Computational exploration of cellular communication in skin from emerging single-cell and spatial transcriptomic data

Biochemical Society transactions

2022 Feb 28

Jin, S;Ramos, R;
PMID: 35191953 | DOI: 10.1042/BST20210863

Tissue development and homeostasis require coordinated cell-cell communication. Recent advances in single-cell sequencing technologies have emerged as a revolutionary method to reveal cellular heterogeneity with unprecedented resolution. This offers a great opportunity to explore cell-cell communication in tissues systematically and comprehensively, and to further identify signaling mechanisms driving cell fate decisions and shaping tissue phenotypes. Using gene expression information from single-cell transcriptomics, several computational tools have been developed for inferring cell-cell communication, greatly facilitating analysis and interpretation. However, in single-cell transcriptomics, spatial information of cells is inherently lost. Given that most cell signaling events occur within a limited distance in tissues, incorporating spatial information into cell-cell communication analysis is critical for understanding tissue organization and function. Spatial transcriptomics provides spatial location of cell subsets along with their gene expression, leading to new directions for leveraging spatial information to develop computational approaches for cell-cell communication inference and analysis. These computational approaches have been successfully applied to uncover previously unrecognized mechanisms of intercellular communication within various contexts and across organ systems, including the skin, a formidable model to study mechanisms of cell-cell communication due to the complex interactions between the different cell populations that comprise it. Here, we review emergent cell-cell communication inference tools using single-cell transcriptomics and spatial transcriptomics, and highlight the biological insights gained by applying these computational tools to exploring cellular communication in skin development, homeostasis, disease and aging, as well as discuss future potential research avenues.

The technological landscape and applications of single-cell multi-omics

Nature reviews. Molecular cell biology

2023 Jun 06

Baysoy, A;Bai, Z;Satija, R;Fan, R;
PMID: 37280296 | DOI: 10.1038/s41580-023-00615-w

Single-cell multi-omics technologies and methods characterize cell states and activities by simultaneously integrating various single-modality omics methods that profile the transcriptome, genome, epigenome, epitranscriptome, proteome, metabolome and other (emerging) omics. Collectively, these methods are revolutionizing molecular cell biology research. In this comprehensive Review, we discuss established multi-omics technologies as well as cutting-edge and state-of-the-art methods in the field. We discuss how multi-omics technologies have been adapted and improved over the past decade using a framework characterized by optimization of throughput and resolution, modality integration, uniqueness and accuracy, and we also discuss multi-omics limitations. We highlight the impact that single-cell multi-omics technologies have had in cell lineage tracing, tissue-specific and cell-specific atlas production, tumour immunology and cancer genetics, and in mapping of cellular spatial information in fundamental and translational research. Finally, we discuss bioinformatics tools that have been developed to link different omics modalities and elucidate functionality through the use of better mathematical modelling and computational methods.

AT2 Cell-Derived IgA Trapped by the Extracellular Matrix and Promoted Pulmonary Fibrosis

Available at SSRN

2023 May 03

Chen, M;Wang, J;Yuan, M;Long, M;Sun, Y;Wang, S;Luo, W;Zhang, W;Jiang, W;Chao, J;
| DOI: 10.2139/ssrn.4431410

Pulmonary fibrosis is an interstitial lung disease caused by various factors such as exposure to workplace environmental contaminants, drugs, or X-rays. Epithelial cells are among the driving factors of pulmonary fibrosis. Immunoglobulin A (IgA), traditionally thought to be secreted by B cells, is an important immune factor involved in COVID-19 infection and vaccination. In current study, we found lung epithelial cells were involved in IgA secretion which, in turn, promoted pulmonary fibrosis. The spatial transcriptomics and single-cell sequencing suggests that Igha transcripts were highly expressed in the fibrotic lesion areas of lungs from silica-treated mice. Reconstruction of B-cell receptor (BCR) sequences revealed a new cluster of AT2-like epithelial cells with a shared BCR and high expression of genes related to IgA production. Furthermore, the secretion of IgA by AT2-like cells were trapped by extracellular matrix and aggravated pulmonary fibrosis by activating fibroblasts. Targeted blockade of IgA secretion by pulmonary epithelial cells may be a potential strategy for treating pulmonary fibrosis.

Small RNA shuffling between murine sperm and their cytoplasmic droplets during epididymal maturation

Developmental cell

2023 Mar 28

Wang, H;Wang, Z;Zhou, T;Morris, D;Chen, S;Li, M;Wang, Y;Zheng, H;Fu, W;Yan, W;
PMID: 37023748 | DOI: 10.1016/j.devcel.2023.03.010

Reports that mouse sperm gain small RNAs from the epididymosomes secreted by epididymal epithelial cells and that these "foreign" small RNAs act as an epigenetic information carrier mediating the transmission of acquired paternal traits have drawn great attention because the findings suggest that heritable information can flow from soma to germ line, thus invalidating the long-standing Weismann's barrier theory on heritable information flow. Using small RNA sequencing (sRNA-seq), northern blots, sRNA in situ hybridization, and immunofluorescence, we detected substantial changes in the small RNA profile in murine caput epididymal sperm (sperm in the head of the epididymis), and we further determined that the changes resulted from sperm exchanging small RNAs, mainly tsRNAs and rsRNAs, with cytoplasmic droplets rather than the epididymosomes. Moreover, the murine sperm-borne small RNAs were mainly derived from the nuclear small RNAs in late spermatids. Thus, caution is needed regarding sperm gaining foreign small RNAs as an underlying mechanism of epigenetic inheritance.

Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology

2023 Feb 27

Caprini, E;D'Agnese, G;Brennan, PA;Rahimi, S;
PMID: 36847112 | DOI: 10.1111/jop.13419

The increase of the incidence of Human Papilloma Virus (HPV) dependent oropharyngeal squamous cell carcinoma (OPSCC) is alarming, although we have greatly progressed in the classification and staging of this disease. We now know that OPSCC-HPV+ is a sub-type of head and neck squamous cell carcinoma with favourable prognosis and good response to therapy that needs a proper system of classification and staging. Thus, in routine practice it is essential to test patients for the presence of HPV. The most popular technique to assess HPV status is immunohistochemistry on biopsy samples with p16, which is an excellent surrogate for high-risk HPV infection. Another highly sensitive and specific tissue-based technique for the detection of HPV is RNAscope In Situ Hybridization (ISH) that has a prohibitive cost, limiting its use in routine practice. Radiomic is an artificial intelligence based non-invasive method of computational analysis of computed tomography, magnetic resonance imaging, positron emission tomography, and ultrasound images. A growing body of evidence suggest that radiomics is able to characterise and detect early relapse after treatment, and enable development of tailored therapy of HPV-positive OPSCC. In this review, we summarise the last findings of radiomic applied to HPV-associated OPSCC.This article is protected by

Distinct biogenesis pathways may have led to functional divergence of the human and Drosophila Arglu1 sisRNA

EMBO reports

2022 Dec 19

Chan, SN;Pek, JW;
PMID: 36533631 | DOI: 10.15252/embr.202154350

Stable intronic sequence RNAs (sisRNAs) are stable, long noncoding RNAs containing intronic sequences. While sisRNAs have been found across diverse species, their level of conservation remains poorly understood. Here we report that the biogenesis and functions of a sisRNA transcribed from the highly conserved Arglu1 locus are distinct in human and Drosophila melanogaster. The Arglu1 genes in both species show similar exon-intron structures where the intron 2 is orthologous and positionally conserved. In humans, Arglu1 sisRNA retains the entire intron 2 and promotes host gene splicing. Mechanistically, Arglu1 sisRNA represses the splicing-inhibitory activity of ARGLU1 protein by binding to ARGLU1 protein and promoting its localization to nuclear speckles, away from the Arglu1 gene locus. In contrast, Drosophila dArglu1 sisRNA forms via premature cleavage of intron 2 and represses host gene splicing. This repression occurs through a local accumulation of dARGLU1 protein and inhibition of telescripting by U1 snRNPs at the dArglu1 locus. We propose that distinct biogenesis of positionally conserved Arglu1 sisRNAs in both species may have led to functional divergence.

Safety De-risking Approaches for Advanced Modalities

pharmafocusasia.com

2022 Jan 01

Gaskin, P;Singh, P;

Artificial intelligence (AI) is now a powerful tool which can be applied to significantly improve the safety de-risking process early in discovery, with AI-driven pipelines of biotechs expanding at a very fast rate. Data from screening studies with DNA-encoded libraries together with high throughput in silico data are screened through AI-enabled computational platforms. These platforms leverage a wide range of in vitro and in vivo models and along with computational predictive models to help identify targets, predicting ‘druggable’ characteristics and target selectivity of molecules from a vast space. In terms of safety, AI can also be used to predict potential interactions and by leveraging publicly available data or proprietary databases can predict potential on- and off-target safety liabilities. A major advantage of AI systems is that they include an active learning loop, referred to as machine learning, which helps to improve the accuracy of prediction and to identify advanceable lead series or candidate molecules leading to a very high success rate, which improves as more data is gathered. Critically AI can also be used to screen billions of molecules virtually, reducing costs and resource requirements and improving the discovery process by more efficient use of molecular biology, public and private databases and other resources.

Unravelling the landscape of skin cancer through single-cell transcriptomics

Translational oncology

2022 Oct 17

Srivastava, A;Bencomo, T;Das, I;Lee, CS;
PMID: 36257209 | DOI: 10.1016/j.tranon.2022.101557

The human skin is a complex organ that forms the first line of defense against pathogens and external injury. It is composed of a wide variety of cells that work together to maintain homeostasis and prevent disease, such as skin cancer. The exponentially rising incidence of skin malignancies poses a growing public health challenge, particularly when the disease course is complicated by metastasis and therapeutic resistance. Recent advances in single-cell transcriptomics have provided a high-resolution view of gene expression heterogeneity that can be applied to skin cancers to define cell types and states, understand disease evolution, and develop new therapeutic concepts. This approach has been particularly valuable in characterizing the contribution of immune cells in skin cancer, an area of great clinical importance given the increasing use of immunotherapy in this setting. In this review, we highlight recent skin cancer studies utilizing bulk RNA sequencing, introduce various single-cell transcriptomics approaches, and summarize key findings obtained by applying single-cell transcriptomics to skin cancer.

Consensus guidelines on the construct validity of rodent models of restless legs syndrome

Disease models & mechanisms

2022 Aug 01

Salminen, AV;Clemens, S;García-Borreguero, D;Ghorayeb, I;Li, Y;Manconi, M;Ondo, W;Rye, D;Siegel, JM;Silvani, A;Winkelman, JW;Allen, RP;Ferré, S;International Restless Legs Syndrome Study Group (IRLSSG), ;
PMID: 35946581 | DOI: 10.1242/dmm.049615

Our understanding of the causes and natural course of restless legs syndrome (RLS) is incomplete. The lack of objective diagnostic biomarkers remains a challenge for clinical research and for the development of valid animal models. As a task force of preclinical and clinical scientists, we have previously defined face validity parameters for rodent models of RLS. In this article, we establish new guidelines for the construct validity of RLS rodent models. To do so, we first determined and agreed on the risk, and triggering factors and pathophysiological mechanisms that influence RLS expressivity. We then selected 20 items considered to have sufficient support in the literature, which we grouped by sex and genetic factors, iron-related mechanisms, electrophysiological mechanisms, dopaminergic mechanisms, exposure to medications active in the central nervous system, and others. These factors and biological mechanisms were then translated into rodent bioequivalents deemed to be most appropriate for a rodent model of RLS. We also identified parameters by which to assess and quantify these bioequivalents. Investigating these factors, both individually and in combination, will help to identify their specific roles in the expression of rodent RLS-like phenotypes, which should provide significant translational implications for the diagnosis and treatment of RLS.

VMHvllCckar cells dynamically control female sexual behaviors over the reproductive cycle

Neuron

2022 Jul 21

Yin, L;Hashikawa, K;Hashikawa, Y;Osakada, T;Lischinsky, JE;Diaz, V;Lin, D;
PMID: 35896109 | DOI: 10.1016/j.neuron.2022.06.026

Sexual behavior is fundamental for the survival of mammalian species and thus supported by dedicated neural substrates. The ventrolateral part of ventromedial hypothalamus (VMHvl) is an essential locus for controlling female sexual behaviors, but recent studies revealed the molecular complexity and functional heterogeneity of VMHvl cells. Here, we identify the cholecystokinin A receptor (Cckar)-expressing cells in the lateral VMHvl (VMHvllCckar) as the key controllers of female sexual behaviors. The inactivation of VMHvllCckar cells in female mice diminishes their interest in males and sexual receptivity, whereas activating these cells has the opposite effects. Female sexual behaviors vary drastically over the reproductive cycle. In vivo recordings reveal reproductive-state-dependent changes in VMHvllCckar cell spontaneous activity and responsivity, with the highest activity occurring during estrus. These in vivo response changes coincide with robust alternation in VMHvllCckar cell excitability and synaptic inputs. Altogether, VMHvllCckar cells represent a key neural population dynamically controlling female sexual behaviors over the reproductive cycle.

Prss29 Cre recombinase mice are useful to study adult uterine gland function

Genesis (New York, N.Y. : 2000)

2022 Jul 22

Kelleher, AM;Allen, CC;Davis, DJ;Spencer, TE;
PMID: 35866844 | DOI: 10.1002/dvg.23493

All mammalian uteri contain glands in their endometrium that develop only or primarily after birth. In mice, those endometrial glands govern post implantation pregnancy establishment via regulation of blastocyst implantation, stromal cell decidualization, and placental development. Here, we describe a new uterine glandular epithelium (GE) specific Cre recombinase mouse line that is useful for the study of uterine gland function during pregnancy. Utilizing CRISPR-Cas9 genome editing, Cre recombinase was inserted into the endogenous serine protease 29 precursor (Prss29) gene. Both Prss29 mRNA and Cre recombinase activity was specific to the GE of the mouse uterus following implantation, but was absent from other areas of the female reproductive tract. Next, Prss29-Cre mice were crossed with floxed forkhead box A2 (Foxa2) mice to conditionally delete Foxa2 specifically in the endometrial glands. Foxa2 was absent in the glands of the post-implantation uterus, and Foxa2 deleted mice exhibited complete infertility after their first pregnancy. These results establish that Prss29-Cre mice are a valuable resource to elucidate and explore the functions of glands in the adult uterus.

Curated variation benchmarks for challenging medically relevant autosomal genes

Nature biotechnology

2022 Feb 07

Wagner, J;Olson, ND;Harris, L;McDaniel, J;Cheng, H;Fungtammasan, A;Hwang, YC;Gupta, R;Wenger, AM;Rowell, WJ;Khan, ZM;Farek, J;Zhu, Y;Pisupati, A;Mahmoud, M;Xiao, C;Yoo, B;Sahraeian, SME;Miller, DE;Jáspez, D;Lorenzo-Salazar, JM;Muñoz-Barrera, A;Rubio-Rodríguez, LA;Flores, C;Narzisi, G;Evani, US;Clarke, WE;Lee, J;Mason, CE;Lincoln, SE;Miga, KH;Ebbert, MTW;Shumate, A;Li, H;Chin, CS;Zook, JM;Sedlazeck, FJ;
PMID: 35132260 | DOI: 10.1038/s41587-021-01158-1

The repetitive nature and complexity of some medically relevant genes poses a challenge for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has provided variant benchmark sets, but these exclude nearly 400 medically relevant genes due to their repetitiveness or polymorphic complexity. Here, we characterize 273 of these 395 challenging autosomal genes using a haplotype-resolved whole-genome assembly. This curated benchmark reports over 17,000 single-nucleotide variations, 3,600 insertions and deletions and 200 structural variations each for human genome reference GRCh37 and GRCh38 across HG002. We show that false duplications in either GRCh37 or GRCh38 result in reference-specific, missed variants for short- and long-read technologies in medically relevant genes, including CBS, CRYAA and KCNE1. When masking these false duplications, variant recall can improve from 8% to 100%. Forming benchmarks from a haplotype-resolved whole-genome assembly may become a prototype for future benchmarks covering the whole genome.

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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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