Krzysztof Polański
A5090126209- Single-cell and spatial transcriptomics
- Immune Cell Function and Interaction
- T-cell and B-cell Immunology
- IL-33, ST2, and ILC Pathways
- Cancer-related molecular mechanisms research
- Extracellular vesicles in disease
- Congenital heart defects research
- Neonatal Respiratory Health Research
- SARS-CoV-2 and COVID-19 Research
- RNA modifications and cancer
- COVID-19 Clinical Research Studies
- Cell Image Analysis Techniques
- Immune responses and vaccinations
- Metabolomics and Mass Spectrometry Studies
- Reproductive System and Pregnancy
- Immune cells in cancer
- Gene Regulatory Network Analysis
- Cancer Genomics and Diagnostics
- Cancer, Lipids, and Metabolism
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- Pregnancy and preeclampsia studies
- Cancer Immunotherapy and Biomarkers
- Immunotherapy and Immune Responses
- Congenital gastrointestinal and neural anomalies
Wellcome Sanger Institute
2018-2025
Wellcome/MRC Cambridge Stem Cell Institute
2024
University of Cambridge
2024
University of Warwick
2013-2024
Coventry University
2016-2017
Silesian University of Technology
2014
University of Łódź
2009
Abstract Cardiovascular disease is the leading cause of death worldwide. Advanced insights into mechanisms and therapeutic strategies require a deeper understanding molecular processes involved in healthy heart. Knowledge full repertoire cardiac cells their gene expression profiles fundamental first step this endeavour. Here, using state-of-the-art analyses large-scale single-cell single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight...
Abstract Motivation Increasing numbers of large scale single cell RNA-Seq projects are leading to a data explosion, which can only be fully exploited through integration. A number methods have been developed combine diverse datasets by removing technical batch effects, but most computationally intensive. To overcome the challenge enormous datasets, we BBKNN, an extremely fast graph-based integration algorithm. We illustrate power BBKNN on mouse atlasing data, and favourably benchmark its run...
Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T B lymphocyte antigen receptor analyses over 780,000 peripheral mononuclear from a cross-sectional cohort 130 patients with varying severities COVID-19. identified expansion nonclassical monocytes expressing complement transcripts (CD16
Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the compartment 16 from 12 adult donors by single-cell RNA sequencing VDJ generating a dataset ~360,000 cells. To systematically resolve cell heterogeneity across tissues, we developed CellTypist, machine learning tool for rapid precise type annotation. Using this approach, combined with detailed curation, determined tissue distribution finely phenotyped types,...
Thymus development, cell by The human thymus is the organ responsible for maturation of many types T cells, which are immune cells that protect us from infection. However, it not well known how these develop with a full complement contains necessary variation to variety pathogens. By performing single-cell RNA sequencing on more than 250,000 Park et al. examined changes occur in over course life. They found development occurs coordinated manner among and their developmental microenvironment....
Abstract The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing response to functional requirements environmental exposures. Here, comprehensively map cell lineages, we use single-cell RNA sequencing antigen receptor analysis almost half a million cells from up 5 anatomical regions 11 distinct healthy paediatric adult gut. This reveals existence transcriptionally BEST4 epithelial tract. Furthermore, implicate IgG sensing as function...
Abstract The endometrium, the mucosal lining of uterus, undergoes dynamic changes throughout menstrual cycle in response to ovarian hormones. We have generated dense single-cell and spatial reference maps human uterus three-dimensional endometrial organoid cultures. dissect signaling pathways that determine cell fate epithelial lineages lumenal glandular microenvironments. Our benchmark organoids reveals states regulating differentiation secretory ciliated both vivo vitro. In vitro...
The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for delivery such an atlas. However, delays between fresh sample collection and processing may lead poor difficulties in experimental design.This study assesses effect cold storage on healthy spleen, esophagus, lung from ≥ 5 donors over 72 h. We collect 240,000 single-cell transcriptomes with detailed type annotations whole...
The skin confers biophysical and immunological protection through a complex cellular network established early in embryonic development. We profiled the transcriptomes of more than 500,000 single cells from developing human fetal skin, healthy adult with atopic dermatitis psoriasis. leveraged these datasets to compare cell states across development, homeostasis, disease. Our analysis revealed an enrichment innate immune during first trimester clonal expansion disease-associated lymphocytes...
Immune landscape of the human kidney Single-cell RNA sequencing has begun to shed light on full cellular diversity specific organs. However, these studies rarely examine organ-specific immune cells. Stewart et al. sequenced healthy adult and fetal samples at a single-cell level define heterogeneity in epithelial, myeloid, lymphoid From this dataset, they identified zonation cells, with relevance disease varied perturbations that occur different tumor settings. This profiling generates...
Abstract Tumors subvert immune cell function to evade responses, yet the complex mechanisms driving evasion remain poorly understood. Here we show that tumors induce de novo steroidogenesis in T lymphocytes anti-tumor immunity. Using a transgenic steroidogenesis-reporter mouse line identify and characterize steroidogenic cells, defining global gene expression identity of these steroid-producing cells regulatory networks by using single-cell transcriptomics. Genetic ablation restricts primary...
It is not fully understood why COVID-19 typically milder in children
Single-cell genomics studies have decoded the immune cell composition of several human prenatal organs but were limited in describing developing system as a distributed network across tissues. We profiled nine tissues combining single-cell RNA sequencing, antigen-receptor and spatial transcriptomics to reconstruct system. This revealed late acquisition immune-effector functions by myeloid lymphoid subsets maturation monocytes T cells before peripheral tissue seeding. Moreover, we uncovered...
The function of a cell is defined by its intrinsic characteristics and niche: the tissue microenvironment in which it dwells. Here we combine single-cell spatial transcriptomics data to discover cellular niches within eight regions human heart. We map cells microanatomical locations integrate knowledge-based unsupervised structural annotations. also profile cardiac conduction system
We present a multiomic cell atlas of human lung development that combines single-cell RNA and ATAC sequencing, high-throughput spatial transcriptomics, imaging. Coupling methods with analysis has allowed comprehensive cellular survey the epithelial, mesenchymal, endothelial, erythrocyte/leukocyte compartments from 5–22 post-conception weeks. identify previously uncharacterized states in all compartments. These include developmental-specific secretory progenitors subtype neuroendocrine...
Abstract Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture lung and airways, we profiled five proximal-to-distal locations healthy lungs depth using multi-omic single cell/nuclei (queryable at lungcellatlas.org ). Using computational data integration analysis, extend beyond suspension paradigm discover macro micro-anatomical compartments including...
The extraembryonic yolk sac (YS) ensures delivery of nutritional support and oxygen to the developing embryo but remains ill-defined in humans. We therefore assembled a comprehensive multiomic reference human YS from 3 8 postconception weeks by integrating single-cell protein gene expression data. Beyond its recognized role as site hematopoiesis, we highlight roles metabolism, coagulation, vascular development, hematopoietic regulation. reconstructed emergence decline stem progenitor cells...
Abstract Human limbs emerge during the fourth post-conception week as mesenchymal buds, which develop into fully formed over subsequent months 1 . This process is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common 2 Decades of work with model organisms have defined fundamental mechanisms underlying vertebrate limb development, but an in-depth characterization this humans has yet to be performed. Here we...
The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the dynamics early cellular responses to this disease remains limited
Skeletal muscle aging is a key contributor to age-related frailty and sarcopenia with substantial implications for global health. Here we profiled 90,902 single cells 92,259 nuclei from 17 donors map the process in adult human intercostal muscle, identifying cellular changes each compartment. We found that distinct subsets of stem exhibit decreased ribosome biogenesis genes increased CCL2 expression, causing different phenotypes. Our atlas also highlights an expansion associated...
Abstract Children infected with SARS-CoV-2 rarely progress to respiratory failure. However, the risk of mortality in people over 85 years age remains high. Here we investigate differences cellular landscape and function paediatric (<12 years), adult (30–50 years) older (>70 ex vivo cultured nasal epithelial cells response infection SARS-CoV-2. We show that cell tropism SARS-CoV-2, expression ACE2 TMPRSS2 subtypes, differ between groups. While ciliated are viral replication centres...