Biology subjects

Mulaw, M. A.

Publications and source records attributed to Mulaw, M. A..

5 recordsLinked to original sources

bioRxiv2026

A divergent mutational and clonal landscape in aged HSCs is not linked to aging-associated clonal hematopoiesis

Somatic mutations accumulate throughout life and can serve as endogenous markers to trace cellular lineage relationships. In hematopoietic stem cells (HSCs), aging is associated with functional decline and clonal skewing, yet how somatic mutational histories shape clonal architecture at single-cell resolution remains incompletely understood. Here, we leverage single-cell RNA sequencing from murine and human long-term HSCs to identify expressed somatic single-nucleotide variants and reconstruct mutation-based genealogies. To address technical noise inherent to single-cell transcriptomes, we implement a stringent joint variant filtering strategy that exploits daughter cell relationships and probabilistic modeling to distinguish true somatic events from artifacts. Using these high-confidence variants, we infer phylogenetic and clonal relationships among individual HSCs and uncover striking age-dependent differences in lineage structure. Whereas young HSCs show little evidence of hierarchical clonal organization, aged HSCs frequently exhibit structured genealogies consistent with clonal expansion. Integration of mutational, transcriptional, and signature-based analyses further reveals that genetically distinct clones in aged samples are transcriptionally divergent and enriched for pathways linked to aging and DNA damage responses. Together, our findings demonstrate that somatic mutations recovered from single-cell transcriptomes can resolve HSC clonal evolution and reveal age-associated alterations in stem cell dynamics.

genomics↗

bioRxiv2026

The extent of myeloid skewing in blood is a biomarker of biological aging in mice and humans

Myeloid skewing is a central and therefore often cited hallmark of hematopoietic aging. Myeloid skewing refers to an elevated myeloid-to-lymphoid cell ratio in aged compared to young mice. Interestingly, whether the extent of myeloid skewing might be in itself a quantitative biological marker of aging has not been addressed yet, nor whether this parameter has also relevance for the extent of aging in humans. Aged mice with high level of myeloid skewing (>50% myeloid cells in blood) showed accelerated hematopoietic aging compared to mice with a low level of myeloid skewing (<30% of myeloid cells in blood), as well as an increased level of inflammatory cytokines and elevated levels of diseases. Hematopoietic stem cells (HSCs) from mice with high myeloid skewing showed an impaired repopulation capacity. Epigenetic clock analyses demonstrated that mice with a high level of myeloid skewing present with a biological age that is older than their chronological age. In humans, a high degree of myeloid skewing was associated with elevated levels of inflammatory markers, reduced mobility, a greater burden of comorbidities, and an increased mortality hazard ratio. The data support that, besides overall myeloid skewing being a central hallmark of aging in mice, the extent of the frequency of myeloid cells in blood might serve as a biological marker of aging and disease in both mice and humans. Key PointsThe extent of myeloid skewing in aged mice correlates to an increased hematological and epigenetic age and increased disease burden. The extent of myeloid skewing in older adults is associated with an increased hazard ratio of mortality and correlates with higher frailty and inflammatory markers.

cell biology↗

bioRxiv2025

Deep Learning links TP53 genotype to expression-defined transcriptional program in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a hematological cancer characterized by genetic diversity and poor clinical outcomes. Among various genetic mutations in AML, TP53 mutations have relatively low prevalence and present very dismal survival rates. While the genetic features of AML are well understood, the transcriptional programs associated with TP53 dysfunction are less clear, especially across different clinical groups. To fill this gap, we used deep learning on four bulk RNA-seq datasets grouped by p53 expression and a single-cell TARGET-seq dataset classified by TP53 genotype. The bulk data revealed disruptions in chromatin regulation, DNA repair, and immune pathways, with the low-p53 state showing activation of chemokine and interleukin signaling. In the single-cell data, deep learning classifiers successfully distinguished WT from multi-hit TP53-mutant cells, while heterozygous TP53 cells remained transcriptionally similar to WT. Comparing bulk and single-cell results, we found a strong positive correlation between p53-low expression states and TP53-inactive genotypes, linking the expression-based and mutation-based axes of p53 activity. Our study identifies a consistent TP53-related transcriptional signature that connects p53-low expression patterns with underlying TP53 AML.

bioinformatics↗

bioRxiv2020

Is zebrafish heart regeneration complete? Lineage-restricted cardiomyocytes proliferate to pre-injury numbers but some fail to differentiate in fibrotic hearts

Adult zebrafish are frequently described to be able to "completely" regenerate the heart. Yet, the extent to which cardiomyocytes lost to injury are replaced is unknown, since only indirect or non-quantitative evidence for cardiomyocyte proliferation exists. We established stereological methods to quantify the number of cardiomyocytes at several time-points post cryoinjury. Intriguingly, after cryoinjuries that killed about 1/3 of the ventricular cardiomyocytes, pre-injury cardiomyocyte numbers were restored already within 30 days. Yet, many hearts retained small residual scars, and a subset of cardiomyocytes bordering these fibrotic areas remained smaller, lacked differentiated sarcomeric structures, and displayed defective calcium signaling. Thus, a subset of regenerated cardiomyocytes failed to fully mature. While lineage-tracing experiments have shown that regenerating cardiomyocytes are derived from differentiated cardiomyocytes, technical limitations have previously made it impossible to test whether cardiomyocyte trans-differentiation contributes to regeneration of non-myocyte cell lineages. Using Cre responder lines that are expressed in all major cell types of the heart, we found no evidence for cardiomyocyte transdifferentiation into endothelial, epicardial, fibroblast or immune cell lineages. Overall, our results imply a refined answer to the question whether zebrafish can completely regenerate the heart: in response to cryoinjury, preinjury cardiomyocyte numbers are indeed completely regenerated, while restoration of cardiomyocyte differentiation and function, as well as resorption of scar tissue, is less robustly achieved.

developmental biology↗

bioRxiv2019

An actin nucleation complex catalyzes filament formation at sites of exocytosis

Due to the local enrichment of factors that influence its formation, dynamics, and organization, the actin cytoskeleton displays different shapes and functions within the same cell. In yeast cells post-Golgi vesicles ride on long actin cables to the bud tip. The scaffold proteins Boi1 and Boi2 participate in tethering and docking these vesicles to the plasma membrane. Here we show that Boi1/2 also recruit nucleation and elongation factors to form actin filaments at sites of exocytosis. Disrupting the physical connection between Boi1/2 and the nucleation factor Bud6 impairs filament formation in the bud, reduces the directed movement of the vesicles to the tip, and shortens their tethering time at the cortex. Artificially transplanting Boi1 from the bud tip to the peroxisomal membrane partially redirects the actin cytoskeleton and the vesicular flow towards the peroxisome, and creates an alternative, rudimentary vesicle-docking zone. We conclude that Boi1/2 is sufficient to induce the formation of a cortical actin structure that receives and aligns incoming vesicles before fusing with the membrane.

cell biology↗