Biology subjects

Lautwein, T.

Publications and source records attributed to Lautwein, T..

12 recordsLinked to original sources

bioRxiv2026

An immunophenotype-coupled transcriptomic atlas of mouse hematopoietic progenitors

Decoding the bone marrow (BM) hematopoietic progenitor compartment is central to understanding the development of mature immune cells in health and disease. Single-cell multimodal approaches are transforming the analysis of this heterogeneous compartment by simultaneously capturing transcriptomic and proteomic information. Still, integrated studies covering the full spectrum of murine hematopoietic stem and progenitor cells (HSPCs) remain scarce. Here, we report a Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) based atlas of 9,281 low-frequency mouse BM HSPCs, profiled using a 123 antibody-derived tag (ADT) panel coupled with genome-wide single-cell transcriptomes. Multimodal analysis resolved 28 progenitor stages across eight blood lineages, each defined by distinctive surface marker and transcription factor (TF) profiles, and provided novel marker combinations to dissect transcriptionally closely related progenitor stages. Classical mouse progenitor surface markers, such as CD117, CD34, and CD115, were detected in accordance with well-established lineage relationships, whereas CD43 and CD48 showed, unexpectedly, broader expression patterns. Neglected surface molecules such as CD27, CD36, CD106, and PIR-A/B are nominated as novel stage-specific markers. ADT versus transcriptome comparison revealed transcription-translation inconsistencies for markers, including CD54 and CD68. A CITE-seq-guided gating strategy translates these population definitions into FACS-compatible panels for prospective isolation and functional interrogation of previously unresolved progenitor stages. Comprehensive TF network analysis delineated lineage- and stage-specific transcriptional programs. This contributes to clarifying unresolved ontogenies and functions, including the lympho-myeloid dual origin of pDCs or rapid neutrophil turnover. This new and comprehensive resource enables exploration of mouse hematopoietic progenitor states driving discoveries in hematology and immunology.

immunology↗

bioRxiv2026

CITE-seq of murine bone marrow plasmacytoid dendritic cells and haematopoietic progenitor cells in sepsis

This dataset contains single-cell transcriptomic and surface protein profiles of bone marrow cells enriched for plasmacytoid dendritic cells (pDCs) and haematopoietic progenitor populations from septic and sham-operated mice. Sepsis was induced in BALB/c wild-type mice using cecal ligation and puncture (CLP) of moderate severity, with sham surgery as control. Bone marrow was collected 36 hours after surgery, depleted for selected lineage-positive cells by fluorescence-activated cell sorting, and processed using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq). Sample demultiplexing was performed using hashtag oligonucleotides. The dataset includes gene expression matrices, antibody-derived tag counts, and barcode assignments for 13,725 cells, with a comparable distribution of sham and CLP samples across the total cell number. It may be used to study transcriptional states, surface marker expression, and phenotypic diversity of bone marrow cells in sepsis, to compare with other immunological and haematological single-cell datasets, or to train and benchmark computational tools for multimodal single-cell data analysis.

immunology↗

bioRxiv2025

Artificial Soil (ArtSoil): recreating soil conditions in synthetic plant growth media

Controlled plant growth in laboratories can be achieved by cultivating plants in sterile or axenic conditions on pre-defined synthetic growth media typically supplemented with sugar. In nature, plants do not receive exogenous sugar supply, form symbiosis with microbes, and plant growth is influenced by soil edaphic factors. Thus, physiological and multi-omic analyses from plants grown on synthetic media will differ from those of soil-grown plants due to the influence of sucrose, and the lack of influence from microbiota and soil edaphic factors on plant growth. The rapid advancements in spatial-omics call for accurate characterization of plants grown in conditions similar to soil. To address the issue, we developed Artificial Soil (ArtSoil), a growth medium containing essential nutrients for plant growth, and aqueous soil extract (ASE) to maintain soil microbiomes and edaphic factors, simultaneously eliminating the need for sugar supplementation in the medium. We compared Arabidopsis thaliana grown on conventional media to ArtSoil under various growth conditions, and showed that complex soil microbiota in ArtSoil promote plant growth without physiological side effects induced by sucrose. We demonstrate an application for ArtSoil in single-cell transcriptomics and report microbiota-induced cell-type specificity in immune and nitrogen signaling. We tested ArtSoil with six types of ASEs to present the potential of ArtSoil in decoupling the effects of nutrients from microbiota in plant growth. We conclude that ArtSoil recapitulates the soil environment compared to conventional media, hence, enabling physiologically relevant plant growth. Significance statementLaboratory plant growth commonly relies on sugar-supplemented media and sterile growth conditions, which introduces physiological artifacts and fails to capture the natural influences of soil microbiota and edaphic factors, leading to analyses that diverge from native conditions. We developed Artificial Soil (ArtSoil), a medium containing aqueous soil extract that supports microbiota and sugar-independent growth, and demonstrate its utility in recapitulating native soil properties and enabling physiologically relevant plant development in vitro.

plant biology↗

bioRxiv2025

Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development

Grass inflorescences are composite structures, featuring complex sets of meristems as stem cell niches that are initiated in a repetitive manner. Meristems differ in identity and longevity, generate branches or split to form flower meristems that finally produce seeds. Within meristems, distinct cell types are determined by positional information and the regional activity of gene regulatory networks. Understanding these local microenvironments requires precise spatio-temporal information on gene expression profiles, which current technology cannot achieve. Here we investigate transcriptional changes during barley development, from the specification of meristem and organ founder cells to the initiation of distinct floral organs, based on an imputation approach integrating deep single-cell RNA sequencing with spatial gene expression data. The expression profiles of more than 40.000 genes can be analysed at cellular resolution in multiple barley tissues using the web-based graphical interface BARVISTA, which enables precise virtual microdissection to analyse any sub-ensemble of cells. Our study pinpoints previously inaccessible key transcriptional events in founder cells during primordia initiation and specification, characterises complex branching mutant phenotypes by barcoding gene expression profiles, and defines spatio-temporal trajectories during flower development. We thus uncover the genetic basis of complex developmental processes, providing novel opportunities for precisely targeted manipulation of barley traits.

plant biology↗

bioRxiv2025

Host-parasite interactions of an avian blood parasite elucidated by single-cell transcriptomics

Parasites and hosts perform fine-tuned cellular and molecular interactions, known from few well-explored model systems. Recent methodological advances now allow such deep insights into non-model parasites, their hosts, and their intense reciprocal manipulation. We applied single cell RNA-sequencing to blood samples of a long-lived bird host, infected at high and low intensity with malaria-related parasites. We identify diverse parasitic traits for immune evasion and potential manipulation of the avian host immune response. The transcriptomic response of immune cells was decoupled from the infection load, consistent with evidently low pathogenicity. Changes of immune cell populations showed low activation of adaptive immunity, such as clonal expansion of lymphoid cells. This absence of antagonism indicates immunosuppression by the parasite, which may mitigate virulence and thereby facilitate host-parasite coadaptation. The identified cell-type specific markers provide an important reference and will help to understand the evolutionary forces that shape host immunity in birds. Our study illuminates in rare molecular detail a benign host-parasite interaction and bridges a large coevolutionary knowledge gap of the gradient from parasitism to commensalism and mutualism.

ecology↗

bioRxiv2024

Defining the cardiac fibroblast secretome in the healthy and infarcted mouse heart

Cardiac fibroblasts (CF) are key players after myocardial infarction (MI), but their signaling is only incompletely understood. Here we report a first secretome atlas of CF in control (cCF) and post-MI hearts (miCF), combining a rapid cell isolation technique with SILAC and click chemistry. In CF, numerous paracrine factors involved in immune homeostasis were identified. Comparing secretome, transcriptome (SLAMseq), and cellular proteome disclosed protein turnover. In miCF at day 5 post-MI, significantly upregulated proteins included SLIT2, FN1, and CRLF1 in mouse and human samples. Comparing the miCF secretome at day 3 and 5 post-MI showed the dynamic nature of protein secretion. Specific in-vivo labeling of miCF proteins via biotin ligase TurboID using the POSTN promotor mirrored the in-vitro data. In summary, we have identified numerous paracrine factors specifically secreted from CF in mice and humans. This secretome atlas may lead to new biomarkers and/or therapeutic targets for the activated CF.

physiology↗

bioRxiv2024

Linker histone H1-0 is a specific mediator of the repressive ETV6::RUNX1 transcriptional landscape

ETV6::RUNX1 is the most common oncogenic fusion in pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL). It induces a clinically silent preleukemic state that requires secondary mutations for progression to leukemia. However, the molecular mechanisms contributing to the characteristic quiescence of ETV6::RUNX1+ preleukemic cells remain elusive. Here, we detect factors involved in the preleukemic state by generating human induced pluripotent stem cell (hiPSC) models using CRISPR/Cas9 gene editing. We identified upregulation of linker histone H1-0 in our preleukemic models, which was preserved upon hematopoietic differentiation and transformation to BCP-ALL. ETV6::RUNX1 induces H1-0 promoter activity whereas depletion of H1-0 specifically inhibited ETV6::RUNX1 signature genes, indicating its role as a key mediator of the ETV6::RUNX1 transcriptome. Single-cell gene expression analysis revealed high H1-0 levels in quiescent cells during hematopoiesis and inverse correlation with transcriptional activity. Pharmacologically, H1-0 protein levels correspond to susceptibility of BCP-ALL towards histone deacetylase inhibitors (HDACi). Altogether, our study provides novel insights into ETV6::RUNX1-induced quiescence and suggests that further investigation into combinatorial treatment of BCP-ALL using the H1-0- inducing HDACi Quisinostat may be worthwhile.

cancer biology↗

bioRxiv2022

Complete sequences of six Major Histocompatibility Complex haplotypes, including all the major MHC class II structures

Accurate and comprehensive immunogenetic reference panels are key to the successful implementation of population-scale immunogenomics. The 5Mbp Major Histocompatibility Complex (MHC) is the most polymorphic region of the human genome and associated with multiple immune-mediated diseases, transplant matching and therapy responses. Analysis of MHC genetic variation is severely complicated by complex patterns of sequence variation, linkage disequilibrium and a lack of fully resolved MHC reference haplotypes, increasing the risk of spurious findings on analyzing this medically important region. Integrating Illumina and ultra-long Nanopore sequencing as well as bespoke bioinformatics, we completed five of the alternative MHC reference haplotypes of the current (B38) build of the human reference genome and added one other. The six assembled MHC haplotypes encompass the DR1 and DR4 haplotype structures in addition to the previously completed DR2 and DR3, as well as six distinct classes of the structurally variable C4 region. Analysis of the assembled haplotypes showed that MHC class II sequence structures, including repeat element positions, are generally conserved within the DR haplotype supergroups, and that sequence diversity peaks in three regions around HLA-A, HLA-B+C, and the HLA class II genes. Demonstrating the potential for improved short-read analysis, the number of proper read pairs recruited to the MHC was found to be increased by 0.32% - 0.69% in a 1000 Genomes Project read re-mapping experiment with seven diverse samples. Furthermore, the assembled haplotypes can serve as references for the community and provide the basis of a structurally accurate genotyping graph of the complete MHC region.

genomics↗

bioRxiv2021

Intra-ocular dendritic cells are increased in HLA-B27 associated acute anterior uveitis

Uveitis describes a heterogeneous group of inflammatory eye diseases characterized by infiltration of leukocytes into the uveal tissues. HLA-B27-associated uveitis is a common subtype of uveitis and a prototypical ocular autoimmune disease. Local immune mechanisms driving human uveitis are poorly characterized mainly due to the limited available biomaterial and subsequent technical limitations. Here, we provide the first high-resolution characterization of intraocular leukocytes in HLA-B27 positive and negative anterior uveitis and an infectious endophthalmitis control by combining single cell RNA-sequencing (scRNA-seq) with flow cytometry and low-input proteomics. Ocular cell infiltrates consisted primarily of lymphocytes in uveitis and of myeloid cells in infectious endophthalmitis. HLA-B27 positive uveitis exclusively featured an plasmacytoid and classical dendritic cells (cDC) infiltrate, and of plasma cells. Moreover, cDCs were central in predicted local cell-cell communication. The data suggests a unique pattern of ocular leukocyte infiltration in HLA-B27 positive uveitis with relevance of particular dendritic cells.

immunology↗

bioRxiv2021

Single-cell transcriptomics defines heterogeneity of epicardial cells and fibroblasts within the infarcted heart

In the adult heart, the epicardium becomes activated after injury, contributing to cardiac healing by secretion of paracrine factors. Here we analyzed by single-cell RNA sequencing combined with RNA in situ hybridization and lineage tracing of WT1+ cells the cellular composition, location, and hierarchy of epicardial stromal cells (EpiSC) in comparison to activated myocardial fibroblasts/stromal cells in infarcted mouse hearts. We identified 11 transcriptionally distinct EpiSC populations, that can be classified in three groups each containing a cluster of proliferating cells. Two groups expressed cardiac specification makers and sarcomeric proteins suggestive of cardiomyogenic potential. Transcripts of HIF-1 and HIF-responsive genes were enriched in EpiSC consistent with an epicardial hypoxic niche. Expression of paracrine factors was not limited to WT1+ cells but was a general feature of activated cardiac stromal cells. Our findings provide the cellular framework by which myocardial ischemia may trigger in EpiSC the formation of cardioprotective/regenerative responses.

cell biology↗

bioRxiv2020

Phloem loading via the abaxial bundle sheath cells in maize leaves

Leaves are asymmetric, with differential functionalization of abaxial and adaxial tissues. The bundle sheath (BS) surrounding the vasculature of the C3 crop barley is dorsoventrally differentiated into three domains: adaxial structural, lateral S-type, and abaxial L-type. S-type cells seem to transfer assimilates towards the phloem. Here we used single-cell RNA sequencing to investigate BS differentiation in C4 maize. Abaxial BS (abBS) cells of rank-2 intermediate veins specifically expressed three SWEET sucrose uniporters (SWEET13a, b, and c) and UmamiT amino acid efflux transporters. SWEET13a, b, c were also identified in the phloem parenchyma (PP). Thus maize acquired a unique mechanism for phloem loading in which abBS cells provide the main pathway for apoplasmic sucrose transfer towards the phloem. This pathway predominates in veins responsible for phloem loading (rank-2 intermediate), while rank-1 intermediate and major veins export sucrose from the phloem parenchyma (PP) adjacent to the sieve element companion cell (SE/CC) complex, as in Arabidopsis. We surmise that abBS identity is subject to dorsoventral patterning and has components of PP identity. These observations provide first insights into the unique transport-specific properties of abBS cells and support for a modification to the canonical phloem loading pathway of maize, which may be generalizable to other C4 monocots.

plant biology↗

bioRxiv2018

Single-cell transcriptomics identifies drivers of local inflammation in multiple sclerosis

Cerebrospinal fluid (CSF) protects the central nervous system (CNS) and analyzing CSF aids the diagnosis of CNS diseases, but our understanding of CSF leukocytes remains superficial. Here, we firstly provide a transcriptional map of single leukocytes in CSF compared to blood. Leukocyte composition and transcriptome were compartment-specific with CSF-enrichment of myeloid dendritic cells and a border-associated phenotype of monocytes.\n\nWe secondly tested how multiple sclerosis (MS) - an autoimmune disease of the CNS - affected both compartments. MS increased transcriptional diversity in blood, while it preferentially increased cell type diversity in CSF. In addition to the known expansion of B lineage cells, we identified an increase of cytotoxic-phenotype and follicular T helper (TFH) cells in the CSF. In mice, TFH cells accordingly promoted B cell infiltration into the CNS and severity of MS animal models. Immune mechanisms in MS are thus highly compartmentalized and indicate local T/B cell interaction.

immunology↗