Publications

iScience | January, 2025

Tumor-derived colorectal cancer organoids induce a unique Treg cell population by directing CD4+ T cell differentiation

This study investigates how colorectal cancer (CRC) tumors influence the differentiation of CD4+ regulatory T (Treg) cells, which are linked to tumor progression, immunotherapy resistance, and poor prognosis. Researchers developed an in vitro co-culture system using CD4+ T cells from Foxp3eGFP mice and CRC tumor-derived organoids. This co-culture led to a significant increase in Treg cell numbers. Bulk RNA sequencing by Single Cell Discoveries played a crucial role in the study by identifying the distinct transcriptional profile of CRC organoid-induced Treg cells. The sequencing revealed upregulation of genes associated with CRC Treg cells in vivo. These findings were significant because high expression of these genes correlated with shorter progression-free intervals and overall survival in CRC patients.

Bulk RNA sequencing Mouse

Nature Cardiovascular Research | January, 2025

Cross-species comparison reveals that Hmga1 reduces H3K27me3 levels to promote cardiomyocyte proliferation and cardiac regeneration

The study compares the regenerative abilities of adult zebrafish and mammalian hearts, focusing on the protein Hmga1. Zebrafish hearts can efficiently replace lost cardiomyocytes (CMs) after injury, while mammalian hearts cannot. Hmga1 is crucial for inducing CM proliferation and heart regeneration by reactivating developmentally silenced genes through H3K27me3 modulation. Single Cell Discoveries performed SORT-seq and Bulk RNA sequencing and the researchers found similar histone modifications in mouse and zebrafish hearts, suggesting Hmga1 drives chromatin remodeling and a regenerative program, making it a potential therapeutic target.

Bulk RNA sequencing SORT-seq Human Mouse Zebrafish Heart

Immunity | December, 2024

Synovial tissue myeloid dendritic cell subsets exhibit distinct tissue-niche localization and function in health and rheumatoid arthritis

This study identified specific dendritic cell clusters in human synovial tissue that could help restore immune tolerance in Rheumatoid Arthritis (RA). The researchers utilized SORT-seq, performed by Single Cell Discoveries, to validate their sorting strategy and confirm the accuracy of their findings. This technique was crucial in pinpointing the roles of pathogenic DC3s and tolerogenic DC2s. Targeting these cells could be key to achieving immune homeostasis in RA joints.

SORT-seq Human Blood Connective tissue

Cell Death Discovery | November, 2024

Reformed islets: a long-term primary cell platform for exploring mouse and human islet biology

This study from the Department of Diabetes at King’s College London developed a long-term biomimetic method to model native mouse and human islets ex vivo, maintaining long-term islet functionality. Single Cell Discoveries confirmed through bulk RNA sequencing that reformed islets mimic primary islets and can survive for extended periods in culture. This platform is ideal for studying β-cell proliferation and immune cell-islet cell interactions, making it a game-changer for diabetes research. Reformed islets exhibit physiological characteristics similar to primary islets, enabling high-resolution imaging and repeated functional assessment.

Bulk RNA sequencing Human Mouse Pancreatic islets

Oncogene | August, 2024

Differential transcriptional invasion signatures from patient derived organoid models define a functional prognostic tool for head and neck cancer

This study by Peter D. Haughton and colleagues uses patient-derived organoid models to explore invasive growth in HPV-negative head and neck squamous cell carcinoma (HNSCC). Single-cell RNA sequencing services from Single Cell Discoveries revealed distinct transcriptional programs for collective and single-cell invasion, highlighting YAP-centered pathways and potential prognostic markers. These findings may guide new therapeutic strategies for HNSCC, offering hope for improved clinical outcomes.

SORT-seq Human Head and neck squamous cell carcinoma

Journal of Autoimmunity | November, 2024

Trained innate immunity in response to nuclear antigens in systemic lupus erythematosus

This study investigates whether nuclear autoantigens can induce trained immunity in SLE patients. Researchers stimulated isolated monocytes with SLE-typical nuclear antigens, NETs, and MPs, observing increased pro-inflammatory cytokine production and deregulation in histone 3 lysine 4 trimethylation. The findings suggest that trained immunity contributes to immunological dysregulation in SLE, highlighting potential biomarkers for assessing flare risks. **Single Cell Discoveries** contributed to this research by performing RNA sequencing on monocytes, identifying transcriptomic changes associated with trained immunity in SLE patients.

Bulk RNA sequencing Human Blood

The Journal of Immunology | October, 2024

Single-cell Sequencing of Circulating Human Plasmablasts during Staphylococcus aureus Bacteremia

This study investigates the immune response in patients with Staphylococcus aureus bacteremia by analyzing circulating plasmablasts. The authors utilized our 10x Genomics service to identify over 300 unique antibody sequences, leading to the discovery of four monoclonal antibodies that can bind to S. aureus, with three also showing cross-reactivity with Staphylococcus epidermidis. These antibodies were produced and assessed for their ability to bind to the bacterial surface and elicit Fc-effector functions, potentially enhancing the immune system’s ability to target and eliminate these bacteria.

10x Genomics Human Blood

Science Advances | October, 2024

Isolation and tracing of matrix-producing notochordal and chondrocyte cells using ACAN-2A-mScarlet reporter human iPSC lines

The study focuses on developing human induced pluripotent stem cell (iPSC) lines that can be used to isolate and trace matrix-producing notochordal and chondrocyte cells. These cell types are crucial for treating conditions like low back pain and osteoarthritis, which are caused by the degeneration of intervertebral discs and hyaline cartilage, respectively. The researchers created two iPSC lines with an ACAN-2A-mScarlet reporter, which allows for the identification and isolation of cells producing the proteoglycan aggrecan (ACAN). Our Bulk RNA service was employed in this study to analyze the gene expression profiles during chondrogenic differentiation.

Bulk RNA sequencing Human iPSCs

Communications Biology | October, 2024

Spatial multi-omics in whole skeletal muscle reveals complex tissue architecture

The study explores the complex tissue architecture of skeletal muscle using advanced spatial multi-omics techniques. Researchers combined RNA tomography and mass spectrometry imaging to map the spatial transcriptomic, metabolomic, and lipidomic organization of the murine tibialis anterior muscle. By leveraging our SORT-seq service, they identified distinct transcription profiles in myonuclei related to myofiber type. This approach revealed significant regionalization of gene expression and metabolic differences along the proximal-distal axis of the muscle. These findings highlight the intricate spatial organization and metabolic compartmentalization within skeletal muscle, providing new insights into muscle biology.

SORT-seq Mouse Muscle

Acta Neuropathologica Communications | September, 2024

Molecular pathology, developmental changes and synaptic dysfunction in (pre-) symptomatic human C9ORF72-ALS/FTD cerebral organoids

The most common genetic cause for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is an hexanucleotide repeat expansion (HRE) in the C9ORF72 gene. The authors generated an iPSC-derived cerebral organoid models from C9-ALS/FTD patients, presymptomatic C9ORF72-HRE carriers, and controls in order to better understand the early events driving disease development. By means of our 10X Genomics 3′ single-cell RNA sequencing service, researchers identified changes in cell type abundance and distribution, including a reduction in the number of deep layer cortical neurons and the distribution of neural progenitors.

10x Genomics Human Brain Organoids

Cell Reports | August, 2024

Trained immunity is regulated by T cell-induced CD40-TRAF6 signaling

After exposure to inflammatory signals, innate immune cells undergo metabolic changes that provide trained immunity, leading to heightened responsiveness to secondary stimuli. In this work, the authors show that T cells modulate trained immunity via CD40-TRAF6 signaling. Our Bulk-seq service was used to profile the effects of CD40-TRAF6 inhibition, revealing the repression of essential transcriptional programs related to inflammation and metabolic rewiring. The results reveal that trained immunity is modulated by CD40-TRAF6 signaling between myeloid and adaptive immune cells and that this can be leveraged for therapeutic purposes, such as in organ transplantation.

Bulk RNA sequencing Data Consultancy Human Immune system

Cardiovascular Research | August, 2024

Nuclear factor of activated T-cells 5 is indispensable for a balanced adaptive transcriptional response of lung endothelial cells to hypoxia

Sustained hypoxia causes structural alterations in the lung, which may lead to pulmonary hypertension, however determinants controlling the initial adaptation of the lung endothelium to hypoxia remain largely unexplored. In this study, the authors used SCD’s 10x Genomics and Data Consultancy services to characterize the responses of a transient subpopulation of murine lung endothelial cells to hypoxia. These responese may determine the degree of organ dysfunction in later stages. The authors found out that NFAT5 acts as a protective transcription factor required to rapidly adjust the endothelial transcriptome to cope with hypoxia.

10x Genomics Data Consultancy Mouse Immune system Lung

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