Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches

AbstractThe epithelial lining of the small intestine consists of multiple cell types, including Paneth cells and goblet cells, that work in cohort to maintain gut health. 3D in vitro cultures of human primary epithelial cells, called organoids, have become a key model to study the functions of Paneth cells and goblet cells in normal and diseased conditions. Advances in these models include the ability to skew differentiation to particular lineages, providing a useful tool to study cell type specific function/dysfunction in the context of the epithelium. Here, we use comprehensive profiling of mRNA, microRNA and long non-coding RNA expression to confirm that Paneth cell and goblet cell enrichment of murine small intestinal organoids (enteroids) establishes a physiologically accurate model. We employ network analysis to infer the regulatory landscape altered by skewing differentiation, and using knowledge of cell type specific markers, we predict key regulators of cell type specific functions: Cebpa, Jun, Nr1d1 and Rxra specific to Paneth cells, Gfi1b and Myc specific for goblet cells and Ets1, Nr3c1 and Vdr shared between them. Links identified between these regulators and cellular phenotypes of inflammatory bowel disease (IBD) suggest that global regulatory rewiring during or after differentiation of Paneth cells and goblet cells could contribute to IBD aetiology. Future application of cell type enriched enteroids combined with the presented computational workflow can be used to disentangle multifactorial mechanisms of these cell types and propose regulators whose pharmacological targeting could be advantageous in treating IBD patients with Crohn’s disease or ulcerative colitis.Table of contentsWe demonstrate the application of network biology techniques to increase understanding of intestinal dysbiosis through studying transcriptomics data from Paneth and goblet cell enriched enteroids.

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P004 Critical paralog proteins has a cell-type specific rewiring role in Ulcerative Colitis associated signalling processes

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjab076.133 ◽

2021 ◽

Vol 15 (Supplement_1) ◽

pp. S126-S127

Author(s):

P Kornilova ◽

L Potari-Gul ◽

D Modos ◽

M Madgwick ◽

W Haerty ◽

...

Keyword(s):

Ulcerative Colitis ◽

Notch Pathway ◽

Cell Types ◽

Goblet Cells ◽

Signalling Pathways ◽

Cell Type ◽

Altered Expression ◽

Hypoxia Response ◽

Cell Functions ◽

Cell Type Specific

Abstract Background Cell functions are regulated by signalling pathways that often cross-talk with each other. These cross-talks are usually cell-type specific and, as we showed earlier, often mediated by so called critical paralog proteins (proteins resulted due to gene duplication but then diverged both in terms of their regulation and their functions). As dysregulation of cell functions is a hallmark of chronic inflammatory diseases, including Ulcerative Colitis (UC), here we investigated the role of such critical paralog proteins in the regulation of some key functions, in UC-associated cell types. Methods In this study, we compared healthy and diseased (non-inflamed UC) conditions. Using network biology approaches combined with single-cell RNAseq data, we identified critical paralog groups in myofibroblasts, regulatory T cells and goblet cells that show cell and/or condition specificity in the process of autophagy, Notch and T-cell receptor signalling. Results We focused our analysis on the Notch pathway-related processes, in particular the EGLN paralogs (EGLN1-3). The EGLN enzymes are prolyl hydroxylases and EGLN1, EGLN3 can directly inhibit the HIF1A transcription factor, while HIF1A induces the expression of all the three EGLN gene upon hypoxia. This negative feedback loop tends to control the amount of EGLNs and the activation status of the HIF1A proteins, therefore maintaining an adequate hypoxia response. In the intestine, EGLN2 and EGLN3 are described as potential regulators of inflammation, and both are downregulated in UC patients. Importantly, we found that the expression of EGLN paralogs shows cell-type and condition specificity. While goblet cells express all three paralogs in both healthy and UC conditions, myofibroblasts express EGLN3 only in the healthy condition. As EGLN3 is responsible for tight junction integrity, and it can regulate hypoxia response, the lack of EGLN3 in UC could contribute to the disrupted epithelial barrier function and dysregulation of myofibroblasts. Accordingly, in mice, depletion of Egln3 causes an increased susceptibility to colitis. Conclusion We have developed a bioinformatic pipeline to reconstruct cell-type specific signalling networks to identify the key differences among critical regulators of the signalling flow (ie., critical paralog proteins) in UC-associated cell types and in comparison of healthy and non-inflamed UC conditions. We analysed the altered expression of paralog genes in signalling pathways in UC-associated cell-types, and demonstrated their role with the condition and cell-type specific expression of EGLN3.

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Connectivity characterization of the mouse basolateral amygdalar complex

Nature Communications ◽

10.1038/s41467-021-22915-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Houri Hintiryan ◽

Ian Bowman ◽

David L. Johnson ◽

Laura Korobkova ◽

Muye Zhu ◽

...

Keyword(s):

Granular Cell ◽

Cell Types ◽

Projection Neurons ◽

Cell Type ◽

Connectivity Map ◽

Analysis Techniques ◽

Domain Specific ◽

Cell Type Specific ◽

Unique Domain

AbstractThe basolateral amygdalar complex (BLA) is implicated in behaviors ranging from fear acquisition to addiction. Optogenetic methods have enabled the association of circuit-specific functions to uniquely connected BLA cell types. Thus, a systematic and detailed connectivity profile of BLA projection neurons to inform granular, cell type-specific interrogations is warranted. Here, we apply machine-learning based computational and informatics analysis techniques to the results of circuit-tracing experiments to create a foundational, comprehensive BLA connectivity map. The analyses identify three distinct domains within the anterior BLA (BLAa) that house target-specific projection neurons with distinguishable morphological features. We identify brain-wide targets of projection neurons in the three BLAa domains, as well as in the posterior BLA, ventral BLA, posterior basomedial, and lateral amygdalar nuclei. Inputs to each nucleus also are identified via retrograde tracing. The data suggests that connectionally unique, domain-specific BLAa neurons are associated with distinct behavior networks.

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Shisa6 mediates cell-type specific regulation of depression in the nucleus accumbens

Molecular Psychiatry ◽

10.1038/s41380-021-01217-8 ◽

2021 ◽

Author(s):

Hee-Dae Kim ◽

Jing Wei ◽

Tanessa Call ◽

Nicole Teru Quintus ◽

Alexander J. Summers ◽

...

Keyword(s):

Nucleus Accumbens ◽

Molecular Mechanisms ◽

Cell Types ◽

Current Treatment ◽

Specific Cell ◽

Excitatory Synapses ◽

Cell Type ◽

Cell Type Specific ◽

Specific Regulation ◽

Circuit Function

AbstractDepression is the leading cause of disability and produces enormous health and economic burdens. Current treatment approaches for depression are largely ineffective and leave more than 50% of patients symptomatic, mainly because of non-selective and broad action of antidepressants. Thus, there is an urgent need to design and develop novel therapeutics to treat depression. Given the heterogeneity and complexity of the brain, identification of molecular mechanisms within specific cell-types responsible for producing depression-like behaviors will advance development of therapies. In the reward circuitry, the nucleus accumbens (NAc) is a key brain region of depression pathophysiology, possibly based on differential activity of D1- or D2- medium spiny neurons (MSNs). Here we report a circuit- and cell-type specific molecular target for depression, Shisa6, recently defined as an AMPAR component, which is increased only in D1-MSNs in the NAc of susceptible mice. Using the Ribotag approach, we dissected the transcriptional profile of D1- and D2-MSNs by RNA sequencing following a mouse model of depression, chronic social defeat stress (CSDS). Bioinformatic analyses identified cell-type specific genes that may contribute to the pathogenesis of depression, including Shisa6. We found selective optogenetic activation of the ventral tegmental area (VTA) to NAc circuit increases Shisa6 expression in D1-MSNs. Shisa6 is specifically located in excitatory synapses of D1-MSNs and increases excitability of neurons, which promotes anxiety- and depression-like behaviors in mice. Cell-type and circuit-specific action of Shisa6, which directly modulates excitatory synapses that convey aversive information, identifies the protein as a potential rapid-antidepressant target for aberrant circuit function in depression.

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Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle

Scientific Reports ◽

10.1038/s41598-021-82539-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

John A. Halsall ◽

Simon Andrews ◽

Felix Krueger ◽

Charlotte E. Rutledge ◽

Gabriella Ficz ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Histone Modifications ◽

Expression Patterns ◽

Cell Types ◽

Cell Type ◽

Bar Code ◽

Genes Encoding ◽

Cell Type Specific ◽

Rolling Windows

AbstractChromatin configuration influences gene expression in eukaryotes at multiple levels, from individual nucleosomes to chromatin domains several Mb long. Post-translational modifications (PTM) of core histones seem to be involved in chromatin structural transitions, but how remains unclear. To explore this, we used ChIP-seq and two cell types, HeLa and lymphoblastoid (LCL), to define how changes in chromatin packaging through the cell cycle influence the distributions of three transcription-associated histone modifications, H3K9ac, H3K4me3 and H3K27me3. We show that chromosome regions (bands) of 10–50 Mb, detectable by immunofluorescence microscopy of metaphase (M) chromosomes, are also present in G1 and G2. They comprise 1–5 Mb sub-bands that differ between HeLa and LCL but remain consistent through the cell cycle. The same sub-bands are defined by H3K9ac and H3K4me3, while H3K27me3 spreads more widely. We found little change between cell cycle phases, whether compared by 5 Kb rolling windows or when analysis was restricted to functional elements such as transcription start sites and topologically associating domains. Only a small number of genes showed cell-cycle related changes: at genes encoding proteins involved in mitosis, H3K9 became highly acetylated in G2M, possibly because of ongoing transcription. In conclusion, modified histone isoforms H3K9ac, H3K4me3 and H3K27me3 exhibit a characteristic genomic distribution at resolutions of 1 Mb and below that differs between HeLa and lymphoblastoid cells but remains remarkably consistent through the cell cycle. We suggest that this cell-type-specific chromosomal bar-code is part of a homeostatic mechanism by which cells retain their characteristic gene expression patterns, and hence their identity, through multiple mitoses.

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Emc3 maintains intestinal homeostasis by preserving secretory lineages

Mucosal Immunology ◽

10.1038/s41385-021-00399-2 ◽

2021 ◽

Author(s):

Meina Huang ◽

Li Yang ◽

Ning Jiang ◽

Quanhui Dai ◽

Runsheng Li ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Er Stress ◽

Dominant Role ◽

Paneth Cell ◽

Intestinal Barrier ◽

Goblet Cells ◽

Paneth Cells ◽

Intestinal Barrier Function ◽

Endoplasmic Reticulum Membrane ◽

Mucus Production

AbstractIntestinal exocrine secretory lineages, including goblet cells and Paneth cells, provide vital innate host defense to pathogens. However, how these cells are specified and maintained to ensure intestinal barrier function remains poorly defined. Here we show that endoplasmic reticulum membrane protein complex subunit 3 (Emc3) is essential for differentiation and function of exocrine secretory lineages. Deletion of Emc3 in intestinal epithelium decreases mucus production by goblet cells and Paneth cell population, along with gut microbial dysbiosis, which result in spontaneous inflammation and increased susceptibility to DSS-induced colitis. Moreover, Emc3 deletion impairs stem cell niche function of Paneth cells, thus resulting in intestinal organoid culture failure. Mechanistically, Emc3 deficiency leads to increased endoplasmic reticulum (ER) stress. Mitigating ER stress with tauroursodeoxycholate acid alleviates secretory dysfunction and restores organoid formation. Our study identifies a dominant role of Emc3 in maintaining intestinal mucosal homeostasis.

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An analytical method for the identification of cell type-specific disease gene modules

Journal of Translational Medicine ◽

10.1186/s12967-020-02690-5 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Jinting Guan ◽

Yiping Lin ◽

Yang Wang ◽

Junchao Gao ◽

Guoli Ji

Keyword(s):

Disease Gene ◽

Gene Interaction ◽

Cell Types ◽

Autism Spectrum ◽

Specific Gene ◽

Cell Type ◽

Specific Disease ◽

Cell Type Specific ◽

Gene Modules ◽

Disease Associated Genes

Abstract Background Genome-wide association studies have identified genetic variants associated with the risk of brain-related diseases, such as neurological and psychiatric disorders, while the causal variants and the specific vulnerable cell types are often needed to be studied. Many disease-associated genes are expressed in multiple cell types of human brains, while the pathologic variants affect primarily specific cell types. We hypothesize a model in which what determines the manifestation of a disease in a cell type is the presence of disease module comprised of disease-associated genes, instead of individual genes. Therefore, it is essential to identify the presence/absence of disease gene modules in cells. Methods To characterize the cell type-specificity of brain-related diseases, we construct human brain cell type-specific gene interaction networks integrating human brain nucleus gene expression data with a referenced tissue-specific gene interaction network. Then from the cell type-specific gene interaction networks, we identify significant cell type-specific disease gene modules by performing statistical tests. Results Between neurons and glia cells, the constructed cell type-specific gene networks and their gene functions are distinct. Then we identify cell type-specific disease gene modules associated with autism spectrum disorder and find that different gene modules are formed and distinct gene functions may be dysregulated in different cells. We also study the similarity and dissimilarity in cell type-specific disease gene modules among autism spectrum disorder, schizophrenia and bipolar disorder. The functions of neurons-specific disease gene modules are associated with synapse for all three diseases, while those in glia cells are different. To facilitate the use of our method, we develop an R package, CtsDGM, for the identification of cell type-specific disease gene modules. Conclusions The results support our hypothesis that a disease manifests itself in a cell type through forming a statistically significant disease gene module. The identification of cell type-specific disease gene modules can promote the development of more targeted biomarkers and treatments for the disease. Our method can be applied for depicting the cell type heterogeneity of a given disease, and also for studying the similarity and dissimilarity between different disorders, providing new insights into the molecular mechanisms underlying the pathogenesis and progression of diseases.

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Cytoplasmic, nuclear, membrane-bound and secreted [35S]methionine-labelled polypeptide pattern in differentiating fibroblast stem cells in vitro

Journal of Cell Science ◽

10.1242/jcs.92.2.231 ◽

1989 ◽

Vol 92 (2) ◽

pp. 231-239

Author(s):

P.I. Francz ◽

K. Bayreuther ◽

H.P. Rodemann

Keyword(s):

Protein Fraction ◽

Fibroblast Cell ◽

Cell Types ◽

Specific Marker ◽

Human Skin Fibroblast ◽

Nuclear Fraction ◽

Cell Type ◽

Marker Proteins ◽

Cell Type Specific ◽

Membrane Bound

Methods for the selective enrichment of various subpopulations of the human skin fibroblast cell line HH-8 have been developed. These methods permit the selection of homogeneous populations of the three mitotic fibroblast cell types MF I, II and III, and the four postmitotic cell types PMF IV, V, VI and VII. These seven cell types exhibit differentiation-dependent and cell-type-specific patterns of [35S]methionine-labelled polypeptides in total soluble cytoplasmic and nuclear proteins, also in membrane-bound proteins, and in secreted proteins. In the differentiation sequence MF II-MF III-PMF IV - PMF V - PMF VI 14 cell-type-specific marker proteins have been found in the cytoplasmic and nuclear fraction, also 24 cell-type-specific marker proteins have been found in the membrane-bound protein fraction, and 11 cell-type-specific marker proteins in the secreted protein fraction. Markers in spontaneously arising and experimentally selected or induced populations of a single fibroblast cell type were found to be identical.

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Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts

Scientific Reports ◽

10.1038/s41598-017-08492-y ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 21

Author(s):

Natallia Shved ◽

Gregor Warsow ◽

Felix Eichinger ◽

David Hoogewijs ◽

Simone Brandt ◽

...

Keyword(s):

Network Analysis ◽

Renal Cell ◽

Cell Type ◽

Cell Type Specific

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A scalable platform for the development of cell-type-specific viral drivers

eLife ◽

10.7554/elife.48089 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 12

Author(s):

Sinisa Hrvatin ◽

Christopher P Tzeng ◽

M Aurel Nagy ◽

Hume Stroud ◽

Charalampia Koutsioumpa ◽

...

Keyword(s):

Gene Expression ◽

Heterologous Gene Expression ◽

High Specificity ◽

Cell Types ◽

Regulatory Elements ◽

Cell Type ◽

Cell Type Specificity ◽

Cell Type Specific ◽

The Many ◽

Dna Regulatory Elements

Enhancers are the primary DNA regulatory elements that confer cell type specificity of gene expression. Recent studies characterizing individual enhancers have revealed their potential to direct heterologous gene expression in a highly cell-type-specific manner. However, it has not yet been possible to systematically identify and test the function of enhancers for each of the many cell types in an organism. We have developed PESCA, a scalable and generalizable method that leverages ATAC- and single-cell RNA-sequencing protocols, to characterize cell-type-specific enhancers that should enable genetic access and perturbation of gene function across mammalian cell types. Focusing on the highly heterogeneous mammalian cerebral cortex, we apply PESCA to find enhancers and generate viral reagents capable of accessing and manipulating a subset of somatostatin-expressing cortical interneurons with high specificity. This study demonstrates the utility of this platform for developing new cell-type-specific viral reagents, with significant implications for both basic and translational research.

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Cell-type specific analysis of physiological action of estrogen in mouse oviducts

10.1101/2020.12.18.423483 ◽

2020 ◽

Author(s):

Emily A. McGlade ◽

Gerardo G. Herrera ◽

Kalli K. Stephens ◽

Sierra L. W. Olsen ◽

Sarayut Winuthayanon ◽

...

Keyword(s):

Hormone Replacement ◽

Cell Types ◽

Normal Embryo ◽

Developmental Defect ◽

Cell Type ◽

Specific Analysis ◽

Cell Type Specific ◽

17Β Estradiol ◽

Oviductal Cell

AbstractOne of the endogenous estrogens, 17β-estradiol (E2) is a female steroid hormone secreted from the ovary. It is well established that E2 causes biochemical and histological changes in the uterus. The oviduct response to E2 is virtually unknown in an in vivo environment. In this study, we assessed the effect of E2 on each oviductal cell type, using an ovariectomized-hormone-replacement mouse model, single cell RNA-sequencing (scRNA-seq), in situ hybridization, and cell-type-specific deletion in mice. We found that each cell type in the oviduct responded to E2 distinctively, especially ciliated and secretory epithelial cells. The treatment of exogenous E2 did not drastically alter the transcriptomic profile from that of endogenous E2 produced during estrus. Moreover, we have identified and validated genes of interest in our datasets that may be used as cell- and region-specific markers in the oviduct. Insulin-like growth factor 1 (Igf1) was characterized as an E2-target gene in the mouse oviduct and was also expressed in human Fallopian tubes. Deletion of Igf1 in progesterone receptor (Pgr)-expressing cells resulted in female subfertility, partially due to an embryo developmental defect and embryo retention within the oviduct. In summary, we have shown that oviductal cell types are differentially regulated by E2 and support gene expression changes that are required for normal embryo development and transport in mouse models.

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