Single-Cell Transcriptional Profiling of the Intestinal Epithelium

Intestinal epithelial damage is associated with most digestive diseases and results in detrimental effects on nutrient absorption and production of hormones and antimicrobial defense molecules. Thus, understanding epithelial repair and regeneration following damage is essential in developing therapeutics that assist in rapid healing and restoration of normal intestinal function. Here we used a well-characterized enteric virus (rotavirus) that damages the epithelium at the villus tip but does not directly damage the intestinal stem cell, to explore the regenerative transcriptional response of the intestinal epithelium at the single-cell level. We found that there are specific Lgr5+ cell subsets that exhibit increased cycling frequency associated with significant expansion of the epithelial crypt. This was accompanied by an increase in the number of immature enterocytes. Unexpectedly, we found rotavirus infects tuft cells. Transcriptional profiling indicates tuft cells respond to viral infection through interferon-related pathways. Together these data provide insights as to how the intestinal epithelium responds to insults by providing evidence of stimulation of a repair program driven by stem cells with involvement of tuft cells that results in the production of immature enterocytes that repair the damaged epithelium.

Download Full-text

Integrating readout of somatic mutations in individual cells with single-cell transcriptional profiling

STAR Protocols ◽

10.1016/j.xpro.2021.100673 ◽

2021 ◽

Vol 2 (3) ◽

pp. 100673

Author(s):

Shichen Liu ◽

Maximilian Nguyen ◽

Sahand Hormoz

Keyword(s):

Single Cell ◽

Somatic Mutations ◽

Transcriptional Profiling

Download Full-text

Spatially defined single-cell transcriptional profiling characterizes diverse chondrocyte subtypes and nucleus pulposus progenitors in human intervertebral discs

Bone Research ◽

10.1038/s41413-021-00163-z ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Yibo Gan ◽

Jian He ◽

Jun Zhu ◽

Zhengyang Xu ◽

Zhong Wang ◽

...

Keyword(s):

Single Cell ◽

Nucleus Pulposus ◽

Molecular Mechanisms ◽

Transcriptional Profiling ◽

Intervertebral Discs ◽

Cellular Heterogeneity ◽

Effector Functions ◽

Cartilage Endplate ◽

Intervertebral Disks ◽

Ivd Degeneration

AbstractA comprehensive understanding of the cellular heterogeneity and molecular mechanisms underlying the development, homeostasis, and disease of human intervertebral disks (IVDs) remains challenging. Here, the transcriptomic landscape of 108 108 IVD cells was mapped using single-cell RNA sequencing of three main compartments from young and adult healthy IVDs, including the nucleus pulposus (NP), annulus fibrosus, and cartilage endplate (CEP). The chondrocyte subclusters were classified based on their potential regulatory, homeostatic, and effector functions in extracellular matrix (ECM) homeostasis. Notably, in the NP, a PROCR+ resident progenitor population showed enriched colony-forming unit-fibroblast (CFU-F) activity and trilineage differentiation capacity. Finally, intercellular crosstalk based on signaling network analysis uncovered that the PDGF and TGF-β cascades are important cues in the NP microenvironment. In conclusion, a single-cell transcriptomic atlas that resolves spatially regulated cellular heterogeneity together with the critical signaling that underlies homeostasis will help to establish new therapeutic strategies for IVD degeneration in the clinic.

Download Full-text

Single Cell Transcriptional Profiling of Adult Mouse Cardiomyocytes

Journal of Visualized Experiments ◽

10.3791/3302 ◽

2011 ◽

Cited By ~ 1

Author(s):

James M. Flynn ◽

Luis F. Santana ◽

Simon Melov

Keyword(s):

Single Cell ◽

Adult Mouse ◽

Transcriptional Profiling

Download Full-text

Probing Plasmodium falciparum sexual commitment at the single-cell level

Wellcome Open Research ◽

10.12688/wellcomeopenres.14645.4 ◽

2018 ◽

Vol 3 ◽

pp. 70 ◽

Cited By ~ 14

Author(s):

Nicolas M.B. Brancucci ◽

Mariana De Niz ◽

Timothy J. Straub ◽

Deepali Ravel ◽

Lauriane Sollelis ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Life Cycle ◽

Single Cell ◽

Transcriptional Profiling ◽

Quantitative Imaging ◽

Complex Life Cycle ◽

Major Transitions ◽

Transcriptional Signature ◽

Life Cycle Stages ◽

Parasite Populations

Background: Malaria parasites go through major transitions during their complex life cycle, yet the underlying differentiation pathways remain obscure. Here we apply single cell transcriptomics to unravel the program inducing sexual differentiation in Plasmodium falciparum. Parasites have to make this essential life-cycle decision in preparation for human-to-mosquito transmission. Methods: By combining transcriptional profiling with quantitative imaging and genetics, we defined a transcriptional signature in sexually committed cells. Results: We found this transcriptional signature to be distinct from general changes in parasite metabolism that can be observed in response to commitment-inducing conditions. Conclusions: This proof-of-concept study provides a template to capture transcriptional diversity in parasite populations containing complex mixtures of different life-cycle stages and developmental programs, with important implications for our understanding of parasite biology and the ongoing malaria elimination campaign.

Download Full-text

Faculty Opinions recommendation of Comprehensive single-cell transcriptional profiling of a multicellular organism.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.728772367.793553294 ◽

2018 ◽

Author(s):

Stephen Schwartz

Keyword(s):

Single Cell ◽

Transcriptional Profiling ◽

Multicellular Organism

Download Full-text

Single-Cell RNA-Sequencing Identifies Infrapatellar Fat Pad Macrophage Polarization in Acute Synovitis/Fat Pad Fibrosis and Cell Therapy

Bioengineering ◽

10.3390/bioengineering8110166 ◽

2021 ◽

Vol 8 (11) ◽

pp. 166

Author(s):

Dimitrios Kouroupis ◽

Thomas M. Best ◽

Lee D. Kaplan ◽

Diego Correa ◽

Anthony J. Griswold

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Transcriptional Profiling ◽

Macrophage Polarization ◽

Myeloid Cells ◽

Cellular Heterogeneity ◽

Joint Disease ◽

Infrapatellar Fat Pad ◽

Fat Pad ◽

Single Cell Rna Sequencing

The pathogenesis and progression of knee inflammatory pathologies is modulated partly by residing macrophages in the infrapatellar fat pad (IFP), thus, macrophage polarization towards pro-inflammatory (M1) or anti-inflammatory (M2) phenotypes is important in joint disease pathologies. Alteration of M1/M2 balance contributes to the initiation and progression of joint inflammation and can be potentially altered with mesenchymal stem cell (MSC) therapy. In an acute synovial/IFP inflammation rat model a single intra-articular injection of IFP-MSC was performed, having as controls (1) diseased rats not receiving IFP-MSC and (2) non-diseased rats. After 4 days, cell specific transcriptional profiling via single-cell RNA-sequencing was performed on isolated IFP tissue from each group. Eight transcriptomically distinct cell populations were identified within the IFP across all three treatment groups with a noted difference in the proportion of myeloid cells across the groups. Largely myeloid cells consisted of macrophages (>90%); one M1 sub-cluster highly expressing pro-inflammatory markers and two M2 sub-clusters with one of them expressing higher levels of canonical M2 markers. Notably, the diseased samples (11.9%) had the lowest proportion of cells expressing M2 markers relative to healthy (14.8%) and MSC treated (19.4%) samples. These results suggest a phenotypic polarization of IFP macrophages towards the pro-inflammatory M1 phenotype in an acute model of inflammation, which are alleviated by IFP-MSC therapy inducing a switch towards an alternate M2 status. Understanding the IFP cellular heterogeneity and associated transcriptional programs may offer insights into novel therapeutic strategies for disabling joint disease pathologies.

Download Full-text

Spatial and Single-Cell Transcriptional Profiling Identifies Functionally Distinct Human Dermal Fibroblast Subpopulations

Journal of Investigative Dermatology ◽

10.1016/j.jid.2018.01.016 ◽

2018 ◽

Vol 138 (4) ◽

pp. 811-825 ◽

Cited By ~ 106

Author(s):

Christina Philippeos ◽

Stephanie B. Telerman ◽

Bénédicte Oulès ◽

Angela O. Pisco ◽

Tanya J. Shaw ◽

...

Keyword(s):

Single Cell ◽

Dermal Fibroblast ◽

Transcriptional Profiling ◽

Human Dermal Fibroblast

Download Full-text

Transcribing the heart: faithfully interpreting cardiac transcriptional insights

Regenerative Medicine ◽

10.2217/rme-2019-0063 ◽

2019 ◽

Vol 14 (9) ◽

pp. 805-810

Author(s):

Oscar Echeagaray ◽

Mark A Sussman

Keyword(s):

Regenerative Medicine ◽

Single Cell ◽

Transcriptional Profiling ◽

Bioinformatic Analysis ◽

Therapeutic Approaches ◽

Improve Efficiency ◽

Accurate Interpretation ◽

Bioinformatic Approaches ◽

Selection Of

Transcriptional profiling continues to produce phenotypical data essential for understanding of basic cardiac biology and required to improve efficiency of cardiac regenerative and therapeutic approaches after injury. Accurate interpretation of cardiac transcriptional data comes with the unique challenges of heart biology including cardiomyocyte morphology, cryopreservation of limited samples and adequate selection of transcriptional platform at a single-cell resolution. Consequently, development and implementation of novel transcriptional platforms and creative bioinformatic analysis are essential to resolve standing questions in the field of cardiac regenerative medicine. Targeted bioinformatic approaches, advancing technological access, increase technical availability and fostering communication between interdisciplinary groups is critical to improve therapeutic approaches and to overcome challenges inherent to transcriptomic cardiac research.

Download Full-text