Biology subjects

Lindskog, C.

Publications and source records attributed to Lindskog, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Pubertal maturation and chemotherapy-associated disruption of the pediatric ovary revealed by multimodal single-cell profiling

Ovarian tissue cryopreservation enables fertility preservation in females undergoing gonadotoxic therapies, restoring fertility in adults. Although offered even before puberty, the childhood ovary and its vulnerability to therapy remain poorly characterized. Here, ovarian tissue from 16 patients undergoing fertility preservation (aged 1-16 years) and 11 adult controls (aged 22-32 years) was analyzed using single-cell RNA sequencing, spatial transcriptomics, and multiplex immunostaining. In chemotherapy-naive samples, 13 somatic cell populations underwent extracellular matrix remodeling, vascular, neural, and stromal maturation during puberty, whereas changes in germline related to chromatin remodeling. Spatial transcriptomics resolved 23 clusters across, revealing distinct tissue organization and follicular niche composition between children and adults. Chemotherapy exposure depleted perifollicular and vascular cells, suppressed intercellular signaling, and dysregulated over half of puberty-associated genes, converging on stress responses and extracellular matrix remodeling, with SEPTIN7 as a potential biomarker. These findings uncover critical developmental vulnerabilities of the pediatric ovary relevant to fertility preservation.

developmental biology↗

bioRxiv2026

A cell type-resolved proteomic atlas of the human body

Proteins define what cells do, yet their systematic quantification across human cell types has remained out of reach. Using Deep Visual Proteomics on tissue from a healthy female donor, we built an atlas of 27 cell types across 14 tissues, quantifying two-thirds of all human protein-coding genes, with up to 8,500 per population. The proteome partitions bimodally into a universal core and highly specialized programs. Integration into the Human Protein Atlas Single Cell Resource enabled comparison of RNA and protein abundance at cell type resolution, revealing that concordance depends on pathway rather than cellular identity. This resolution uncovered cancer-testis antigens in oocytes invisible to bulk profiling. Our openly accessible resource provides a foundation for cell type-resolved proteomics in health and disease.

biochemistry↗

bioRxiv2026

Expression landscape of the genetic hearing loss protein whirlin across human tissues and cell types.

Whirlin (WHRN/DFNB31) is a cytosekeltal scaffolding protein essential for the development and function of sensory cells in the inner ear and retina, yet its distribution and potential roles in other human tissues remain poorly defined. Here, we present a comprehensive expression map of whirlin by integrating bulk RNA, single-cell RNA, and antibody-based proteomics data generated as part of the Human Protein Atlas consortium. WHRN was detected in most human tissues, with highest levels observed in endocrine organs, reproductive tissues, and the nervous system. Single-cell analysis revealed that this distribution is driven by enrichment in specific cell types, including endocrine, ciliated, and specialized epithelial cells, as well as different immune cells. Immunohistochemistry confirmed broad protein expression with cell type-specific patterns consistent with transcriptomic data. Analysis of cancer tissues showed that whirlin is widely expressed, with levels generally reflecting those of corresponding normal tissues. In addition, several commonly used human cell lines were found to express endogenous WHRN. Together, this work provides the first comprehensive body-wide expression landscape of whirlin and establishes an important resource for further studies on its roles beyond hearing and vision. SUBJECTSCells; Genetics; Immunology; Peptides and proteins; Protein expression O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/713511v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@169a7corg.highwire.dtl.DTLVardef@1f87a54org.highwire.dtl.DTLVardef@27419borg.highwire.dtl.DTLVardef@1445140_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2026

Cell type-resolved transcriptomic map of skeletal muscle in women with polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is associated with skeletal muscle insulin resistance, fibrosis, and lipotoxicity, yet the cellular origins remain unknown. Here, we present a comprehensive cellular atlas of skeletal muscle from hyperinsulinemic and hyperandrogenic women with PCOS and controls of similar age, weight, and BMI. Analysis of 72,247 nuclei from 19 biopsies revealed cell-type-specific dysregulation in PCOS, with fiber-type-specific metabolic impairment, converging with pro-fibrotic reprogramming of fibro-adipogenic progenitors (FAPs) and enhanced FAP-myofiber crosstalk, characterized by enhanced collagen and laminin signaling. Metformin intervention for 16-weeks selectively reversed PCOS-associated transcriptional dysregulation in FAPs, revealing heterogeneous cellular responses in skeletal muscle. In vitro, PCOS myotubes retained metabolic dysfunction, yet show normalized glucose responsiveness, indicating plasticity despite metabolic memory. Systemic hyperinsulinemia and hyperandrogenemia correlated with transcriptional signatures in muscle fibers and FAPs, linking endocrine imbalance to pro-fibrotic remodeling. These findings identify novel therapeutic targets beyond conventional insulin-sensitizing approaches. Highlights- First single-nuclei atlas of human skeletal muscle in women with PCOS - FAPs subpopulations display activated pro-fibrotic phenotype - Metformin selectively targets distinct cell populations - Hyperinsulinemia and hyperandrogenemia correlate with transcriptional signatures of skeletal muscle fibers and FAPs

physiology↗

bioRxiv2026

Regional epithelial architecture and spatial distribution of T and B lymphocytes in the human fallopian tube

The human fallopian tube plays a critical role in reproduction, yet its structural organization and immune landscape remain incompletely characterized. Here, we analyzed tissue from women of reproductive age across three anatomical regions (isthmus, ampulla, and fimbriae) throughout the menstrual cycle. By using antibody-based imaging together with automated image analysis, the epithelial thickness and spatial distribution of T and B lymphocytes was assessed. No significant differences in epithelial thickness were observed between proliferative and secretory phases. However, significant regional variation was identified, with the epithelium thickest in the isthmus and thinnest in the ampulla. Both CD8A+ T lymphocytes and CD20+ B lymphocytes were present throughout the fallopian tube, with their abundance strongly correlated across patients. Spatial analysis further revealed that both lymphocyte populations were preferentially localized to the mucosal compartment adjacent to the lumen, and intraepithelial B lymphocytes were consistently observed. Together, these findings provide new insight into epithelial organization and immune cell distribution in the human fallopian tube, highlighting the complexity of the tubal immune microenvironment and its potential relevance for reproductive biology.

immunology↗

bioRxiv2026

A high-resolution spatial map of cilia-associated proteins in the human fallopian tube

Molecular alterations in the fallopian tubes play a pivotal role in the development of cancer and reproductive disorders, yet their molecular landscape at the protein level remains poorly defined. Here, we map key fallopian tube proteins at single-cell resolution utilizing an integrated transcriptomics and proteomics approach. Based on RNA-seq analysis we identify 310 genes with elevated expression in fallopian tube, the majority of which are associated with motile cilia function. We spatially characterize 133 of the corresponding proteins in fallopian tube and other human tissues with motile cilia to subcellular structures of ciliated cells, validating the findings with single-cell RNA-seq and mass-spectrometry data. Eleven proteins previously only studied on the transcript level without information in cilia databases are further analyzed in a hydrosalpinx patient, showing a thinner epithelium, lower density of FOXJ1 expression, and reduced expression of FHAD1, RIIAD1, and C2orf81. Our high-resolution spatial map aids in dissecting the pathways underlaying infertility and diseases linked to cilia-specific functions.

molecular biology↗

bioRxiv2025

A high-resolution subcellular map of proteins in ciliated cells

Motile cilia are complex structures regulated by thousands of genes, essential for various physiological functions like respiration and reproduction. Their dysfunction can result in severe conditions like primary ciliary dyskinesia (PCD), highlighting the need for a deeper molecular understanding of their specific ciliary compartments. Interestingly, ciliated cells harbor multiple proteins with limited evidence on biological function, as defined by Functional Evidence (FE) scores, a grading system developed by the Human Proteome Project (HPP). Building upon the stringent antibody validation pipeline of the Human Protein Atlas (HPA) project, we developed a high-throughput workflow that combines a novel multiplex immunohistochemistry protocol with image analysis to investigate protein expression and subcellular localization in motile ciliated cells across five human tissues: nasopharynx, bronchus, fallopian tube, endometrium, and cervix. We spatially mapped >180 proteins, out of which 73% have FE scores 2-5, suggesting that further evidence is needed to establish these proteins biological function. Notably, expression patterns varied between tissues, suggesting that motile cilia proteins are not universally expressed across the different epithelia. Our pipeline constitutes a promising resource for comprehensive mapping of the motile cilia proteome, and a first step towards identifying cilia proteins for functional studies to understand the molecular mechanisms underlying ciliopathies.

cell biology↗

bioRxiv2024

Intrinsic Diversity in Primary Cilia Revealed Through Spatial Proteomics

Primary cilia are a critical organelle found on most human cells, and their dysfunction is linked to hereditary ciliopathies with a wide phenotypic spectrum. Despite their significance, the specific roles of cilia in different cell types remain poorly understood due to limitations in analyzing ciliary protein composition. We employed antibody-based spatial proteomics to expand the Human Protein Atlas to primary cilia. Our analysis identified the subciliary locations of 715 proteins across three cell lines, examining 128,156 individual cilia. We found that 69% of the ciliary proteome is cell-type specific, and 78% exhibited single-cilia heterogeneity. Our findings portray cilia as sensors tuning their proteome to effectively sense the environment and compute cellular responses. We identified 91 novel cilia proteins and found a genetic candidate variant in CREB3 in one clinical case with features overlapping ciliopathy phenotypes. This open, spatial cilia atlas advances research on cilia and ciliopathies.

cell biology↗

bioRxiv2024

A spatiotemporal atlas of human spermatogenesis based on single-cell transcriptomics and multiplex antibody imaging

Understanding how transcriptional programs are translated into functional protein landscapes within intact tissues remains a major challenge in biology. While single-cell RNA sequencing (scRNA-seq) has enabled high-resolution identification of cellular states, corresponding protein expression within its spatial context remains poorly resolved at scale. Here, we present a scalable framework that integrates scRNA-seq with multiplex immunohistochemistry (mIHC) and automated image analysis to achieve spatially resolved, single-cell-level protein mapping across human spermatogenesis. Using this approach, we quantified the expression of nearly 500 proteins across 12 discrete germ cell states within intact human testis tissue, generating a high-resolution spatiotemporal proteomic atlas. Comparative analysis of mRNA and protein expression revealed widespread temporal discordance, indicating that transcriptional state is not always predictive of protein abundance. Notably, we identify delayed translation of key regulators such as PIWIL4, whose protein expression peaks at later differentiation stages than its mRNA expression. Together, our results establish a generalizable strategy for proteome-wide spatial mapping of single-cell states and demonstrate the importance of integrating protein-level measurements to resolve cellular identity and function in complex tissues.

molecular biology↗

bioRxiv2024

Dissecting autonomous enzyme variability in single cells

Metabolic enzymes perform life-sustaining functions in various cellular compartments. Anecdotally, metabolic activity is observed to vary between genetically identical cells, which impacts drug resistance, differentiation, and immune cell activation. However, no large-scale resource systematically reporting metabolic cellular heterogeneity exists. Here, we leverage imaging-based single-cell spatial proteomics to reveal the extent of non-genetic variability of the human enzymatic proteome, as a proxy for metabolic states. Nearly two fifths of enzymes exhibit cell-to-cell variable expression, and half localize to multiple cellular compartments. Metabolic heterogeneity arises largely autonomously of cell cycling, and individual cells reestablish these myriad metabolic phenotypes over several cell divisions. Multiplexed imaging revealed that metabolic states are continuous and that the correlation between metabolic pathways is metabolic state dependent. These results establish cell-to-cell enzymatic heterogeneity as an organizing principle of cell biology that may rewire our understanding of drug resistance, treatment design, and other aspects of medicine.

cell biology↗

bioRxiv2024

Flexible and robust cell type annotation for highly multiplexed tissue images

Identifying cell types in highly multiplexed images is essential for understanding tissue spatial organization. Current cell type annotation methods often rely on extensive reference images and manual adjustments. In this work, we present a tool, Robust Image-Based Cell Annotator (RIBCA), that enables accurate, automated, unbiased, and fine-grained cell type annotation for images with a wide range of antibody panels, without requiring additional model training or human intervention. Our tool has successfully annotated over 3 million cells, revealing the spatial organization of various cell types across more than 40 different human tissues. It is open-source and features a modular design, allowing for easy extension to additional cell types.

bioinformatics↗

bioRxiv2024

PTEN and ARID1A haploinsufficiency equip colonic epithelium for oncogenic transformation

Normal aged tissues are thought to exist as a patchwork of mutant clones. However, the relevance of driver mutations in normal tissue in terms of cancer initiation has not been well described. Here, we sought a quantitative understanding of how different cancer drivers achieve an age-related mutational footprint in the human colonic epithelium and to relate the clonal behaviours they generate to cancer risk. Metanalysis of contemporary multiregional sampling studies of colorectal tumours revealed many of the weak or moderate cancer drivers are trunk mutations present in the last common ancestor from which cancers arise. To study the processes by which such driver mutations could contribute to cancer predisposition, immunohistochemistry was used to detect PTEN, SMAD4 and ARID1A deficient clones in normal colon FFPE surgical resection samples (N=182 patients). Age-related changes in clone size and frequency identified positive biases in clone dynamics that acted to increase the mutational footprint for ARID1A and PTEN but not SMAD4. In vitro engineered monoallelic loss of PTEN and ARID1A implicated specific altered downstream pathways and acquired pro-oncogenic cellular fates corresponding to haploinsufficiency for these genes. In situ analysis confirmed enhanced proliferation in both PTEN and ARID1A deficient clones and creation of an immune exclusive microenvironment associated with ARID1A deficiency. The behaviours resulting from haploinsufficiency of PTEN and ARID1A exemplify how priming of the tissue through somatic mosaicism could contribute alternative combinations of genetic events leading to transformation.

cancer biology↗

bioRxiv2024

ANKRD55 interacts with an IFT-B-like complex in microglia

IntroductionSNPs associated with genome-wide risk for multiple sclerosis (MS) modulate expression of ankyrin repeat domain protein 55 (ANKRD55). The function of ANKRD55 is not well understood. A role for ANKRD55 in ciliar transport in multiciliated cells has been reported. To gain deeper insight in how ANKRD55 may modulate neuro-inflammatory parameters, we identified the ANKRD55 interactomes from human neuroblastoma, astrocytic, microglial and monocytic cell lines. MethodsCell lines were transfected with synthetic ANKRD55 RNA in conjunction with nanoparticles. ANKRD55 interactomes were determined by affinity purification coupled to mass spectrometry (AP-MS) and analyzed bioinformatically. Results were validated and interpreted using confocal immunofluorescence microscopy, RNAseq transcriptomics, and a visible immunoprecipitation assay (VIP). ResultsShared among the interactomes were the 14-3-3 isoforms 14-3-3{eta} and 14-3-3{beta}{eta}. Unique to the microglial interactome were eight proteins belonging to the intraflagellar transport complex B (IFT-B). The IFT-B complex is known to mediate anterograde protein trafficking from the base to the tip of cilia. The dimer IFT46-IFT56 was identified as the minimum entity of IFT-B needed to support interaction with ANKRD55. To verify whether ANKRD55 is a ciliar transport protein, we induced ciliogenesis by serum starvation. Primary ARL13B+ cilia could be induced in the astrocytic and neuroblastoma, but not microglial, cell lines. By confocal microscopy, ANKRD55 was not detectable in these cilia but was enriched at the basal body. In the microglial cell line, ANKRD55 and IFT-B components were enriched at the centrosome. In two human primary myeloid cell models, monocyte-derived microglia (MoMG) and monocyte-derived dendritic cells (MoDC), we were able to recapitulate the co-localization of ANKRD55 and IFT81 at the centrosome. DiscussionOur work shows that an ANKRD55 - IFT-B-like complex is assembled in microglial cells. Together with the finding that ANKRD55 was not detected in primary cilia, the results suggest that ANKRD55 is associated with an IFT-B pathway that can operate independent of ciliogenesis.

immunology↗

bioRxiv2023

A human stomach cell type transcriptome atlas

The identification of cell type-specific genes and their modification under different conditions is central to our understanding of human health and disease. The stomach, a hollow organ in the upper gastrointestinal tract, provides an acidic environment that contributes to microbial defence and facilitates the activity of secreted digestive enzymes to process food and nutrients into chyme. In contrast to other sections of the gastrointestinal tract, detailed descriptions of cell type gene enrichment profiles in the stomach are absent from the major single cell sequencing-based atlases. Here, we use an integrative correlation analysis method to predict human stomach cell type transcriptome signatures using unfractionated stomach RNAseq data from 359 individuals. We profile parietal, chief, gastric mucous, gastric enteroendocrine, mitotic, endothelial, fibroblast, macrophage, neutrophil, T-cell and plasma cells, identifying over 1600 cell type-enriched genes. We uncover the cell type expression profile of several non-coding genes strongly associated with the progression of gastric cancer and, using a sex-based subset analysis, uncover a panel of male-only chief cell-enriched genes. This study provides a roadmap to further understand human stomach biology.

systems biology↗

bioRxiv2023

A tissue centric atlas of cell type transcriptome enrichment signatures

Genes with cell type specific expression typically encode for proteins that have cell type specific functions. Single cell RNAseq (scRNAseq) has facilitated the identification of such genes, but various challenges limit the analysis of certain cell types and lowly expressed genes. Here, we performed an integrative network analysis of over 6000 bulk RNAseq datasets from 15 human organs, to generate a tissue-by-tissue cell type enrichment prediction atlas for all protein coding genes. We profile all the major constituent cell types, including several that are fragile or difficult to process and thus absent from existing scRNAseq-based atlases. The stability and read depth of bulk RNAseq data, and the high number of biological replicates analysed, allowed us to identify lowly expressed cell type enriched genes that are difficult to classify using existing methods. We identify co-enriched gene panels shared by pancreatic alpha and beta cells, chart temporal changes in cell enrichment signatures during spermatogenesis, and reveal that cells in the hair root are a major source of skin enriched genes. In a cross-tissue analysis, we identify shared gene enrichment signatures between highly metabolic and motile cell types, and core identity profiles of cell types found in across tissue types. Our study provides the only cell type gene enrichment atlas generated independently of scRNAseq, representing a new addition to our existing toolbox of resources for the understanding of gene expression across human tissues.

systems biology↗

bioRxiv2023

Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms

The development of a reference atlas of the healthy human body requires automated image segmentation of major anatomical structures across multiple organs based on spatial bioimages generated from various sources with differences in sample preparation. We present the setup and results of the "Hacking the Human Body" machine learning algorithm development competition hosted by the Human Biomolecular Atlas (HuBMAP) and the Human Protein Atlas (HPA) teams on the Kaggle platform. We showcase how 1,175 teams from 78 countries engaged in community- driven, open-science code development that resulted in machine learning models which successfully segment anatomical structures across five organs using histology images from two consortia and that will be productized in the HuBMAP data portal to process large datasets at scale in support of Human Reference Atlas construction. We discuss the benchmark data created for the competition, major challenges faced by the participants, and the winning models and strategies.

bioinformatics↗

bioRxiv2022

Genome-wide single cell annotation of the human protein-coding genes

An important quest for the life science community is to deliver a complete annotation of the human building-blocks of life, the genes and the proteins. Here, we report on a genome-wide effort to annotate all protein-coding genes based on single cell transcriptomics data representing all major tissues and organs in the human body, integrated with data from bulk transcriptomics and antibody-based tissue profiling. Altogether, 25 tissues have been analyzed with single cell transcriptomics resulting in genome-wide expression in 444 single cell types using a strategy involving pooling data from individual cells to obtain genome-wide expression profiles of individual cell type. We introduce a new genome-wide classification tool based on clustering of similar expression profiles across single cell types, which can be visualized using dimensional reduction maps (UMAP). The clustering classification is integrated with a new "tau" score classification for all protein-coding genes, resulting in a measure of single cell specificity across all cell types for all individual genes. The analysis has allowed us to annotate all human protein-coding genes with regards to function and spatial distribution across individual cell types across all major tissues and organs in the human body. A new version of the open access Human Protein Atlas (www.proteinatlas.org) has been launched to enable researchers to explore the new genome-wide annotation on an individual gene level.

systems biology↗

bioRxiv2021

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

The endometrium, the mucosal lining of the uterus, undergoes dynamic changes throughout the menstrual cycle in response to ovarian hormones. We have generated single-cell and spatial reference maps of the human uterus and 3D endometrial organoid cultures. We dissect the signalling pathways that determine cell fate of the epithelial lineages in the lumenal and glandular microenvironments. Our benchmark of the endometrial organoids highlights common pathways regulating the differentiation of secretory and ciliated lineage in vivo and in vitro. We show in vitro that downregulation of WNT or NOTCH pathways increases the differentiation efficiency along the secretory and ciliated lineages, respectively. These mechanistic insights provide a platform for future development of treatments for a range of common endometrial disorders including endometriosis and carcinoma.

genomics↗