Biology subjects

Schlaeger, T. M.

Publications and source records attributed to Schlaeger, T. M..

5 recordsLinked to original sources

bioRxiv2026

RNA splicing factor mutations drive myeloid neoplasm oncogenesis through protein complex poisoning

RNA splicing factor mutations (SFmut) are founding oncogenic events which cause RNA splicing errors with unpredictable gene expression dynamics. Despite extensive transcriptomic studies, SFmut cancer-initiating mechanisms remain elusive. Among SFmut cancers, myeloid neoplasms (MN) alone offer a setting where true cancer-driving SFmut stem cells can be identified, namely the hematopoietic stem cell (HSC). Within a cohort of 62 MN patients and 20 healthy donors, we conducted long/short-read single-cell transcriptomics (10X-ONT, n = 21) and immunophenotype-resolved low-cell proteomics (pauciproteomics, n = 78) to resolve gene expression, RNA splicing and protein expression dynamics across healthy and SFmut MN hematopoiesis. During hematopoietic differentiation, SFmut RNA mis-splicing decouples proteotranscriptomic dynamics in a mutation-specific manner. Pauciproteomics defines the functional effects of SFmut RNA mis-splicing on the protein layer, identifying early-stage protein effects which poison entire functional protein complexes and progressively disrupt the proteome-wide network during cellular maturation. Importantly, this information could neither be resolved nor predicted by transcriptomic analyses. Finally, we functionally validate the proteome dynamics of HSC through induced pluripotent stem cell culture models of early hematopoietic differentiation, identifying candidate mechanisms for SFmut oncogenesis. Overall, these data elucidate SFmut MN disease biology with unprecedented granularity, defining the molecular consequences of SFmut RNA mis-splicing and offering a generalizable framework for cancer stem cell studies.

cancer biology↗

bioRxiv2023

Matrin3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and YY1 mediated enhancer-promoter interactions

Although emerging evidence indicates that alterations in proteins within nuclear compartments elicit changes in chromosomal architecture and differentiation, the underlying mechanisms are not well understood. Here we investigate the direct role of the abundant nuclear complex protein Matrin3 (Matr3) in chromatin architecture and development in the context of myogenesis. Using an acute targeted protein degradation platform (dTAG-Matr3), we reveal the dynamics of development-related chromatin reorganization. Upon acute depletion of Matr3, gains in chromatin accessibility and MyoD binding were observed, prior to widespread loss in the steady-state Matr3-knockout. These initial changes correlated with gene expression changes later in development. High-throughput chromosome conformation capture (Hi-C) experiments revealed substantial chromatin loop rearrangements soon after Matr3 depletion. Notably, YY1 binding was detected in close proximity to enhancer and promoter regions, accompanied by the emergence of novel YY1-mediated enhancer-promoter loops, which occurred concurrently with changes in histone modifications and chromatin-level binding patterns. Overall, our results suggest that Matr3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and highlight a conserved and direct role for Matr3 in maintenance of chromosomal architecture.

molecular biology↗

bioRxiv2023

Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts

Reprogramming human fibroblasts to induced pluripotent stem cells (iPSCs) is inefficient, with heterogeneity among transcription factor (TF) trajectories driving divergent cell states. Nevertheless, the impact of TF dynamics on reprogramming efficiency remains uncharted. Here, we identify the successful reprogramming trajectories of the core pluripotency TF, OCT4, and design a genetic controller that enforces such trajectories with high precision. By combining a genetic circuit that generates a wide range of OCT4 trajectories with live-cell imaging, we track OCT4 trajectories with clonal resolution and find that a distinct constant OCT4 trajectory is required for colony formation. We then develop a synthetic genetic circuit that yields a tight OCT4 distribution around the identified trajectory and outperforms in terms of reprogramming efficiency other circuits that less accurately regulate OCT4. Our synthetic biology approach is generalizable for identifying and enforcing TF dynamics for cell fate programming applications. One-sentence summaryGenetic controllers and live-cell imaging offer a versatile strategy for probing the role of transcription factor dynamics in cell fate transitions.

synthetic biology↗

bioRxiv2022

Extracellular vesicles improve GABAergic transmission in Huntington's disease iPSC-derived neurons

Extracellular vesicles (EVs) carry bioactive molecules associated with various biological processes, including miRNAs. In both Huntingtons disease (HD) models and human samples, altered expression of miRNAs involved in synapse regulation were reported. Recently, the use of EV cargo to reverse phenotypic alterations in disease models with synaptopathy as the end-result of the pathophysiological cascade has become an interesting possibility. Here, we assessed the contribution of EVs to GABAergic synaptic alterations using a human HD model and studied the miRNA content of isolated EVs. After differentiating HD human induced-pluripotent stem cells into electrophysiologically active striatal-like GABAergic neurons, we found that HD-derived neurons displayed reduced density of inhibitory synapse markers and of GABA receptor-mediated ionotropic signaling. Treatment with EVs secreted by control (CTR) fibroblasts reversed the deficits in GABAergic synaptic transmission and increased the density of inhibitory synapses on HD-neuron cultures, while EVs from HD-derived fibroblasts had the opposite effects on CTR-neurons. Moreover, analysis of miRNAs from purified EVs identified a set of differentially expressed miRNAs between manifest HD, premanifest and CTR lines with predicted synaptic targets. The EVs-mediated reversal of the abnormal GABAergic phenotype in HD-derived neurons reinforces the potential role of EVs-miRNAs on synapse regulation.

neuroscience↗

bioRxiv2020

Derivation of Airway Basal Stem Cells from Human Pluripotent Stem Cells

The derivation of self-renewing tissue-specific stem cells from human induced pluripotent stem cells (iPSCs) would shorten the time needed to engineer mature cell types in vitro and would have broad reaching implications for the field of regenerative medicine. Here we report the directed differentiation of human iPSCs into putative airway basal cells ("iBCs"), a population resembling the epithelial stem cell of lung airways. Using a dual fluorescent reporter system (NKX2-1GFP;TP63tdTomato) we track and purify these cells over time, as they first emerge from iPSC-derived foregut endoderm as developmentally immature NKX2-1GFP+ lung progenitors which then augment a TP63 program during subsequent proximal airway epithelial patterning. These cells clonally proliferate, initially as NKX2-1GFP+/TP63tdTomato+ immature airway progenitors that lack expression of the adult basal cell surface marker NGFR. However, in response to primary basal cell medium, NKX2-1GFP+/ TP63tdTomato+ cells upregulate NGFR and display the molecular and functional phenotype of airway basal stem cells, including the capacity to clonally self-renew or undergo multilineage ciliated and secretory epithelial differentiation in air-liquid interface cultures. iBCs and their differentiated progeny recapitulate several fundamental physiologic features of normal primary airway epithelial cells and model perturbations that characterize acquired and genetic airway diseases. In an asthma model of mucus metaplasia, the inflammatory cytokine IL-13 induced an increase in MUC5AC+ cells similar to primary cells. CFTR-dependent chloride flux in airway epithelium generated from cystic fibrosis iBCs or their syngeneic CFTR-corrected controls exhibited a pattern consistent with the flux measured in primary diseased and normal human airway epithelium, respectively. Finally, multiciliated cells generated from an individual with primary ciliary dyskinesia recapitulated the ciliary beat and ultrastructural defects observed in the donor. Thus, we demonstrate the successful de novo generation of a tissue-resident stem cell-like population in vitro from iPSCs, an approach which should facilitate disease modeling and future regenerative therapies for a variety of diseases affecting the lung airways.

developmental biology↗