Biology subjects

Gronska-Peski, M.

Publications and source records attributed to Gronska-Peski, M..

6 recordsLinked to original sources

bioRxiv2025

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes

Detecting somatic mutations in normal tissues is challenging due to sequencing errors and the low allele fractions of post-zygotic variants. Duplex sequencing greatly reduces errors and can detect mutations at any allele fraction, but systematic, cross-platform comparisons are lacking. We present a comprehensive benchmarking of six duplex sequencing technologies used by the SMaHT Network: CODEC, CompDuplex-seq, HiDEF-seq, NanoSeq, ppmSeq, and VISTA-seq. We evaluated their performance using cord blood DNA, a tumor-normal cell line mixture, and homogenates from six human tissues. Each method shows distinct profiles in genomic footprint, sensitivity, and cost. Despite differences in library construction and sequencing platforms, estimates of mutation rates and mutational signatures are highly concordant. Integration with ultra-deep whole-genome sequencing shows that duplex approaches sensitively capture mutations and signatures beyond embryonic or clonally expanded variants. These results provide a foundation for selecting duplex methods and interpreting their data, enabling scalable single-molecule analyses of somatic mutation landscapes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/692823v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@123b221org.highwire.dtl.DTLVardef@83ba0aorg.highwire.dtl.DTLVardef@2b0ab0org.highwire.dtl.DTLVardef@1cae35e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Controlled Delivery of a Neurotrophic Factor in the Adult Mouse Brain Using Engineered Microglia

Microglia, the resident immune cells of the central nervous system, have been proposed as vehicles for delivering therapeutic biologics. These cells can be genetically engineered in vitro and transplanted into host animals following ablation of endogenous microglia, enabling repopulation of the brain parenchyma. However, current replacement strategies often rely on radiation or transgenic models, limiting their clinical relevance. CSF1R inhibitors offer a more translational approach to microglia ablation, though surviving host cells can compete with transplanted microglia during repopulation. In this study, we successfully ablated endogenous microglia using a CSF1R inhibitor in adult mice and developed a method to transplant engineered microglia expressing Brain-Derived Neurotrophic Factor (BDNF) in a doxycycline-inducible manner. To enhance engraftment, transplanted cells also expressed a constitutively active CSF1R mutant (caCSF1R). BDNF-expressing transplanted microglia spread through large areas of host mice brains, displayed similar morphology and transcriptional profile to repopulating host microglia, and responded to pro-inflammatory stimuli. Treatment with doxycycline resulted in increased BDNF expression and TrkB phosphorylation in the host brain. Expression of caCSF1R provided transplanted cells with a competitive advantage over endogenous repopulating cells, resulting in the accelerated spread of the transplants. Our results demonstrate the functional integration and therapeutic potential of microglia as vehicles for delivering neurotrophic factors to the brain in a controllable manner. Furthermore, we show that caCSF1R expression is able to enhance the spread of transplanted microglia. SIGNIFICANCEThis study demonstrates the potential of engineered microglia to deliver the protein Brain-Derived Neurotrophic Factor to the brain parenchyma, under the control of orally-administered doxycycline. The technique can be generalized to a wide array of proteins, offering a novel paradigm for neurological therapy.

neuroscience↗

bioRxiv2025

Divergent somatic mutation patterns among human cerebellar neuron types

Neurons in the human brain accumulate somatic mutations with age. However, it is largely unknown how somatic mutation rates and patterns vary among the brains diverse types of neurons. Characterizing this variability is critical for elucidating the role of genome integrity in human brain function and disease. Moreover, the significant physiological differences among the brains cell types provides an opportunity to learn more general underlying factors that determine mutation rates and patterns. Here, we utilized high-fidelity duplex DNA sequencing to profile somatic mutation processes across the lifespan in the two major cell types of the human cerebellum, Purkinje neurons and granule neurons, which have dramatically different sizes, functions, and physiologies. Surprisingly, these cell types exhibited similar rates of substitution mutations, including similar rates of signature SBS5 that is responsible for most mutations in the body yet whose mechanism remains unknown. However, we identified differences in Purkinje and granule neurons patterns of substitutions and in their rates and patterns of insertions and deletions, with transcription playing a key role in mediating these differences. Our work indicates that different types of neurons in the brain can differ in their aging-related somatic mutation processes. Our results further suggest that key features that distinguish Purkinje neurons from granule neurons, such as cell size, metabolic rates, and neuronal firing rates, are unlikely to be intrinsic determinants of the total substitution mutation rate and of signature SBS5, which is the most prevalent aging-related mutational process.

genomics↗

bioRxiv2023

Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing

Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other genetic diseases1-4. Almost all of these mosaic mutations begin as nucleotide mismatches or damage in only one of the two strands of the DNA prior to becoming double-strand mutations if unrepaired or misrepaired5. However, current DNA sequencing technologies cannot resolve these initial single-strand events. Here, we developed a single-molecule, long-read sequencing method that achieves single-molecule fidelity for single-base substitutions when present in either one or both strands of the DNA. It also detects single-strand cytosine deamination events, a common type of DNA damage. We profiled 110 samples from diverse tissues, including from individuals with cancer-predisposition syndromes, and define the first single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumors deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples deficient in only polymerase proofreading. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. Since the double-strand DNA mutations interrogated by prior studies are only the endpoint of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable new studies of how mutations arise in a variety of contexts, especially in cancer and aging.

genomics↗

bioRxiv2021

Donor-derived vasculature is required to support neocortical cell grafts after stroke

Neural precursor cells (NPCs) transplanted into the adult neocortex generate neurons that synaptically integrate with host neurons, supporting the possibility of achieving functional tissue repair. However, poor survival of transplanted NPCs greatly limits efficient engraftment. Here, we test the hypothesis that combining blood vessel-forming vascular cells with neuronal precursors improves engraftment. By transplanting mixed embryonic neocortical cells into adult mice with neocortical strokes, we show that transplant-derived neurons synapse with appropriate targets while donor vascular cells form vessels that fuse with the host vasculature to perfuse blood within the graft. Although all grafts became vascularized, larger grafts had greater contributions of donor-derived vessels that increased as a function of their distance from the host-graft border. Moreover, excluding vascular cells from the donor cell population strictly limited graft size. Thus, inclusion of vessel-forming vascular cells with NPCs is required for more efficient engraftment and ultimately for tissue repair.

neuroscience↗

bioRxiv2020

Role of Drosophila Rap/Fzr (DCdh1) in Retinal Axon Targeting and its Interactions with Loco and Liprin-alpha

The development of the wild type Drosophila compound eye involves stereotypical targeting of photoreceptor axons to the specific layers of the optic ganglion, medulla and lamina, in the third instar larvae. To test the hypothesis that ubiquitin ligases play an important role during retinal axon targeting we have examined the patterns of axon targeting in the developing eye of the retina aberrant in pattern (rap/fzr) mutants. Rap/Fzr is a homolog of mammalian Cdh1, an activator of anaphase promoting complex (APC), a multi-subunit E3 ubiquitin ligase, regulating the cell cycle progression. Previous work has shown that Rap/Fzr is required during eye development for proper cell cycle regulation, glia differentiation and pattern formation. It was also necessary for proper neuromuscular junction development and circadian rhythms. Our results show that Rap/Fzr is required for proper retinal axon targeting in the developing eye. Using ro-tau-lacZ, we show that the R2-R5 axons fail to stop in the lamina and mis-target to the medulla levels. Also, mosaic analyses experiments using FLP-FRT and GAL4-UAS techniques show that Rap/Fzr functions in a cell autonomous manner. To test for possible role of other signalling molecules and interactions with Rap/Fzr, we have examined rap/fzr axon projection phenotypes in double mutant combinations with the RGS protein, locomotion defective (loco) mutants and a scaffolding protein, Liprin-. Our studies suggest that Rap/Fzr is required for proper axon targeting during Drosophila visual system development, and the phenotype is enhanced in double mutants with either loco or Liprin-. These results are consistent with other mammalian studies reporting a role of Cdh1 in axon growth and targeting and provides further insights into neuronal functions of the ubiquitin ligase APC/CCdh1. HighlightsO_LILoss of rap/fzr in the third instar Drosophila eye disc leads to photoreceptor axon overgrowth C_LIO_LIOverexpression of rap/fzr leads to photoreceptor axon leads to axon shortening and clumping C_LIO_LILoss of LocoP452 leads to photoreceptor overgrowth C_LIO_LIDouble mutants of rap and loco or rap and Liprin- show axon enhancement of the axon targeting defects in the Drosophila third instar larvae eye imaginal discs. C_LI

genetics↗