Biology subjects

Nowak, K.

Publications and source records attributed to Nowak, K..

10 recordsLinked to original sources

bioRxiv2026

Cardiac unloading via a transvalvular pump prevents arrhythmias following myocardial ischemia / reperfusion by preserving coronary microcirculation and cardiomyocyte nanostructure

Cardiac damage in the aftermath of myocardial ischemia / reperfusion (MI/R) compromises both electrical and mechanical function, predisposing patients to arrhythmia and heart failure. Microvascular obstruction (MVO) is increasingly recognized as a sequela of MI/R and a contributor to proarrhythmic cardiac remodeling. While transvalvular unloading (TVU) using a percutaneously delivered pump is garnering appreciation as a means of limiting infarct size and preserving mechanical function following percutaneous coronary intervention, its benefits for arrhythmia prevention remain unclear. We used a porcine model to test the hypothesis that cardiac unloading prior to and through reperfusion mitigates MVO, preserves cardiomyocyte nanostructure, and alleviates arrhythmias following MI/R. Anesthetized domestic swine undergoing acute ischemia (LAD occlusion, 90 mins) and reperfusion (120 mins) were randomized to TVU (n=5) and no treatment (control; n=6) treatments. Thioflavin-S was infused into the mid-LAD to assess coronary microcirculation and quantify MVO. Arrhythmia burden was assessed by in vivo electrocardiography using 3 lead EKG. Cardiac tissues were preserved for histology and optical microscopy studies. Compared to no treatment controls, TVU hearts evidenced significantly reduced infarct area (48 +/- 5 % vs. 59 +/- 11 % p = 0.03) and MVO (19 +/- 4 % vs. 27 +/- 5% , p = 0.03) normalized to area at risk and a higher myocardial salvage index (52 +/- 5 % vs. 41 +/- 11% p = 0.03). Extensive perivascular edema, and neutrophil infiltration observed in controls was markedly reduced in TVU hearts. Confocal microscopy and spatial pattern analysis revealed significantly mitigated disruption of gap junctions and NaV1.5 dissociation from N-cadherin in TVU hearts compared to controls. Importantly, severity-adjusted arrhythmia burden during reperfusion was significantly lower in TV-P hearts (8+/-8 vs. 12+/-5 episodes lasting greater than 5seconds in controls). Our results demonstrate that TVU effectively prevents arrhythmias during reperfusion by preserving coronary microvasculature and cardiomyocyte nanostructure.

physiology↗

bioRxiv2026

Focused Ultrasound Blood-Tumor Barrier Opening Rapidly Augments Intratumor CD4 and CD8 T Cell Representation in a Genetically Engineered Mouse Model of Glioma

Glioblastoma (GBM) is a highly aggressive primary brain tumor that remains difficult to treat due in part to its disorganized and heterogeneous vasculature, known as the blood-tumor barrier (BTB), which limits therapeutic delivery and beneficial immune cell infiltration. Focused ultrasound (FUS) with microbubbles (MBs) can transiently disrupt the BTB to enhance drug delivery and may induce sterile inflammation (SI) that can beneficially remodel the tumor immune landscape. However, this concept has only been explored in implanted tumor models with modest immune effects. Here, we utilized a physiologically relevant genetically engineered mouse model (GEMM) generated via in utero electroporation targeting Nf1, Tp53, and Pten to study tumor-vascular-immune interactions. This 3x CRISPR-Cas9 GEMM recapitulates key features of human glioma, including infiltrative growth, histopathology, molecular alterations, and stage-dependent blood-brain barrier disruption. FUS+MBs were applied to transiently disrupt the BTB, and MRI confirmed increased vascular permeability in treated tumors. Flow cytometry revealed robust increases in tumor-infiltrating CD4+ helper and CD8+ effector T cells three days post-FUS treatment, without altering the CD8/Treg ratio. These findings were supported by immunofluorescence imaging. Double-negative and double-positive T cells were detected, but they were not significantly altered by FUS. Ki67 analysis indicated that increased T-cell accumulation was not driven by local proliferation. By seven days post-treatment, immune differences were no longer observed. Collectively, these results demonstrate that FUS-mediated BTB disruption selectively and rapidly enhances lymphocyte infiltration in a clinically relevant glioma model, supporting its potential as a temporally controlled immunomodulatory strategy for GBM.

cancer biology↗

bioRxiv2026

Transcriptomic, Genomic, and Clinical Characterization of Morphological Classes in Localized and Metastatic Pancreatic Cancer

BackgroundHistomorphology is a strong prognostic biomarker correlated with basal-like and classical programs in surgically resected pancreatic ductal adenocarcinoma (PDAC). However, the spectrum of morphology and its biological associations remain poorly defined in advanced disease. ObjectivesWe explored the transcriptomic and genomic underpinnings and clinical relevance of morphological classes across localized and metastatic PDAC. DesignWe unified morphological classifications into four classes: glandular, cribriform, solid, and squamous. We integrated transcriptome and whole-genome sequencing following laser-capture microdissection with morphological classifications in 348 PDAC patients, where half of the cohort included locally advance and metastatic stages to uncover molecular associations. ResultsNon-glandular morphologies comprised three distinct classes that were enriched in metastatic disease. Transcriptomic profiling exhibited that glandular tumours predominantly expressed classical epithelial programs, although a subset displayed partial or full epithelial- mesenchymal transition signatures. In contrast, non-glandular morphologies showed basal-like transcriptional programs with subtype-specific pathways, including ciliogenesis in cribriform tumours, extracellular matrix remodelling and immune evasion in solid tumours, and keratinisation programs in squamous tumours. The solid class was significantly enriched in liver metastatic lesions and was associated with increased intra-tumoural morphological heterogeneity, whole-genome doubling, KRAS major allelic imbalance, and elevated KRAS-ERK signalling. ConclusionNon-glandular morphologies identify biologically distinct PDAC tumour states that are enriched in liver metastases and associated with subtype-specific transcriptional programs and KRAS-driven genomic alterations.

cancer biology↗

bioRxiv2025

A novel CHD4-CTCF regulatory axis drives key developmental programs and transitions in male germ cells.

Sustained gamete production and testis development relies in developmental programs and transitions such as spermatogonia differentiation, meiosis, and spermiogenesis. Chromatin remodeling complexes and CTCF are key regulators of these processes by controlling specific patterns of gene expression across gamete development. Although the CHD4 chromatin remodeler and CTCF have been implicated in spermatogonia development, a mechanism explaining their cooperation is missing. We also do not know CHD4 and CTCF role in later stages of spermatogenesis. Our studies reveal that germ cell-specific deletion of CHD4 results in spermatogonia development defects and affects meiotic-specific functions such as homologous chromosome synapsis. Combined analysis of genome-wide chromatin binding and single cell gene transcription showed that CHD4 controls specific gene expression programs important for spermatogonia differentiation, transition into meiosis, and meiotic specific processes. Mechanistically, this can be explained by a pervasive role for CHD4 in controlling CTCF chromatin binding and transcriptional function. The discovery of a functional interplay between CHD4 and CTCF reveals a novel axis of gene expression control, integrating chromatin structure and transcriptional outcomes. This interaction is essential in orchestrating early testis development and meiotic processes, ensuring that the correct number of chromosomes is faithfully transmitted to the next generation.

developmental biology↗

bioRxiv2025

Integrated spatial proteomics of human PDAC uncovers an expanded tumour-immune-stroma spectrum with genomic associations

Distinctively, pancreatic ductal adenocarcinoma (PDAC) consists of sparse tumour lesions intertwined with extensive desmoplastic stroma. The complexity of tumour-microenvironment interactions within this desmoplasia poses a challenge for accurate tumour profiling and patient stratification, and characterizes a profoundly chemoresistant tumour. Here we mapped the spatial relationships between tumour, stroma, and immune cell compartments delineating tumour and microenvironment types that expand the classical to basal spectrum of human PDAC. We used imaging mass cytometry to profile the in situ multi-cellular organization of 81 cell types in resected cases with paired whole genome sequencing. Cell types, functions, and pathway activation were distributed as highly reproducible environments in discrete locations throughout these tumours, which we deep-profiled using laser-capture mass spectrometry. We show that the connections between tumour phenotypes, vascularization, immune response, and stromal biophysical state are reinforced by genomic aberrations, altered by treatment, and associated with patient outcome. Predictive machine-learning models showed that spatial single cell data outperformed genomic or clinical features but integrated multi-omics models provide the best prediction of patient survival with compressed models requiring only 10 non-redundant robust molecular measures associated with the phenotypic spectrum of PDAC. Together, these findings define a phenotypic and molecular framework of PDAC that captures tumour-microenvironment co-dependencies and offers a refined basis for patient stratification and therapeutic targeting.

cancer biology↗

bioRxiv2024

Molecular Basis of Sperm Methylome Response to Aging and Stress

Changes in the sperm epigenome induced by age and/or stressors often follow common unexplained patterns affecting genes responsible for embryonic development and neurodevelopment. The stochastic epigenetic variation (SEV) hypothesis proposes that in response to stressors naturally variable methylation regions (VMRs) associated with morphogenic genes increase in methylation variation to diversify phenotypes and improve chances of survival of the genetic lineage. Here, we test predictions from the SEV hypothesis using mouse and rat sperm DNA methylation and other -omics data. We demonstrate that the context of DNA regions determines the response of sperm methylome to various factors rather than the stressors and/or timing of these factors. We propose a model explaining age/stress-dependent shifts in methylation in VMRs by an asymmetric increase in methylation variation of these regions. Because methylation variation in VMRs increases with age, sperm methylome response to stressors may be characterized as an acceleration of epigenetic aging.

systems biology↗

bioRxiv2023

The nuclear PIWI-interacting protein Gtsf1 controls the selective degradation of small RNAs in Paramecium

Ciliates undergo developmentally programmed genome elimination, in which small RNAs direct the removal of target DNA segments, including transposable elements. At each sexual generation, the development of the macronucleus (MAC) requires massive and reproducible elimination of a large proportion of the germline micronuclear (MIC) genome, leading to a highly streamlined somatic MAC genome. 25-nt long scnRNAs are produced from the entire germline MIC genome during meiosis, and this initial complex small RNA population is then transported to the maternal MAC, where selection of scnRNAs corresponding to germline (MIC)-specific sequences is thought to take place. Selected scnRNAs, loaded onto the PIWI protein Ptiwi09, guide the deposition of histone H3 post-translational modifications (H3K9me3 and H3K27me3) onto transposable elements in the developing macronucleus, ultimately triggering their specific elimination. How germline-specific MIC scnRNAs are selected remains to be determined. Here, we provide important mechanistic insights into the scnRNA selection pathway by identifying a Paramecium homolog of Gametocyte specific factor 1 (Gtsf1) as essential for the selective degradation of scnRNAs corresponding to retained somatic MAC sequences. Consistently, we also show that Gtsf1 is exclusively localized in the maternal macronucleus and associates with the scnRNA-binding protein Ptiwi09. Furthermore, Gtsf1 is necessary for DNA elimination and correct H3K9me3 and H3K27me3 localization in the new developing macronucleus, demonstrating that the scnRNA selection process is important for genome elimination. We propose that Gtsf1 is required for the coordinated degradation of Ptiwi09-scnRNA complexes that pair with nascent RNA transcribed from the maternal MAC genome, similarly to the mechanism suggested for microRNA target-directed degradation in metazoans.

genetics↗

bioRxiv2020

Development of a mass-spectrometry based method for the identification of the in vivo whole blood and plasma ADP-ribosylomes

Blood and plasma proteins are heavily investigated as biomarkers for different diseases. However, the post-translational modification states of these proteins are rarely analyzed since blood contains many enzymes that rapidly remove these modification after sampling. In contrast to the well-described role of protein ADP-ribosylation in cells and organs, its role in blood remains mostly uncharacterized. Here, we discovered that plasma phosphodiesterases and/or ADP-ribosylhydrolases rapidly demodify in vitro ADP-ribosylated proteins. Thus, to identify the in vivo whole blood and plasma ADP-ribosylomes, we established a novel mass-spectrometry based workflow that was applied to blood samples collected from LPS-treated pigs (Sus scrofa), which serves as a model for human systemic inflammatory response syndrome. These analyses identified 60 ADP-ribosylated proteins, 17 of which were ADP-ribosylated plasma proteins. This new protocol provides an important step forward for the rapidly developing field of ADP-ribosylation and defines the blood and plasma ADP-ribosylomes under both healthy and disease conditions.

molecular biology↗

bioRxiv2020

Some theoretical aspects of reprogramming the standard genetic code

1Reprogramming of the standard genetic code in order to include non-canonical amino acids (ncAAs) opens a new perspective in medicine, industry and biotechnology. There are several methods of engineering the code, which allow us for storing new genetic information in DNA sequences and transmitting it into the protein world. Here, we investigate the problem of optimal genetic code extension from theoretical perspective. We assume that the new coding system should encode both canonical and new ncAAs using 64 classical codons. What is more, the extended genetic code should be robust to point nucleotide mutation and minimize the possibility of reversion from new to old information. In order to do so, we follow graph theory to study the properties of optimal codon sets, which can encode 20 canonical amino acids and stop coding signal. Finally, we describe the set of vacant codons that could be assigned to new amino acids. Moreover, we discuss the optimal number of the newly incorporated ncAAs and also the optimal size of codon blocks that are assigned to ncAAs.

synthetic biology↗

bioRxiv2019

Geographically structured genomic diversity of non-human primate-infecting Treponema pallidum subsp. pertenue

BackgroundIncreasing evidence suggests many non-human primate (NHP) species in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue (TPE), the bacterium causing yaws in humans. In humans, yaws is characterized by lesions of the extremities and face, while Treponema pallidum subsp. pallidum (TPA) causes venereal syphilis and is characterized by primary lesions on the genital, anal or oral mucosae, and has not been detected in NHPs. Due to a paucity of genetic data, it remains unclear whether other Treponema pallidum (TP) subspecies found in humans also occur in NHP and how the genomic diversity of TPE lineages that do occur in NHPs is distributed across hosts and space. MethodologyWe observed a combination of yaws- and syphilis-like symptoms in sooty mangabeys (Cercocebus atys atys) in Tai National Park (TNP), Cote dIvoire and collected swabs and biopsies from symptomatic animals. We also collected NHP bones from eight species from TNP, as well as from 19 species at 12 field sites across sub-Saharan Africa. Samples were screened for TP DNA using PCRs. In-solution hybridization capture coupled with high throughput sequencing was used to sequence TP genomes from positive samples. Principal findingsWe generated four nearly complete TP genomes from biopsies and swabs and five partial genomes from bones. Phylogenomic analyses revealed that both syphilis- and yaws-like lesions of sooty mangabeys within a single social group in TNP were caused by TPE. All TPE genomes determined from these sooty mangabeys were different and exhibited divergence levels not observed in TPE from a single species at any other field site where the disease seems to be epizootic. In general, simian TPE isolates did not form monophyletic clades based on host species or the type of symptoms caused by an isolate, but rather clustered based on geography. ConclusionsThere is a large diversity of TPE strains infecting NHPs in TNP. Our observations within a single social group of sooty mangabeys do not support the epizootic spread of a single clone, but rather points towards frequent independent introductions of the bacterium, which can cause syphilis- and yaws-like lesions. On a larger scale, the geographic clustering of TPE genomes might be compatible with cross-species transmission of TPE within ecosystems or environmental exposure leading to acquisition of closely related strains. Authors summaryIndividuals in several populations of wild non-human primates (NHP) in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue (TPE), a pathogen causing yaws disease in humans. In humans, yaws is characterized by skin lesions of the extremities and face. In contrast, Treponema pallidum subsp. pallidum, which causes venereal syphilis in humans, has not been observed in NHPs. We describe a combination of yaws- and syphilis-like symptoms in a sooty mangabey (Cercocebus atys atys) social group in Tai National Park (TNP), Cote dIvoire. We sampled lesioned animals and collected and tested NHP bones from field sites across sub-Saharan Africa. We were able to reconstruct four genomes from swabs/biopsies and five partial genomes from bone samples. Phylogenomic analyses revealed that syphilis-like lesions and yaws-like lesions in TNP were caused by a large diversity of TPE strains. Additionally, simian TPE isolates did not form monophyletic clades based on the host species or the types of symptoms caused by an isolate, but rather clustered by geographic origin. This is suggestive of cross-species transmission of TPE within ecosystems or environmental exposure leading to acquisition of closely related strains.

genomics↗