Biology subjects

Lonnberg, T.

Publications and source records attributed to Lonnberg, T..

5 recordsLinked to original sources

bioRxiv2025

Adipose tissue-derived fibroblasts engage in immune-stromal crosstalk during obesity-aggravated atherosclerosis in mice

Atherosclerosis involves changes in the vascular wall and surrounding perivascular adipose tissue, yet the cellular contributors to disease progression remain incompletely understood. Obesity exacerbates atherogenesis, but the cell types driving this aggravation are unclear. We aimed to define the key cell populations across tissues in a highly atherogenic mouse model under obese and normal-weight conditions and to identify obesity-associated cellular changes. We employed 5 single-cell RNA sequencing combined with antibody staining in Ldlr-/-Apob100/100 male mice fed either a high-fat or control diet. Aorta, perivascular and epididymal adipose tissues, and spleen were analyzed, with CD45 enrichment of aortic samples and CITE-seq using a 138-antibody panel. Key findings were validated in mice by immunohistochemistry and multiplexed immunofluorescence and explored in human aorta and carotid arteries using spatial transcriptomics. Analysis of [~]46,000 cells enabled characterization of cell states, gene enrichment, regulon activity, and inferred interactions. Adipose-derived fibroblast subsets displayed immune-associated transcriptional programs in obesity. Pi16 progenitor fibroblasts were reduced alongside marked PVAT remodeling, and the top mouse differentially expressed genes exhibited clear spatial patterning in human arteries.

genomics↗

bioRxiv2024

Breast Cancer Remodels Lymphatics in Sentinel Lymph Nodes

Cancer metastasis to sentinel lymph nodes (LNs) is often the first marker of potential disease progression. Although it is recognized that tumor-induced lymphangiogenesis facilitates metastasis into LNs in murine models, tumor-induced alterations in human lymphatic vessels remain obscure. We used single-cell RNA sequencing to profile lymphatic endothelial cell (LEC) subsets in paired metastatic and non-metastatic LNs obtained from patients with treatment-naive breast cancer. Tumor metastasis decreases immunoregulatory LEC subsets, such as PD-L1+ subcapsular sinus LECs, while inducing an increase in capillary-like CD200+ HEY1+ LECs. Matrix Gla protein (MGP) was the most upregulated gene in metastatic LN LECs, and its expression on LECs was TGF-{beta} and VEGF dependent. Upregulated MGP promotes cancer cell adhesion to LN lymphatics. Thus, breast cancer cell metastasis to LNs remodels LEC subsets in human LNs and escalates MGP expression, potentially facilitating cancer cell dissemination through the lymphatic system.

immunology↗

bioRxiv2023

Single-cell transcriptome analysis of the early immune response in the lymph nodes of Borrelia burgdorferi-infected mice

Lyme borreliosis is a disease caused by Borrelia burgdorferi sensu lato bacteria. Borrelia burgdorferi is known to induce prolonged extrafollicular immune responses and abnormal germinal center formation. However, the mechanism behind this is poorly understood. The extrafollicular response is characterized by strong plasmablast induction and by an IgM, IgG3, and IgG2b dominant antibody production. These antibodies do not generate a neutralizing type of immunity, and the bacteria eventually establish a persistent infection. Here, we performed single-cell RNA sequencing to characterize the immune landscape of lymph node lymphocytes in the early Borrelia burgdorferi infection in a murine model. Our results indicate that four days after Borrelia burgdorferi infection, a notable B cell proliferation, immunoglobulin class switching to IgG3 and IgG2b isotypes, and plasma cell differentiation are induced, all of which are hallmarks of the extrafollicular immune response. In addition, we found infection-derived upregulation of suppressor of cytokine signalling genes Socs1 and Socs3, and downregulation of genes involved in MHC II antigen presentation in B cells. Our results support the central role of B cells in the immune response of a Borrelia burgdorferi infection, and provide cues of mechanisms behind the determination between extrafollicular and germinal center responses during Borrelia burgdorferi infection.

molecular biology↗

bioRxiv2023

Cell-type-specific characterization of miRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution

MicroRNAs (miRNAs) are a class of regulatory non-coding RNAs that finetune cellular functions by modulating the stability and abundance of their target mRNAs, thereby contributing to regulation of tissue homeostasis. MiRNA genes are transcribed similarly to protein-coding genes and recent studies have enabled their annotation and quantification genome-wide from bulk nascent transcriptomes. Here, we developed an approach to quantify and integrate miRNA gene signatures into single-cell studies. To characterize miRNA gene expression dynamics, we first compared the suitability of droplet and plate-based single-cell RNA-sequencing (scRNA-seq) platforms using the matched datasets provided by the Tabula Muris Senis and Tabula Sapiens consortiums. We found high concordance between the platforms and with cell type-specific bulk expression data. Based on the comprehensive aging profiles, our analysis comparing spleen immune cells between young and old mice revealed a concordant regulation of miRNAs involved in senescence and inflammatory pathways in multiple immune cell types, including up-regulation of mmu-mir-146a, mmu-mir-101a and mmu-mir-30 family genes. To study the aberrant regulation of immune cell homeostasis and tissue inflammation that pre-dispose to aging-related disease development, we collected transcriptome profiles from atherosclerosis development in LDLR-/-ApoB100/100 mice. We found an elevated myeloid cell proportion in the adipose tissue and further characterized the cell subtypes based on reproducible transcriptome clusters. We then compared miRNA gene expression in early versus late disease and upon inflammatory challenge to monitor different stages during disease progression. At atherosclerotic stage, pro-inflammatory mmu-mir-511 expression increased in several macrophage subtypes, while immunosuppressive mmu-mir-23b[~]mir-24-2[~]mir-27b up-regulation was specific to Trem2+ lipid-associated macrophages. The infiltrating monocytes up-regulated mmu-mir-1938 and mmu-mir-22 expression and in classical monocytes maturation further increased mmu-mir-221[~]222, mmu-mir-511 and mmu-mir-155 expression. To validate that these changes detected from single cell profiles represent miRNA gene transcriptional regulation, we used nascent transcriptomics data from ex vivo macrophage cultures with pro-inflammatory stimulation, confirming both rapid and long-lasting transcriptional activation of the miRNA loci studied. Collectively, our work enables integrating miRNA gene analysis to current single cell genomics pipelines and facilitates characterization of miRNA regulatory networks during aging and disease development.

molecular biology↗

bioRxiv2020

Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1 positive pediatric leukemia identifies drug-targetable transcription factor activities

Tight regulatory loops orchestrate commitment to B-cell fate within bone marrow. Genetic lesions in this gene regulatory network underlie the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). The initial genetic hits, including the common translocation that fuses ETV6 and RUNX1 genes, lead to arrested cell differentiation. Here, we aimed to characterize transcription factor activities along the B-lineage differentiation trajectory as a reference to characterize the aberrant cell states present in leukemic bone marrow, and to identify those transcription factors that maintain cancer-specific cell states for more precise therapeutic intervention. We compared normal B-lineage differentiation and in vivo leukemic cell states using single cell RNA-sequencing (scRNA-seq) and several complementary genomics profiles. Based on statistical tools for scRNA-seq, we benchmarked a workflow to resolve transcription factor activities and gene expression distribution changes in healthy bone marrow lymphoid cell states. We compared these to ALL bone marrow at diagnosis and in vivo during chemotherapy, focusing on leukemias carrying the ETV6-RUNX1 fusion. We show that lymphoid cell transcription factor activities uncovered from bone marrow scRNA-seq have high correspondence with independent ATAC- and ChIP-seq data. Using this comprehensive reference for regulatory factors coordinating B-lineage differentiation, our analysis of ETV6-RUNX1-positive ALL cases revealed elevated activity of multiple ETS-transcription factors in leukemic cells states, including the leukemia genome-wide association study hit ELK3. The accompanying gene expression changes associated with natural killer cell inactivation and depletion in the leukemic immune microenvironment. Moreover, our results suggest that the abundance of G1 cell cycle state at diagnosis and lack of differentiation-associated regulatory network changes during induction chemotherapy represent features of chemoresistance. To target the leukemic regulatory program and thereby overcome treatment-resistance, we show that selective inhibitors of ETS-transcription factors could effectively reduce cell viability. Our data provide a detailed picture of the transcription factor activities that characterize both normal B-lineage differentiation and those acquired in leukemic bone marrow and provide a rational basis for new treatment strategies targeting the immune microenvironment and the active regulatory network in leukemia.

cancer biology↗