Biology subjects

Nowak, D.

Publications and source records attributed to Nowak, D..

13 recordsLinked to original sources

bioRxiv2026

Lineage-aware stochastic modeling reveals gene-expression dynamics in development and disease

Gene expression changes along cell lineages, but most single-cell RNA-seq analyses treat cells as independent snapshots and ignore their phylogenetic relationships. Here we present LaVOUS, a lineage-aware probabilistic framework for modeling sparse single-cell gene-expression counts on reconstructed lineage trees. LaVOUS couples Brownian motion and Ornstein-Uhlenbeck models of latent transcriptional dynamics with negative-binomial observation models and scalable variational inference, enabling likelihood-based tests for gene-expression heritability, branch-specific expression shifts, and ancestral expression reconstruction. In simulations, LaVOUS improved detection of lineage-associated expression changes over Gaussian phylogenetic models and accurately reconstructed expression histories across expression levels. Applied to lineage-resolved single-cell datasets from metastatic lung cancer, class-switching B cells, and the developing brain, LaVOUS identified expression changes associated with metastatic progression, isotype switching, and neuronal differentiation. LaVOUS provides a general framework for studying single-cell expression dynamics across development and disease.

bioinformatics↗

bioRxiv2025

Primary CD34+ cells of patients with VEXAS syndrome are highly sensitive to targeted treatment with TAK-243 and pevonedistat

Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic (VEXAS) syndrome is an autoinflammatory disease characterized by somatically acquired UBA1 mutations in hematopoietic stem cells. VEXAS patients present with significant therapeutic challenges such as severe treatment-resistant inflammation and predisposition to myeloid malignancies. In this study, we evaluated the efficacy of TAK-243, a UBA1 inhibitor, and pevonedistat, a NEDD8 inhibitor, in vitro on primary CD34+ hematopoietic stem and progenitor cells (HSPCs) from patients with VEXAS syndrome (n=5), myelodysplastic neoplasms (MDS) (n=10), as well as healthy controls (n=10). Our findings revealed that VEXAS patient-derived HSPCs exhibited significantly higher sensitivity to both TAK-243 (IC50: 22 nM) and pevonedistat (IC50: 553 nM) compared to MDS (IC50: 133 nM and 1048 nM, respectively) and healthy controls (IC50: 192 nM and 1107 nM, respectively) as demonstrated by reduced cell viability. Furthermore, VEXAS CD34+ cells exhibited significantly higher levels of apoptosis after treatment with both inhibitors. These results suggest that TAK-243 and pevonedistat selectively target UBA1-mutated progenitor cells, and indicate a broad therapeutic window in which malignant cells are eradicated but healthy hematopoiesis is not yet compromised. This study provides a strong rationale for further clinical investigation of TAK-243 and pevonedistat as targeted therapies for VEXAS patients, offering hope for improved management of this clinically challenging disorder and contributing to our understanding of its underlying molecular mechanisms.

cancer biology↗

bioRxiv2024

Repeated cigarette smoke exposure attenuates the proliferation rate of primary human lung fibroblasts in vitro

BackgroundLung fibroblasts are crucial structural cells involved in airway remodelling and tissue maintenance. The study aimed to analyze the effect of cigarette smoke extract (CSE) on primary human lung fibroblasts at various stages of proliferation to assess whether an initial exposure could exert a protective effect against subsequent exposures. MethodsWe examined the effect of CSE on fibroblasts isolated from 15 donors who had undergone lung surgery. Fibroblast cultures were exposed to 2% CSE early (day 5-7), late (day 9-11), or at both time points (double). Cell counts and viability tests were performed every 2 days. Changes in proliferation rates were determined immediately at the end of each 2-day exposure as well as 2 days afterwards, until the end of the experiment with a plateau of proliferation. Differences between exposures were analyzed by comparing proliferation rates by ANOVA with adjusted post-hoc analyses. ResultsEarly-, late- and double-CSE exposed cultures showed lower proliferation rates (p<0.05 each) compared to unexposed cultures. The response to late-CSE exposure varied depending on whether an initial CSE exposure had occurred, suggesting a protective effect from the early exposure. Changes observed over the 2-day exposure period and the subsequent 2 days (a total of 4 days) yielded similar results to those recorded during just the 2-day exposure period. Proliferation rates varied among cells from different donors, but responses correlated across different exposure regimens, indicating inherent differences in susceptibility to CSE. ConclusionsRepeated CSE exposures attenuated the proliferation of primary human lung fibroblasts more strongly than a single exposure, despite the fact that an early CSE exposure appeared to protect against the CSE in repetitively exposed fibroblast cultures. Our results highlight that while significant differences may occur among primary cells from different donors in vitro, responses can remain consistent across various exposure conditions.

cell biology↗

bioRxiv2024

Pain distribution can be determined by classical conditioning

ABSTRACTChronic widespread pain (CWP) - as many other clinical presentations - manifests in ongoing pain without identifiable structural cause, with pain that spreads over multiple body areas. The development and maintenance of symptoms may involve learning mechanisms. Ninety-four healthy volunteers participated in this study and were randomly distributed to four groups. In the classical conditioning combined with verbal suggestion group, US-(small pain distribution) and US+ (large pain distribution) were paired with visual stimuli (CS+ and CS-) and participants were told about this association. In the verbal suggestion group, the conditioning was not performed, whereas in classical conditioning only group, learning was not combined with suggestion. In the control group, conditioning and suggestion did not take place. Ratings of perceived pain distribution (PD) were collected after each trial and ratings of pain intensity after each block of trials. During the testing phase, participants were exposed to electrocutaneous stimuli corresponding to only the small (US-) pain distribution. Results showed significant differences between CS+ and CS-pain distribution ratings across the experimental groups: conditioning + verbal suggestion (p<0.01), conditioning only group (p<0.05) and verbal suggestion only group (p<0.05), but not in the control group (p>0.05). Furthermore, significant differences in the perceived pain distribution were found between the control group and all experimental groups. This result supports our main hypothesis that the perceived pain distribution can be influenced by classical conditioning as well as verbal suggestion, although the effect is stronger when both are combined.

physiology↗

bioRxiv2023

Cell type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells

The functional impact and cellular context of mosaic structural variants (mSVs) in normal tissues is understudied. Utilizing Strand-seq, we sequenced 1,133 single cell genomes from 19 human donors of increasing age, revealing a heterogeneous mSV landscape in hematopoietic stem and progenitor cells (HSPCs). While mSV clonal expansions are confined to individuals over 60, de novo mSV formation occurs consistently across age, frequently leading to megabase-scale segmental aneuploidies. Cells harboring subclonal mosaicism show evidence for increased mSV formation. To enable high-resolution cell-typing of each Strand-seq library, we generated single-cell MNase-seq reference datasets for eight distinct HSPCs. Subclonal mSVs frequently exhibit enrichment in myeloid progenitors, and single-cell multiomic analysis suggests that these mSVs result in recurrent dysregulation of pathways related to proliferation and metabolism, including Ras signaling and lipid metabolism. The comprehensive mSV landscape identified in this study implicates mSVs in cell type-specific molecular phenotypes, establishing a foundation for deciphering links between mSVs, aging, and disease risk.

genomics↗

bioRxiv2022

Reproducibility of spatial summation of pain effect during COVID-19 pandemic

The purpose of this study was to reproduce the previously observed spatial summation of pain effect (SSp) using non-laboratory procedures and commercial equipment. An additional aim was to explore the association between expectations and SSp. The Cold Pressor Task (CPT) was used to induce SSp. Healthy participants (N=68) immersed their non-dominant hands (divided into 5 segments) into cold water (CPT). Two conditions were used 1) gradual hand immersion (ascending condition) and 2) gradual hand withdrawal (descending condition). Pain intensity was measured on a Visual Analogue Scale (VAS). Psychological factors, such as the participants expectations of pain intensity were also measured on a VAS. Results showed significant SSp (X2(4) = 116.90, p < 0.001), reproduced with non-laboratory equipment in a home-based set-up. Furthermore, two novel findings were observed: i) there was a significant correlation between expectations and perceived pain, indicating a link between pain expectations and SSp, ii) spatial summation increased with the increase in duration exposure to the noxious stimulus (Wald X2(8) = 80.80, p < 0.001). This study suggests that SSp is associated with pain expectations and can be formed by a mixture of excitatory and inhibitory mechanisms potentially driven by temporal characteristics of neural excitation. Moreover, this study proposes a new feasible way to induce SSp using a home-based set-up.

physiology↗

bioRxiv2021

Haplotype-aware single-cell multiomics uncovers functional effects of somatic structural variation

Somatic structural variants (SVs) are widespread in cancer genomes, however, their impact on tumorigenesis and intra-tumour heterogeneity is incompletely understood, since methods to functionally characterize the broad spectrum of SVs arising in cancerous single-cells are lacking. We present a computational method, scNOVA, that couples SV discovery with nucleosome occupancy analysis by haplotype-resolved single-cell sequencing, to systematically uncover SV effects on cis-regulatory elements and gene activity. Application to leukemias and cell lines uncovered SV outcomes at several loci, including dysregulated cancer-related pathways and mono-allelic oncogene expression near SV breakpoints. At the intra-patient level, we identified different yet overlapping subclonal SVs that converge on aberrant Wnt signaling. We also deconvoluted the effects of catastrophic chromosomal rearrangements resulting in oncogenic transcription factor dysregulation. scNOVA directly links SVs to their functional consequences, opening the door for single-cell multiomics of SVs in heterogeneous cell populations.

genomics↗

bioRxiv2021

The long non-coding RNA MaTAR20 promotes mammary tumor growth by regulating angiogenesis pathways

Long non-coding RNAs (lncRNAs) are an emerging class of regulatory molecules that have been shown to play important roles in tumorigenesis and cancer progression. Here, we studied the recently identified lncRNA Mammary Tumor Associated RNA 20 (MaTAR20) in mammary cancer progression. A CRISPR/Cas9 knockout of MaTAR20 in the metastatic 4T1 cell line led to reduced cancer cell proliferation and increased cell surface adhesion compared to control cells. Consistent with these knockout results antisense oligonucleotide (ASO) mediated knockdown of MaTAR20 resulted in reduced growth and invasion in 4T1 cells, and in primary mammary tumor organoids derived from the MMTV-PyMT mouse model of breast cancer. Injection of MaTAR20-specific ASOs subcutaneously into tumor bearing MMTV-PyMT mice resulted in smaller and highly necrotic tumors in comparison to mice injected with a scrambled control ASO. To investigate the molecular mechanism by which MaTAR20 acts to advance mammary tumor progression, we applied a combination of RNA-sequencing and RNA-pulldown coupled to DNA-sequencing. These analyses demonstrated that the nuclear retained lncRNA is associated with several essential cancer signaling pathways such as VEGF signaling. In particular, MaTAR20 directly binds to and regulates the expression of Tnfsf15. Our results indicate that MaTAR20 is an important driver of mammary tumor progression and represents a promising new therapeutic target.

cancer biology↗

bioRxiv2021

Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states

Single-cell genomics has transformed our understanding of complex cellular systems. However, excessive costs and a lack of strategies for the purification of newly identified cell types impede their functional characterization and large-scale profiling. Here, we have generated high content single-cell proteo-genomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all major hematopoietic cell types in healthy aging and leukemia. These reference maps enable the automatic design of cost-effective high-throughput cytometry schemes that outperform state-of-the-art approaches, accurately reflect complex topologies of cellular systems, and permit the purification of precisely defined cell states. The systematic integration of cytometry and proteo-genomic data enables measuring the functional capacities of precisely mapped cell states at the single-cell level. Our study serves as an accessible resource and paves the way for a data-driven era in cytometry.

immunology↗

bioRxiv2020

Irradiated mesenchymal stromal cells induce genetic instability in human CD34+ cells

Radiation-induced bystander effects (RIBE) in human hematopoietic stem and progenitor cells may initiate myeloid neoplasms (MN). Here, the occurrence of RIBE caused by genotoxic signaling from irradiated human mesenchymal stromal cells (MSC) on human bone marrow CD34+ cells was investigated. For this purpose, healthy MSC were irradiated in order to generate conditioned medium containing potential genotoxic signaling factors. Afterwards, healthy CD34+ cells from the same donors were grown in conditioned medium and RIBE were analyzed. Increased DNA damage and chromosomal instability were detected in CD34+ cells grown in MSC conditioned medium when compared to CD34+ cells grown in control medium. Furthermore, reactive oxygen species and distinct proteome alterations, e.g., heat-shock protein GRP78, that might be secreted into the extracellular medium, were identified as potential RIBE mediators. In summary, our data provide evidence that irradiated MSC induce genetic instability in human CD34+ cells potentially resulting in the initiation of MN. Furthermore, the identification of key bystander signals, such as GRP78, may lay the framework for the development of next-generation anti-leukemic drugs.

cancer biology↗

bioRxiv2019

Restoration of Direct Corticospinal Communication Across Sites of Spinal Injury

Injury to the spinal cord often disrupts long-distance axon tracts that link the brain and spinal cord, causing permanent disability. Axon regeneration is then prevented by a combination of inhibitory signals that emerge at the injury site and by a low capacity for regeneration within injured neurons. The corticospinal tract (CST) is essential for fine motor control but has proven refractory to many attempted pro-regenerative treatments. Although strategies are emerging to create relay or detour circuits that re-route cortical motor commands through spared circuits, these have only partially met the challenge of restoring motor control. Here, using a murine model of spinal injury, we elevated the intrinsic regenerative ability of CST neurons by supplying a pro-regenerative transcription factor, KLF6, while simultaneously supplying injured CST axons with a growth-permissive graft of neural progenitor cells (NPCs) transplanted into a site of spinal injury. The combined treatment produced robust CST regeneration directly through the grafts and into distal spinal cord. Moreover, selective optogenetic stimulation of regenerated CST axons and single-unit electrophysiology revealed extensive synaptic integration by CST axons with spinal neurons beyond the injury site. Finally, when KLF6 was delivered to injured neurons with a highly effective retrograde vector, combined KLF6/NPC treatment yielded significant improvements in forelimb function. These findings highlight the utility of retrograde gene therapy as a strategy to treat CNS injury and establish conditions that restore functional CST communication across a site of spinal injury. Significance StatementDamage to the spinal cord results in incurable paralysis because axons that carry descending motor commands are unable to regenerate. Here we deployed a two-pronged strategy in a rodent model of spinal injury to promote regeneration by the corticospinal tract, a critical mediator of fine motor control. Delivering pro-regenerative KLF6 to injured neurons while simultaneously transplanting neural progenitor cells to injury sites resulted in robust regeneration directly through sites of spinal injury, accompanied by extensive synapse formation with spinal neurons. In addition, when KLF6 was delivered with improved retrograde gene therapy vectors, the combined treatment significantly improved forelimb function in injured animals. This work represents important progress toward restoring regeneration and motor function after spinal injury.

neuroscience↗

bioRxiv2018

MutaSeq reveals the transcriptomic consequences of clonal evolution in acute myeloid leukemia

Cancer stem cells drive disease progression and relapse in many types of cancer. Despite this, a thorough characterization of these cells remains elusive and with i the ability to eradicate cancer at its source. In acute myeloid leukemia (AML), leukemic stem cells (LSCs) underlie mortality but are difficult to isolate due to their low abundance and high similarity to healthy hematopoietic stem cells (HSCs). Here, we demonstrate that LSCs, HSCs, and pre-leukemic stem cells can be identified and molecularly profiled by combining single-cell transcriptomics with lineage tracing using both nuclear and mitochondrial somatic variants. While mutational status discriminates between healthy and cancerous cells, gene expression distinguishes stem cells and progenitor cell populations. Our approach enables the identification of LSC-specific gene expression programs and the characterization of differentiation blocks induced by leukemic mutations. Taken together, we demonstrate the power of single-cell multi-omic approaches in characterizing cancer stem cells.

genomics↗

bioRxiv2018

Decreased integrity of exercise-induced plasma cell free nuclear DNA - negative association with the increased oxidants production by circulating phagocytes

Strenuous exercise increases circulating cell free DNA (cf DNA) and stimulates blood phagocytes to generate reactive oxygen species (ROS) which may induce DNA strand breaks. We tested whether: (A) elevated cf DNA in response to three repeated bouts of exhaustive exercise has decreased integrity; (B) each bout of exercise increases luminol enhanced whole blood chemiluminescence (LBCL) as a measure of ROS production by polymorphonuclear leukocytes. Eleven men performed three treadmill exercise tests to exhaustion separated by 72 hours of resting. Pre- and post-exercise concentrations and integrity of cf nuclear and mitochondrial DNA (cf n-DNA, cf mt-DNA) and resting and fMLP-stimulated LBCL were determined. Each bout increased concentrations of cf n-DNA by more than 10-times which was accompanied by about 2-times elevated post-exercise rLBCL and fMLP-LBCL. Post-exercise cf n-DNA integrity (integrity index, I206/78) decreased after the first (0.59{+/-}0.19 vs. 0.48{+/-}0.18) and second (0.53{+/-}0.14 vs. 0.44{+/-}0.17) bout of exercise. There were negative correlations between I206/78 and rLBCL (=-0.37) and I206/78 and fMLP-LBCL (=- 0.40) - analysis of pooled pre- and post-exercise data (n=66). cf-mt DNA integrity (I218/97) did not alter in response to exercise. This suggests an involvement of phagocyte ROS in cf n-DNA strand breaks in response to exhaustive exercise.

physiology↗