The Use of Single Cell RNA-seq and Spatial Transcriptomics in Understanding the Pathogenesis and Treatment of Skin Diseases

JID Innovations

2023 Mar 01

Houser, A;Kazmi, A;Nair, A;Ji, A;
| DOI: 10.1016/j.xjidi.2023.100198

The development of multi-omic profiling tools has rapidly expanded in recent years, along with their use in profiling skin tissues in various contexts, including dermatologic diseases. Among these tools, single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST) have emerged as widely adopted and powerful assays for elucidating key cellular components and their spatial arrangement within skin disease. Here, we review recent biological insights gained from the use of scRNA-seq and ST, and the advantages of combining both, for profiling skin disease, including aberrant wound healing, inflammatory skin diseases, and cancer. We discuss the role of scRNA-seq and ST for improving skin disease treatments and moving towards the goal of achieving precision medicine in dermatology, whereby patients can be optimally matched to treatments that maximize therapeutic response.

A new method for the sampling and preservation of placental specimens in low-resource settings for the identification of P. falciparum and analysis of nucleic acids

Journal of histotechnology

2022 Jun 29

Potoczak, PS;Strassmann, BI;Vincenz, C;
PMID: 35766215 | DOI: 10.1080/01478885.2022.2088191

Collection, preservation, and shipment of histological specimens in low-resource settings is challenging. We present a novel method that achieved excellent preservation of placental specimens from rural Mali by using formalin fixation, ethanol dehydration, and long-term storage in a solar-powered freezer. Sample preservation success was 92%, permitting evaluation of current and past malaria infection, anemia, placental maturity, and inflammation. Using RNAscope hybridization we were able to visualize cell-specific gene expression patterns in the formalin-fixed paraffin-embedded (FFPE) specimens. Additionally, our method entailed mirrored sampling from the two cut faces of a cotyledon, one for the FFPE workflows and the other for storage in RNAlater and RNA-seq.

Sigh Generation in Prebötzinger Complex

SSRN Electronic Journal

2022 May 28

Cui, Y;Bondarenko, E;Thörn Perez, C;Chiu, D;Feldman, J;
| DOI: 10.2139/ssrn.4117921

We elucidated neural mechanisms underlying sighing. Photostimulation of parafacial (pF) neuromedin B ( NMB) or gastrin releasing peptide (GRP) or preBötC NMBR or GRPR neurons elicited ectopic sighs with latency inversely related to time from the preceding endogenous sigh. Of particular note, ectopic sighs could be produced without involvement of these peptides or their receptors in preBötC. Moreover, chemogenetic or optogenetic activation of preBötC SST neurons induced sighing, even in the presence of NMBR or GRPR antagonists. We propose that an increase in the excitability of preBötC NMBR or GRPR neurons not requiring activation of their peptide receptors activates partially overlapping pathways to generate sighs, and that preBötC SST neurons are a downstream element in the sigh generation circuit that converts normal breaths into sighs.

Acute Mesenteric Ischemia in Patients with COVID-19: Review of the literature

Journal of the National Medical Association

2021 Dec 29

Chen, C;Li, YW;Shi, PF;Qian, SX;
PMID: 34973847 | DOI: 10.1016/j.jnma.2021.12.003

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a global health emergency. In addition to common respiratory symptoms, some patients with COVID-19 infections may experience a range of extra-pulmonary manifestations, such as digestive system involvement. Patients with COVID-19 have been reported to suffer from acute mesenteric ischemia (AMI) that is associated with disease-related severity and mortality. However, in the context of COVID-19, the exact cause of AMI has yet to be clearly defined. This review provides a comprehensive overview of the available data and elucidates the possible underlying mechanisms linking COVID-19 to AMI, in addition to highlighting therapeutic approaches for clinicians. Finally, given the severe global impact of COVID-19, we emphasize the importance of coordinated vaccination programs.

The Long and the Small Collide: LncRNAs and Small Heterodimer Partner (SHP) in Liver Disease

Molecular and cellular endocrinology

2021 Mar 26

Wu, J;Nagy, LE;Wang, L;
PMID: 33781837 | DOI: 10.1016/j.mce.2021.111262

Long non-coding RNAs (lncRNAs) are a large and diverse class of RNA molecules that are transcribed but not translated into proteins, with a length of more than 200 nucleotides. LncRNAs are involved in gene expression and regulation. The abnormal expression of lncRNAs is associated with disease pathogenesis. Small heterodimer partner (SHP, NR0B2) is a unique orphan nuclear receptor that plays a pivotal role in many biological processes by acting as a transcriptional repressor. In this review, we present the critical roles of SHP and summarize recent findings demonstrating the regulation between lncRNAs and SHP in liver disease.

Genetic deletion of the ghrelin receptor (GHSR) impairs growth and blunts endocrine response to fasting in Ghsr-IRES-Cre mice

Molecular Metabolism

2021 Mar 01

Peris-Sampedro, F;Stoltenborg, I;Le May, M;Zigman, J;Adan, R;Dickson, S;
| DOI: 10.1016/j.molmet.2021.101223

Insertion of the _IRES-Cre_ cassette into the 3’-untranslated region of the _Ghsr_ gene led to a gene-dosage GHSR depletion in the Arc. Whereas heterozygotes remained ghrelin-responsive and more closely resembled wild-types, ghrelin had reduced orexigenic efficacy and failed to induce Arc Fos expression in homozygous littermates. Homozygotes had a lower body weight accompanied by a shorter body length, less fat tissue content, altered bone parameters, and lower insulin-like growth factor-1 levels compared to wild-type and heterozygous littermates. Additionally, both heterozygous and homozygous _Ghsr-IRES-Cre_ mice lacked the usual fasting-induced rise in growth hormone (GH) and displayed an exaggerated drop in blood glucose and insulin compared to wild-types. Unexpectedly, fasting acyl-ghrelin levels were allele-dependently increased.

Temperature and species-dependent regulation of browning in retrobulbar fat

Scientific reports

2021 Feb 04

Rajaii, F;Kim, DW;Pan, J;Mahoney, NR;Eberhart, CG;Qian, J;Blackshaw, S;
PMID: 33542375 | DOI: 10.1038/s41598-021-82672-9

Retrobulbar fat deposits surround the posterior retina and optic nerve head, but their function and origin are obscure. We report that mouse retrobulbar fat is a neural crest-derived tissue histologically and transcriptionally resembles interscapular brown fat. In contrast, human retrobulbar fat closely resembles white adipose tissue. Retrobulbar fat is also brown in other rodents, which are typically housed at temperatures below thermoneutrality, but is white in larger animals. We show that retrobulbar fat in mice housed at thermoneutral temperature show reduced expression of the brown fat marker Ucp1, and histological properties intermediate between white and brown fat. We conclude that retrobulbar fat can potentially serve as a site of active thermogenesis, that this capability is both temperature and species-dependent, and that this may facilitate regulation of intraocular temperature.

Neural mechanisms of comforting: Prosocial touch and stress buffering

Hormones and behavior

2023 Jun 08

Lim, KY;Hong, W;
PMID: 37301130 | DOI: 10.1016/j.yhbeh.2023.105391

Comforting is a crucial form of prosocial behavior that is important for maintaining social unity and improving the physical and emotional well-being of social species. It is often expressed through affiliative social touch toward someone in distress, providing relief for their distressed state. In the face of increasing global distress, these actions are paramount to the continued improvement of individual welfare and the collective good. Understanding the neural mechanisms responsible for promoting actions focused on benefitting others is particularly important and timely. Here, we review prosocial comforting behavior, emphasizing synthesizing recent studies carried out using rodent models. We discuss its underlying behavioral expression and motivations, and then explore both the neurobiology of prosocial comforting in a helper animal and the neurobiology of stress relief following social touch in a recipient as part of a feedback loop interaction.

Methods and applications for single-cell and spatial multi-omics

Nature reviews. Genetics

2023 Mar 02

Vandereyken, K;Sifrim, A;Thienpont, B;Voet, T;
PMID: 36864178 | DOI: 10.1038/s41576-023-00580-2

The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome from single cells is transforming our understanding of cell biology in health and disease. In less than a decade, the field has seen tremendous technological revolutions that enable crucial new insights into the interplay between intracellular and intercellular molecular mechanisms that govern development, physiology and pathogenesis. In this Review, we highlight advances in the fast-developing field of single-cell and spatial multi-omics technologies (also known as multimodal omics approaches), and the computational strategies needed to integrate information across these molecular layers. We demonstrate their impact on fundamental cell biology and translational research, discuss current challenges and provide an outlook to the future.

Single-cell proteomics enabled by next-generation sequencing or mass spectrometry

Nature methods

2023 Mar 01

Bennett, HM;Stephenson, W;Rose, CM;Darmanis, S;
PMID: 36864196 | DOI: 10.1038/s41592-023-01791-5

In the last decade, single-cell RNA sequencing routinely performed on large numbers of single cells has greatly advanced our understanding of the underlying heterogeneity of complex biological systems. Technological advances have also enabled protein measurements, further contributing to the elucidation of cell types and states present in complex tissues. Recently, there have been independent advances in mass spectrometric techniques bringing us one step closer to characterizing single-cell proteomes. Here we discuss the challenges of detecting proteins in single cells by both mass spectrometry and sequencing-based methods. We review the state of the art for these techniques and propose that there is a space for technological advancements and complementary approaches that maximize the advantages of both classes of technologies.

Spatial profiling technologies illuminate the tumor microenvironment

Cancer cell

2023 Feb 13

Elhanani, O;Ben-Uri, R;Keren, L;
PMID: 36800999 | DOI: 10.1016/j.ccell.2023.01.010

The tumor microenvironment (TME) is composed of many different cellular and acellular components that together drive tumor growth, invasion, metastasis, and response to therapies. Increasing realization of the significance of the TME in cancer biology has shifted cancer research from a cancer-centric model to one that considers the TME as a whole. Recent technological advancements in spatial profiling methodologies provide a systematic view and illuminate the physical localization of the components of the TME. In this review, we provide an overview of major spatial profiling technologies. We present the types of information that can be extracted from these data and describe their applications, findings and challenges in cancer research. Finally, we provide a future perspective of how spatial profiling could be integrated into cancer research to improve patient diagnosis, prognosis, stratification to treatment and development of novel therapeutics.

Alternative Splicing

Methods in Molecular Biology

2022 Jul 27

Scheiffele, P;Mauger, O;
| DOI: 10.1007/978-1-0716-2521-7

This detailed volume collects commonly used and cutting-edge methods to analyze alternative splicing, a key step in gene regulation. After an introduction of the alternative splicing mechanism and its targeting for therapeutic strategies, the book continues with techniques for analyzing alternative splicing profiles in complex biological systems, visualizing and localizing alternative spliced transcripts with cellular and sub-cellular resolution, probing regulators of alternative splicing, as well as assessing the functional consequences of alternative splicing. Written for the highly successful _Methods in Molecular Biology_ series, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.

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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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