Publications

Genome Research | September, 2023

Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear

In contrast to other mammals, the spiny mouse ( Acomys ) regenerates skin and ear tissue scar-free. Here, the authors show that cues originating from the proximal side are required for normal regeneration and use spatially resolved transcriptomics (tomo-seq) to understand the molecular and cellular events underlying this process.

Next Gen Sequencing Spiny mouse Ear

Frontiers in Molecular Neuroscience | September, 2023

Effect of methanol fixation on single cell RNA sequencing of the murine dentate gyrus

The authors evaluated the effect of methanol fixation on murine dentate gyrus single-cell suspensions and on subsequent scRNA-seq downstream analysis with SORT-seq. The results show that MeOH fixation preserves RNA integrity and has no apparent effects on cDNA library construction.

SORT-seq Mouse Brain

Nature Biotechnology | September, 2023

Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis

The authors report the generation of human trunk-like structure organoids that model the co-morphogenesis, patterning and differentiation of the human spine and spinal cord. Single-cell and spatial transcriptomics show that somitic and spinal cord differentiation trajectories organize along this axis and can self-assemble into a neural tube surrounded by somites upon extracellular matrix addition.

10x Genomics Human Central nervous system Embryo Organoids Spine

Nature Communications | September, 2023

Germinal center output is sustained by HELLS-dependent DNA-methylation-maintenance in B cells

Studying a mouse model based on the genetic mutations in a rare immunodeficiency syndrome (ICF), the authors report that germinal center B cells devoid of the HELLS protein form and proliferate normally, but collapse prematurely, preventing the establishment of long-term humoral immunity.

SORT-seq Mouse Lymphatic system

Research from our own scientists

Blood | September, 2023

Neutral sphingomyelinase blockade enhances hematopoietic stem cell fitness through an integrated stress response

Hematopoietic stem and progenitor cell (HSPC) therapy is limited by ex-vivo self-renewal and quiescence. The authors look into nSMase2 blockade in mouse HSPCs at single-cell resolution and find that transient inhibition enables ex vivo graft manipulation with enhanced potency.

10x Genomics Data Consultancy Human Mouse Blood Stem cells

Clinical & Experimental Immunology | August, 2023

Compartment-driven imprinting of intestinal CD4 T cells in inflammatory bowel disease and homeostasis

Crohn’s disease patients suffer from inflammatory bowels. To better understand CD4 T cell regulation of the ileal lamina propria and epithelium during inflammation, the authors performed bulk and single-cell RNA sequencing (SORT-seq) on patient biopsies.

SORT-seq Human Immune system Intestine

Nature Communications | August, 2023

Development of Plasmodium falciparum liver-stages in hepatocytes derived from human fetal liver organoid cultures

After infection their human hosts, the malaria parasite P. falciparum first develops in liver cells. It can be interesting for malaria medicine to interupt this vulnerable life-cycle stage. With this in the back of their minds, the authors explore hepatic organoids for in vitro study. They use SORT-seq to establish P. falciparum gene expression in single cells & simultaneously decode transcriptional changes in the host hepatocytes.

SORT-seq Human P. falciparum Liver Organoids Parasites

Journal of Cachexia, Sarcopenia and Muscle | June, 2023

Iron deficiency is related to lower muscle mass in community-dwelling individuals and impairs myoblast proliferation

This study assesses the relationship between iron deficiency and loss of muscle mass in a large population cohort (readouts: transferrin saturation & creatinine excretion rate) and on mouse muscle cell lines. Using bulk RNA-seq to identify the genes affected by iron deficiency, the authors suggest iron deficiency contributes to loss of muscle mass.

Bulk RNA sequencing Mouse Cell culture Muscle

ACS Nano | June, 2023

Direct In Vivo Activation of T Cells with Nanosized Immunofilaments Inhibits Tumor Growth and Metastasis

This research explores a new perspective for immunotherapy (adoptive T cell therapy) in cancer: to circumvent ex vivo expansion of T cells and utilize in vivo activation instead, with engineered nanosized immunofilaments. The authors used bulk RNA-sequencing of antigen-specific T cells to study the transcriptome changes after immunofilament-aided in vivo activation.

Bulk RNA sequencing Mouse Immune system

Nature | June, 2023

Tumour immune rejection triggered by activation of α2-adrenergic receptors

How can we overcome tumor resistance to immunotherapy? This study finds immune suppressor class ‘alpha-2-adrenergic receptor agonsits’ shows strong anti-tumor activity in resistant tumor models and mouse xenografts. Studying its mode of action with single-cell RNA sequencing, the authors reveal an upregulated innate and adaptive immune response in CD4+ T, CD8+ T cells and macrophages. That suggests this existinting drug class may supplement immunotherapy.

10x Genomics Mouse Intestine Xenograft (mouse)

Viruses | April, 2023

An Endogenous Retrovirus Vaccine Encoding an Envelope with a Mutated Immunosuppressive Domain in Combination with Anti-PD1 Treatment Eradicates Established Tumours in Mice

Targeting the endogenous retrovirus protein ‘Envelope’ may protect against cancer. Here, the authors document their development of a virus-like vaccine technology and employ SORT-seq to study the vaccine’s immunogenicity effect on dendritic cells.

SORT-seq Mouse Bone marrow Immune system

MDPI | March, 2023

The Role of IL-13 and IL-4 in Adipose Tissue Fibrosis

The authors discovered interleukins IL-13 and IL-4 play a role in vivo in inducing white adipose tissue fibrosis. Using bulk RNA sequencing of wildtype and IL-4 deficient mouse bone marrow macrophages, the team identified a basal difference in fibrosis-related gene expression depending on IL-4.

Bulk RNA sequencing Mouse Bone marrow Immune system

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