Applications of Single-Cell Sequencing in Dermatology

Medical science monitor : international medical journal of experimental and clinical research

2021 May 20

Zou, D;Qi, J;Wu, W;Xu, D;Tu, Y;Liu, T;Zhang, J;Li, X;Lu, F;He, L;
PMID: 34011922 | DOI: 10.12659/MSM.931862

Single-cell sequencing (SCS) is a promising new technique used to assess the genomics, transcriptomics, epigenetics, and other multi-omics at the single-cell level. In addition to elucidating the immune microenvironment and revealing the pathomechanisms of disease and drug resistance, SCS can profile the actual state of an individual cell and identify a novel cell type and differentiation trajectories, which cannot be achieved by bulk tissue sequencing technique. SCS technique serves as powerful tools to explore more meaningful biomarkers of diagnosis, prognosis, and new therapeutic targets in clinical practice. The SCS technique has been widely applied in the field of dermatology. In this review, we summarize the advances of SCS in dermatology.

Transcriptomic analysis and EdnrB expression in cochlear intermediate cells reveal developmental differences between inner ear and skin melanocytes

Pigment cell & melanoma research

2021 Jan 23

Renauld, JM;Davis, W;Cai, T;Cabrera, C;Basch, ML;
PMID: 33484097 | DOI: 10.1111/pcmr.12961

In the inner ear the neural crest gives rise to the glia of the VIIIth ganglion and two types of melanocytic cells: the pigmented cells of the vestibular system, and intermediate cells of the stria vascularis. We analyzed the transcriptome of neonatal intermediate cells in an effort to better understand the development of the stria vascularis. We found that expression of endothelin receptor B, which is essential for melanocyte development persists in intermediate cells long after birth. In contrast, skin melanocytes rapidly downregulate expression of EdnrB. Our findings suggest that endothelins might have coopted new functions in the inner ear during evolution of the auditory organ. This article is protected by

Analysis of SNHG14: A Long Non-Coding RNA Hosting SNORD116, Whose Loss Contributes to Prader-Willi Syndrome Etiology

Genes

2022 Dec 29

Ariyanfar, S;Good, D;
| DOI: 10.3390/genes14010097

The Small Nucleolar Host Gene 14 (SNHG14) is a host gene for small non-coding RNAs, including the SNORD116 small nucleolar C/D box RNA encoding locus. Large deletions of the SNHG14 locus, as well as microdeletions of the SNORD116 locus, lead to the neurodevelopmental genetic disorder Prader-Willi syndrome. This review will focus on the SNHG14 gene, its expression patterns, its role in human cancer, and the possibility that single nucleotide variants within the locus contribute to human phenotypes in the general population. This review will also include new in silico data analyses of the SNHG14 locus and new in situ RNA expression patterns of the Snhg14 RNA in mouse midbrain and hindbrain regions.

Emerging approaches for decoding neuropeptide transmission

Trends in neurosciences

2022 Oct 15

Girven, KS;Mangieri, L;Bruchas, MR;
PMID: 36257845 | DOI: 10.1016/j.tins.2022.09.005

Neuropeptides produce robust effects on behavior across species, and recent research has benefited from advances in high-resolution techniques to investigate peptidergic transmission and expression throughout the brain in model systems. Neuropeptides exhibit distinct characteristics which includes their post-translational processing, release from dense core vesicles, and ability to activate G-protein-coupled receptors (GPCRs). These complex properties have driven the need for development of specialized tools that can sense neuropeptide expression, cell activity, and release. Current research has focused on isolating when and how neuropeptide transmission occurs, as well as the conditions in which neuropeptides directly mediate physiological and adaptive behavioral states. Here we describe the current technological landscape in which the field is operating to decode key questions regarding these dynamic neuromodulators.

BS18 Enhanced matrix stiffness prevents vsmc contractility: how calcium signalling and microtubule stability regulate vascular compliance during ageing

Basic science

2022 Jun 01

Johnson, R;Ahmed, S;Solanki, R;Wostear, F;Afewerki, T;Warren, D;
| DOI: 10.1136/heartjnl-2022-bcs.198

Rationale DNA damage accumulation is a hallmark of vascular smooth muscle cell (VSMC) ageing. Importantly, VSMC DNA damage accumulation and ageing has been implicated in the progression of cardiovascular disease (CVD), including atherosclerosis and vascular calcification. Chemotherapy drugs used in the treatment of many cancers are known to induce DNA damage in cardiovascular cells and accelerate CVD. Histone deacetylase (HDAC) inhibitors are drugs being investigated for novel treatments of many cancers. HDACs perform many vital functions in cells; HDAC6 is known to deacetylate alpha-tubulin to regulate microtubule stability and flexibility. We have recently shown that microtubule stability regulates both VSMC morphology and contractility. Therefore, in this study we investigate the impact of HDAC6 inhibition upon VSMC function. Methodology We use polyacrylamide hydrogels (PAHs)

Contemporary Approaches to the Study of Pain

Neuromethods

2022 May 26

Ferreira, DW;Arokiaraj, CM;Seal, RP;
| DOI: 10.1007/978-1-0716-2039-7#page=50

This volume contains experimental approaches that are currently revolutionizing our understanding of the neurobiology of pain. The chapters cover many cutting-edge methods including the identification of gene expression profiles, transcriptomes or translatomes, from individual cells or defined groups of cells in rodents and primates; the electrophysiological investigation of human tissues, such as human dorsal root ganglion neurons; ways to assess modality response profiles of neurons using calcium imaging in vitro and in vivo; and somatosensory behaviors in rodents using high-speed videography and machine learning. In the _Neuromethods_ series style, the chapters include detailed advice from specialists to obtain successful results in your laboratory.

Capybara: A computational tool to measure cell identity and fate transitions

Cell stem cell

2022 Mar 23

Kong, W;Fu, YC;Holloway, EM;Garipler, G;Yang, X;Mazzoni, EO;Morris, SA;
PMID: 35354062 | DOI: 10.1016/j.stem.2022.03.001

Measuring cell identity in development, disease, and reprogramming is challenging as cell types and states are in continual transition. Here, we present Capybara, a computational tool to classify discrete cell identity and intermediate "hybrid" cell states, supporting a metric to quantify cell fate transition dynamics. We validate hybrid cells using experimental lineage tracing data to demonstrate the multi-lineage potential of these intermediate cell states. We apply Capybara to diagnose shortcomings in several cell engineering protocols, identifying hybrid states in cardiac reprogramming and off-target identities in motor neuron programming, which we alleviate by adding exogenous signaling factors. Further, we establish a putative in vivo correlate for induced endoderm progenitors. Together, these results showcase the utility of Capybara to dissect cell identity and fate transitions, prioritizing interventions to enhance the efficiency and fidelity of stem cell engineering.

Adaptive differentiation promotes intestinal villus recovery

Developmental cell

2022 Jan 24

Ohara, TE;Colonna, M;Stappenbeck, TS;
PMID: 35016013 | DOI: 10.1016/j.devcel.2021.12.012

Loss of differentiated cells to tissue damage is a hallmark of many diseases. In slow-turnover tissues, long-lived differentiated cells can re-enter the cell cycle or transdifferentiate to another cell type to promote repair. Here, we show that in a high-turnover tissue, severe damage to the differentiated compartment induces progenitors to transiently acquire a unique transcriptional and morphological postmitotic state. We highlight this in an acute villus injury model in the mouse intestine, where we identified a population of progenitor-derived cells that covered injured villi. These atrophy-induced villus epithelial cells (aVECs) were enriched for fetal markers but were differentiated and lineage committed. We further established a role for aVECs in maintaining barrier integrity through the activation of yes-associated protein (YAP). Notably, loss of YAP activity led to impaired villus regeneration. Thus, we define a key repair mechanism involving the activation of a fetal-like program during injury-induced differentiation, a process we term "adaptive differentiation."

New molecular techniques for exploring neuronal appetite pathways

Current Opinion in Endocrine and Metabolic Research

2022 Feb 01

Tadross, J;Lam, B;Yeo, G;
| DOI: 10.1016/j.coemr.2021.100309

Satiety and hunger are controlled by a complex and distributed neural network. The ‘standard model’ of energy homeostasis as the net product of orexigenic agouti-related protein and anorexigenic pro-opiomelanocortin neurons within the hypothalamus is the cornerstone of our understanding. It is, however, patently incomplete, and fundamental gaps exist in our understanding of the identity and organisation of cell types forming the appetitive neurocircuitry, their functions and the relevance of those identified and characterised in mice to the equivalent human neurocircuitry. Technological advances in single-cell and spatial transcriptomics, increasingly refined genetic tools for neuronal manipulation in mice, and the development of human hypothalamic cell models provide tools capable of addressing these fundamental questions and offer hope of one day approaching a ‘grand unifying theory’ of energy homeostasis.

Batrachochytrium salamandrivorans Can Devour More than Salamanders

Journal of wildlife diseases

2021 Sep 13

Towe, AE;Gray, MJ;Carter, ED;Wilber, MQ;Ossiboff, RJ;Ash, K;Bohanon, M;Bajo, BA;Miller, DL;
PMID: 34516643 | DOI: 10.7589/JWD-D-20-00214

Batrachochytrium salamandrivorans is an emerging fungus that is causing salamander declines in Europe. We evaluated whether an invasive frog species (Cuban treefrog, Osteopilus septentrionalis) that is found in international trade could be an asymptomatic carrier when exposed to zoospore doses known to infect salamanders. We discovered that Cuban treefrogs could be infected with B. salamandrivorans and, surprisingly, that chytridiomycosis developed in animals at the two highest zoospore doses. To fulfill Koch's postulates, we isolated B. salamandrivorans from infected frogs, exposed eastern newts (Notophthalmus viridescens) to the isolate, and verified infection and disease by histopathology. This experiment represents the first documentation of B. salamandrivorans chytridiomycosis in a frog species and substantially expands the conservation threat and possible mobilization of this pathogen in trade.

Is thyroid gland a target of SARS-CoV-2 infection? Results of the analysis of necropsy thyroid specimens from COVID-19 patients

Endocrine Abstracts

2021 May 15

Macedo, S;Pestana, A;Liliana, R;Neves, C;Susana, G;Guimarães, A;Dolhnikoff, M;Saldiva, P;Carneiro, F;Sobrinho-Simões, M;Soares, P;
| DOI: 10.1530/endoabs.73.oc14.3

In the 2002 outbreak of severe acute respiratory syndrome (SARS) a number of patients presented abnormalities in the thyroid functioning, neuroendocrine and calcium homeostasis. It was detected in autopsies from SARS Coronavirus (SARS-CoV) patients that the thyroid gland was significantly affected by the disease, with extensive injury and death of follicular and parafollicular cells. In the present SARS-CoV-2 pandemic some studies start to report acute thyroiditis and alterations in the levels of thyroid hormones [(triiodothyronine (T3), thyroxine (T4), thyroid stimulating hormone (TSH)]. Thyroid cells present high levels of mRNA expression of angiotensin-converting enzyme 2 (ACE2), the host receptor for SARS-CoV-2. It remains poorly studied the thyroid expression of proteins that predispose to SARS-CoV-2 infection and if thyroid cells can be a direct or indirect target of SARS-CoV-2 infection.

Methods to study circRNA-protein interactions

Methods (San Diego, Calif.)

2021 Apr 22

Ulshöfer, CJ;Pfafenrot, C;Bindereif, A;Schneider, T;
PMID: 33894379 | DOI: 10.1016/j.ymeth.2021.04.014

Circular RNAs (circRNAs) have been studied extensively in the last few years, uncovering functional roles in a diverse range of cell types and organisms. As shown for a few cases, these functions may be mediated by trans-acting factors, in particular RNA-binding proteins (RBPs). However, the specific interaction partners for most circRNAs remain unknown. This is mainly due to technical difficulties in their identification and in differentiating between interactors of circRNAs and their linear counterparts. Here we review the currently used methodology to systematically study circRNA-protein complexes (circRNPs), focusing either on a specific RNA or protein, both on the gene-specific or global level, and discuss advantages and challenges of the available approaches.

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	Description
sense Example: Hs-LAG3-sense	Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe.
Intron# Example: Mm-Htt-intron2	Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection
Pool/Pan Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G)	A mixture of multiple probe sets targeting multiple genes or transcripts
No-XSp Example: Hs-PDGFB-No-XMm	Does not cross detect with the species (Sp)
XSp Example: Rn-Pde9a-XMm	designed to cross detect with the species (Sp)
O# Example: Mm-Islr-O1	Alternative design targeting different regions of the same transcript or isoforms
CDS Example: Hs-SLC31A-CDS	Probe targets the protein-coding sequence only
EnEm	Probe targets exons n and m
En-Em	Probe targets region from exon n to exon m
Retired Nomenclature
tvn Example: Hs-LEPR-tv1	Designed to target transcript variant n
ORF Example: Hs-ACVRL1-ORF	Probe targets open reading frame
UTR Example: Hs-HTT-UTR-C3	Probe targets the untranslated region (non-protein-coding region) only
5UTR Example: Hs-GNRHR-5UTR	Probe targets the 5' untranslated region only
3UTR Example: Rn-Npy1r-3UTR	Probe targets the 3' untranslated region only
Pan Example: Pool	A mixture of multiple probe sets targeting multiple genes or transcripts

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