beta} signaling or CREB3L1 activation reduced stromal support for AML cells. These findings identify a specific LSC subtype as a source of niche-remodeling cues that shape specialized leukemia-supportive niches.

molecular biology↗

bioRxiv2026

Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells

CD4+ T cells harbor a disproportionate enrichment of immune disease risk loci and represent the primary cellular context for immune disease biology, yet the genes and regulatory programs these variants affect remain largely unknown. We combined targeted Perturb-seq of 1,032 cis-regulatory elements (CREs) overlapping 4,724 variants across 14 immune diseases with genome-wide Perturb-seq of all expressed genes in primary human CD4+ T cells, spanning 4.1 million cells. We identified 626 CRE-gene pairs, and connected CRE targets to downstream regulatory cascades. At the TYK2 and DEXI/CLEC16A loci, we resolved target genes and linked noncoding variants to inflammatory and metabolic programs. Across diseases, we revealed that dispersed variants converged on shared and disease-specific programs. Our work provides a framework for tracing variant-to-CRE-to-gene-to-network in disease-relevant primary cells.

genetics↗

bioRxiv2025

CryoSiam: self-supervised representation learning for automated analysis of cryo-electron tomograms

Cryo-electron tomography (cryo-ET) enables visualization of macromolecular complexes in their native cellular context, but interpretation remains challenging due to high noise levels, missing information, and lack of ground-truth data. Here, we present CryoSiam (CRYO-electron tomography SIAMese networks), an open-source framework for self-supervised representation learning in cryo-ET. CryoSiam learns hierarchical representations of tomographic data spanning both voxel-level and subtomogram-level information. To train CryoSiam, we generated CryoETSim (CRYO-Electron Tomography SIMulated), a synthetic dataset that systematically models defocus variation, sample thickness, and molecular crowding. CryoSiam trained models transfer directly to experimental data without fine-tuning and support key aspects of cryo-ET data analysis, including tomogram denoising, segmentation of subcellular structures, and macromolecular detection and identification across both prokaryotic and eukaryotic systems. Publicly available pretrained models and the CryoETSim dataset provide a foundation for scalable and automated cryo-ET analysis.

bioinformatics↗

bioRxiv2025

Integrative Multi-Omics Identifies CDK1 as a Key Signaling Regulator of CD4+ T Cell Effector Function

CD4 T cell differentiation is orchestrated by coordinated signaling, transcriptional, and epigenomic programs, yet how signaling connects to chromatin and genetic variation in human T cells remains unclear. Here, we generated an integrative multi-omics map of human CD4 T cell activation and differentiation, combining phosphoproteomics, transcriptomics, and chromatin accessibility under Th0, Th1, and iTreg polarization. Within 10 minutes of activation, we observed rapid phosphorylation changes of RNA-binding proteins accompanied by degradation of effector-associated transcripts, preceding chromatin remodeling and later transcriptional activation of the same genes. Moreover, our data highlights how site-specific phosphorylation refines TF activity during T cell differentiation and activation, and identifies CDK1 as a regulator of Th1 effector function. Indeed, we found that a low dose of CKD1 inhibition impairs IFN-{gamma} expression and pro-inflammatory differentiation, while preserving regulatory features in iTregs. Single-cell multi-omic profiling upon CDK1 inhibition revealed how CDK1 activity shapes subset-specific gene regulatory networks, which are enriched for genetic variants associated with immune-traits. Specifically, CDK1-sensitive TFs, including IRF8, connect immune trait heritability to enhancer accessibility at IFNG and TNF loci. Together, these results establish CDK1 as a signaling hub that couples phosphorylation to gene regulation and genetic risk, with therapeutic relevance in autoimmune disease.

genomics↗

bioRxiv2025

SpliceUp: Predicting SF3B1 mutations in individual cells via aberrant splice site activation from scRNA-seq data

Myeloid neoplasms (MN) are clonal heterogeneous disorders initiated by somatic driver mutations in hematopoietic stem and progenitor cells (HSPCs). Among the most common are mutations in RNA splicing factors, which exert pleiotropic effects but are difficult to study due to altered hematopoietic differentiation and the inability to specifically isolate mutant HSPCs. Single-cell transcriptomics offers a powerful framework to dissect mutant cell states, yet direct genotyping is hampered by data sparsity and often requires costly, labor-intensive approaches. To overcome this limitation, we developed SpliceUp, a computational tool that identifies splice factor-mutant cells through their aberrant RNA splicing signatures. Applied to SF3B1-mutant samples, SpliceUp exploits cryptic 3 splice site usage and exon-skipping events to achieve more than a 7-fold increase in mutant cell detection from low-coverage 10x Genomics datasets. Differential expression analysis revealed cell typespecific programs, including MHC-II upregulation in SF3B1-mutated HSCs and enhanced RNA translation in SF3B1-mutated erythroid precursors.

bioinformatics↗

bioRxiv2025

Dual role of ZIC2 during neural induction: from pioneer transcription factor to enhancer activator

ZIC2, a member of the Zinc Finger of the Cerebellum family of transcription factors (TFs), plays crucial roles during neural development. In humans, defects in ZIC2 cause holoprosencephaly, a congenital brain malformation characterized by the defective cleavage of cerebral hemispheres due to problems in midline patterning. However, the gene regulatory network (GRN) controlled by ZIC2 and the regulatory mechanisms it employs during neural development remain largely unexplored. Here, we combined a mouse embryonic stem cell (mESC) in vitro differentiation model towards anterior neural progenitors (AntNPCs) with genome editing approaches, bulk and single cell (i.e. Multiome scATAC + scRNAseq) genomic methods to elucidate the precise GRN controlled by ZIC2 and the underlying mechanisms. We found that ZIC2 shows widespread binding throughout the genome already in mESC as well as upon pluripotency exit and neural induction. Despite its extensive binding in mESC, ZIC2 function is dispensable in pluripotent cells due to compensation by ZIC3. In contrast, ZIC2 plays a major regulatory function during neural induction, directly controlling the expression of master regulators implicated in the patterning and morphogenesis of specific brain regions, such as the midbrain (e.g., En1, Lmx1b, Pax2, Wnt1) and the roof plate (e.g., Lmx1a, Wnt3a). Mechanistically, ZIC2 plays a dual role in neural differentiation: (i) during pluripotency exit, ZIC2 acts as a pioneer TF, binding de novo to distal enhancers and promoting their chromatin accessibility; (ii) during neural induction, ZIC2 is essential for the activation of a subset of the previously primed enhancers, which in turn control the expression of major neural patterning regulators and signaling pathways (i.e. WNT) that prevent the premature differentiation of neural progenitors. Overall, our work shows that, by sequentially acting as a promiscuous pioneer and selective activator of enhancer elements, ZIC2 canalizes pluripotent cells towards neural progenitors with rostro-dorsal identities.

genomics↗

bioRxiv2025

High-throughput single-cell CRISPRi screens stratify neurodevelopmental functions of schizophrenia-associated genes

Schizophrenia is a complex neuropsychiatric disorder with strong genetic underpinnings, yet the molecular mechanisms linking genetic risk to disrupted brain development remain poorly understood. Transcription factors (TFs) and chromatin regulators (CRs) are increasingly implicated in neuropsychiatric disorders, where their dysregulation may disrupt neurodevelopmental programs. Despite this, systematic functional interrogation in human models has been limited. Here, we combine pooled CRISPR interference (CRISPRi) screens with high- throughput single-cell multiomic profiling in hiPSC-derived neural progenitors and neurons to functionally assess 65 schizophrenia-associated genes. Based on public datasets and literature review, we selected 55 TFs and CRs, along with ten additional risk genes whose loss-of-function has been linked to schizophrenia. Our single-cell CRISPRi readouts revealed that perturbations in TFs and CRs converge on disrupting neurodevelopmental timing. CRISPRi of several factors delayed neural differentiation, whereas others, such as the knockdown of MCRS1, drove precocious neural commitment. Validation screens combined with cell cycle and metabolic indicators confirmed the differentiation-restricting or -promoting roles of these TFs and CRs. Multimodal trajectory analysis uncovered discrete transcriptional and epigenomic states representing delayed and accelerated neurodevelopment, enriched for schizophrenia GWAS loci and disease-relevant pathways. Gene regulatory network (GRN) inference identified TCF4 and ZEB1 as critical mediators opposing the neural differentiation trajectory. Functional overexpression of these TFs followed by chromatin profiling demonstrated that TCF4 restrains, while ZEB1 promotes, neural differentiation in a stage-specific and competitive manner. Furthermore, we show that MCRS1 represses ZEB1 expression, positioning MCRS1 as a key brake on premature neurodevelopment. Together, our study establishes a scalable framework that integrates genetic perturbation, single- cell multiomics, and GRN modeling to functionally annotate disease-linked genes. We reveal convergent regulatory axes that underlie altered neurodevelopmental timing in schizophrenia, offering mechanistic insights into how chromatin misregulation contributes to disease pathogenesis.

neuroscience↗

bioRxiv2025

FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data

SummarySingle molecule footprinting profiles the heterogeneity of TF occupancy at cis-regulatory elements across cell populations at unprecedented resolution. The single molecule nature of the data in principle allows for observing the footprint of individual transcription factors and nucleosomes. However, we currently lack algorithms to quantify these occupancy patterns of chromatin binding factors in an automated way and without prior assumptions on their genomic location. Here we present FootprintCharter, an unsupervised tool to detect and quantify footprints for transcription factors (TFs) and nucleosomes from single molecule footprinting data. FootprintCharter allows for the quantification of complex molecular states such as positioning of unphased nucleosomes and combinatorial co-binding of multiple TFs. Availability and implementationFootprintCharter is freely available on Bioconductor with version 2.1.6 of https://bioconductor.org/packages/SingleMoleculeFootprinting with the functions FootprintCharter, PlotFootprints and Plot_FootprintCharter_SM.

bioinformatics↗

bioRxiv2025

Cumulative TF binding and H3K27 Acetylation drive enhancer activation frequency

In eukaryotes, transcription factors (TFs) must continuously compete with nucleosomes to access their binding sites, leading to cell-to-cell variability in chromatin accessibility at regulatory regions. Although critical to understand enhancer function in transcription, the mechanisms that define how frequently an enhancer is active in a cell population remain unclear. Here, we used single molecule footprinting to quantify the frequency at which chromatin is accessible at enhancers in response to TF perturbations, and changes of their chromatin environment. We find that individually most TFs open chromatin in a small fraction of the cells, and that cumulative TF binding controls enhancers activation frequency. Moreover, testing the functionality of hundreds of enhancers when inserted at an ectopic genomic location identifies H3K27Ac as a chromatin mark required for their full activation. Our data support a model where enhancer activation frequency depends on the cumulative function of multiple TFs, enhanced by activating chromatin marks.

molecular biology↗

bioRxiv2025

A kinetics-based model of hematopoiesis reveals extrinsic regulation of skewed lineage output from stem cells

Residing at the top of the hematopoietic hierarchy, long-term hematopoietic stem cells (HSCs) are capable of self-renewal and sustained blood cell regeneration. Over the past decades, single-cell and clonal analyses have revealed substantial functional and molecular heterogeneity within this compartment, challenging the notion that self-renewal is inherently tied to balanced, multi-lineage blood production. However, a cohesive model that explains the relationships among these diverse HSC states remains elusive. Here, we combined single-cell transplantations of over 1,000 highly purified murine long-term HSCs with in-depth phenotyping of their clonal progeny to achieve a detailed, time-resolved understanding of heterogeneous reconstitution outcomes. We identified reconstitution kinetics as an overall unifying metric of HSC functional potency, with the most potent HSCs displaying the greatest delay in hematopoietic reconstitution. Importantly, a progressive acceleration in reconstitution kinetics was also associated with a gradual shift in mature cell production from platelet and erythro-myeloid bias to balanced, and eventually lymphoid bias. Serial single-cell transplantations of HSCs revealed a unidirectional acceleration in reconstitution kinetics accompanied by a gradual decline in functional potency of daughter HSCs, aligning diverse phenotypes along a linear hierarchical trajectory. Mathematical modeling, together with experimental modulation of lineage-biased blood production, demonstrated that apparent lineage biases actually arise from cell-extrinsic feedback regulation and clonal competition between slow- and fast-engrafting clones to occupy the limited compartment sizes of mature lineages. Our study reconciles multiple layers of HSC heterogeneity into a unifying framework, prompting a reevaluation of the meaning of lineage biases in both normal and diseased hematopoiesis, with broad implications for other regenerating tissues during development, homeostasis, and repair.

cell biology↗

bioRxiv2024

Inflammatory Mesenchymal Stromal Cells and IFN-responsive T cells are key mediators of human bone marrow niche remodeling in CHIP and MDS

Somatic mutations in hematopoietic stem/progenitor cells (HSPCs) can lead to clonal hematopoiesis of indeterminate potential (CHIP), potentially progressing to myelodysplastic syndromes (MDS). Here, we investigated how CHIP and MDS remodel the human bone marrow (BM) niche relative to healthy elderly donors, using single cell and anatomical analyses in a large BM cohort. We found distinct inflammatory remodeling of the BM in CHIP and MDS. Furthermore, the stromal compartment progressively lost its HSPC-supportive adipogenic CXCL12-abundant reticular cells while an inflammatory mesenchymal stroma cell (iMSCs) population emerged in CHIP, which expanded in MDS. iMSCs exhibited distinct functional signatures in CHIP and MDS, retaining residual HSPC-support and angiogenic activity in MDS, corresponding with an increase in microvasculature in the MDS niche. Additionally, an IFN-responsive T cell population was linked to fueling inflammation in the stroma. Overall, these findings open new avenues for early intervention in hematological malignancies.

molecular biology↗

bioRxiv2024

Contextualising transcription factor binding during embryogenesis using natural sequence variation

Understanding how genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F1 crosses with extensive genetic diversity to profile allele-specific binding of four TFs at several embryonic time-points, using Drosophila as a model. Using a combined haplotype test, we identified 9-18% of TF bound regions impacted by genetic variation. By expanding WASP (a tool for allele-specific read mapping) to examine INDELs, we increased detection of allele imbalanced (AI) peaks by 30-50%. This fine-grained mutagenesis could reconstruct functionalized binding motifs of all factors. To prioritise potential causal variants, we trained a convolutional neural network (Basenji) to predict TF binding from DNA sequence. The model could accurately predict experimental AI for strong effect variants, providing a mechanistic interpretation for how genetic variation impacted TF binding. This revealed unexpected relationships between TFs, including potential cooperative pairs, and mechanisms of tissue specific recruitment of the ubiquitous factor CTCF.

genetics↗

bioRxiv2024

Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumourigenesis

Cell fate plasticity enables development, yet unlocked plasticity is a cancer hallmark. Regulating cell identity requires gene activation and repression. While master regulators induce lineage-specific genes to restrict plasticity, it remains unclear whether unwanted plasticity is actively suppressed by lineage-specific repressors. Here, we computationally predict so-called safeguard repressors for 18 cell types that block phenotypic plasticity lifelong. We validated hepatocyte-specific candidates using reprogramming, revealing that Prospero homeobox protein 1 (PROX1) enhanced hepatocyte identity by direct repression of alternate fate master regulators. In mice, Prox1 was required for efficient hepatocyte regeneration after injury and acted as a tumour suppressor in multiple liver cancer models. In line with patient data, Prox1 depletion caused hepatocyte fate loss in vivo, and promoted transition of hepatocellular carcinoma to cholangiocarcinoma, conversely, overexpression promoted cholangiocarcinoma to hepatocellular carcinoma transdifferentiation. Our findings provide mechanistic evidence for PROX1 as a hepatocyte-specific safeguard and support a model where individual cell type-specific repressors actively suppress plasticity throughout life to safeguard lineage choice and prevent disease.

cancer biology↗

bioRxiv2024

Role of Stem-Like Cells in Chemotherapy Resistance and Relapse in pediatric T Cell Acute Lymphoblastic Leukemia

T cell acute lymphoblastic leukemia (T-ALL) is an aggressive leukemia predominantly affecting adolescents and young adults. T-ALL relapses are characterized by chemotherapy resistance, cellular heterogeneity and dismal outcome. To gain a deeper understanding of the cellular heterogeneity and mechanisms driving relapse, we conducted single-cell full-length RNA sequencing of 13 matched pediatric T-ALL patient-derived xenografts (PDX) samples obtained at initial diagnosis and relapse, generating the to date most comprehensive longitudinal single cell study in paired T-ALL samples, along with 5 non-relapsing PDX samples collected at initial diagnosis. This dataset identifies considerable transcriptomic diversity among individual T-ALL cell populations. Notably however, 11 of the 18 patients exhibit a small T-ALL cell subpopulation with a shared set of gene regulatory networks characterized by a common set of active regulons, expression patterns and splice isoforms. This profile involves the upregulation of a stem-like cell signature with enrichment of cell adhesion, and inhibition of the cell cycle and metabolic activity. Comprehensive investigations of these networks identify transcripts enforcing drug resistance through NF-{kappa}B expression and TGF-{beta} signaling and of anti-apoptotic T cell signaling. Longitudinal monitoring of these stem-like cells demonstrates this subpopulation to account for only a small proportion of leukemia cells initially with a substantial expansion at relapse suggesting resistance to first line therapy. Chemotherapy resistance is functionally corroborated through in vitro and in vivo drug testing. We thus report the discovery of inherently treatment-resistant stem-like T-ALL cell populations underscoring the potential for devising future therapeutic strategies aimed at targeting stemness pathways in pediatric T-ALL. Key PointsO_LISingle-cell full-length RNA sequencing reveals dormant, treatment-resistant cells expanding upon T cell acute lymphoblastic leukemia relapse. C_LIO_LIStem-like T-ALL cells exhibit a shared gene regulatory network conferring chemotherapy resistance and relapse. C_LI

cancer biology↗

bioRxiv2024

Functional phenotyping of genomic variants using multiomic scDNA-scRNA-seq

Genomic variation ranging from single nucleotide polymorphisms to structural variants can impact gene function and expression, contributing to disease mechanisms such as cancer progression. The systematic study of this variation is hindered by inefficient precision editing tools making it challenging to confidently link genotype and gene expression in pooled screens. Additionally, assessing heterogenous variants in primary tumor samples at scale is difficult with current single-cell technologies. We developed droplet-based multiomic targeted scDNA-scRNAseq (SDR-seq) to precisely link genotypes with gene expression profiles in high-throughput. SDR-seq simultaneously assesses up to 480 RNA and gDNA targets with high coverage and sensitivity across thousands of cells. Using SDR-seq, we associate coding and non-coding variants with distinct gene expression profiles in human iPSCs. Furthermore, we demonstrate that in primary B-cell lymphoma samples, cells with a higher mutational burden exhibit elevated B-cell receptor signaling and tumorigenic gene expression. SDR-seq has broad potential for gaining functional insights into regulatory mechanisms encoded by genetic variants at diverse loci, advancing our ability to study gene expression regulation and its implications for disease.

molecular biology↗

bioRxiv2024

Mechanistic basis of gene-specific transcription regulation by the Integrator complex

The Integrator complex (INT) regulates gene expression via premature transcription termination of RNA polymerase II (RNAP2) at promoter-proximal pausing sites. This attenuation of transcription is required for cellular response to external stimuli, cell differentiation and neurodevelopment. How gene-specific regulation is achieved by INT in an inducible manner remains unclear. Here, we identify two sites on INT subunits 13/14 that serve as direct binding hubs for diverse sets of sequence-specific transcription factors (TFs) and other transcription effector complexes. The TFs co-localize with INT genome-wide, increase INT abundance on target genes and co-regulate inducible transcriptional programs. Consistently, disruption of INT-TF contacts impairs sensory cilia formation in response to glucose starvation. Structural analysis places INTs TF binding hubs upstream of the transcription bubble when attached to paused RNAP2, consistent with simultaneous TF-promoter association. Our data establish TF-mediated recruitment of INT to promoters as a widespread mechanism for targeted and inducible transcription attenuation.

molecular biology↗