scholarly journals Modeling Cell-Specific Dynamics and Regulation of the Common Gamma Chain Cytokines

2019 ◽  
Author(s):  
Ali M. Farhat ◽  
Adam C. Weiner ◽  
Cori Posner ◽  
Zoe S. Kim ◽  
Brian Orcutt-Jahns ◽  
...  
Keyword(s):  
Immune Cell ◽  
Cell Types ◽  
Reaction Model ◽  
Cell Populations ◽  
List Type ◽  
Tensor Factorization ◽  
Gamma Chain ◽  
Receptor Ligand ◽  
The Family ◽  
The Common

AbstractMany receptor families exhibit both pleiotropy and redundancy in their regulation, with multiple ligands, receptors, and responding cell populations. Any intervention, therefore, has multiple effects, confounding intuition about how to precisely manipulate signaling for therapeutic purposes. The common γ-chain cytokine receptor dimerizes with complexes of the cytokines interleukin (IL)-2, IL-4, IL-7, IL-9, IL-15, and IL-21 and their corresponding “private” receptors. These cytokines have existing uses and future potential as immune therapies due to their ability to regulate the abundance and function of specific immune cell populations. However, engineering cell specificity into a therapy is confounded by the complexity of the family across responsive cell types. Here, we build a binding-reaction model for the ligand-receptor interactions of common γ-chain cytokines enabling quantitative predictions of response. We show that accounting for receptor-ligand trafficking is essential to accurately model cell response. This model accurately predicts ligand response across a wide panel of cell types under diverse experimental designs. Further, we can predict the effect and specificity of natural or engineered ligands across cell types. We then show that tensor factorization is a uniquely powerful tool to visualize changes in the input-output behavior of the family across time, cell types, ligands, and concentration. In total, these results present a more accurate model of ligand response validated across a panel of immune cell types, and demonstrate an approach for generating interpretable guidelines to manipulate the cell type-specific targeting of engineered ligands. These techniques will in turn help to study and therapeutically manipulate many other complex receptor-ligand families.Summary pointsA dynamical model of the γ-chain cytokines accurately models responses to IL-2, IL-15, IL-4, and IL-7.Receptor trafficking is necessary for capturing ligand response.Tensor factorization maps responses across cell populations, receptors, cytokines, and dynamics to visualize cytokine specificity.An activation model coupled with tensor factorization provides design specifications for engineering cell-specific responses.

scholarly journals Full-Length Transcriptome: A Reliable Alternative for Single-Cell RNA-Seq Analysis in the Spleen of Teleost Without Reference Genome

2021 ◽  
Vol 12 ◽  
Author(s):  
Lixing Huang ◽  
Ying Qiao ◽  
Wei Xu ◽  
Linfeng Gong ◽  
Rongchao He ◽  
...  
Keyword(s):  
Data Analysis ◽  
B Cells ◽  
Single Cell ◽  
Reference Genome ◽  
Immune Cell ◽  
Cell Types ◽  
Full Length ◽  
Cell Populations ◽  
Epinephelus Coioides ◽  
Rna Seq

Fish is considered as a supreme model for clarifying the evolution and regulatory mechanism of vertebrate immunity. However, the knowledge of distinct immune cell populations in fish is still limited, and further development of techniques advancing the identification of fish immune cell populations and their functions are required. Single cell RNA-seq (scRNA-seq) has provided a new approach for effective in-depth identification and characterization of cell subpopulations. Current approaches for scRNA-seq data analysis usually rely on comparison with a reference genome and hence are not suited for samples without any reference genome, which is currently very common in fish research. Here, we present an alternative, i.e. scRNA-seq data analysis with a full-length transcriptome as a reference, and evaluate this approach on samples from Epinephelus coioides-a teleost without any published genome. We show that it reconstructs well most of the present transcripts in the scRNA-seq data achieving a sensitivity equivalent to approaches relying on genome alignments of related species. Based on cell heterogeneity and known markers, we characterized four cell types: T cells, B cells, monocytes/macrophages (Mo/MΦ) and NCC (non-specific cytotoxic cells). Further analysis indicated the presence of two subsets of Mo/MΦ including M1 and M2 type, as well as four subsets in B cells, i.e. mature B cells, immature B cells, pre B cells and early-pre B cells. Our research will provide new clues for understanding biological characteristics, development and function of immune cell populations of teleost. Furthermore, our approach provides a reliable alternative for scRNA-seq data analysis in teleost for which no reference genome is currently available.

scholarly journals Heterogeneity of Circulating Tumor Cell Neoplastic Subpopulations Outlined by Single-Cell Transcriptomics

Cancers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 4885
Author(s):  
Christine M. Pauken ◽  
Shelby Ray Kenney ◽  
Kathryn J. Brayer ◽  
Yan Guo ◽  
Ursa A. Brown-Glaberman ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Single Cell ◽  
Immune Cell ◽  
Metastatic Breast ◽  
Gene Expression Signature ◽  
Circulating Tumor Cell ◽  
Therapeutic Interventions ◽  
Cell Populations ◽  
Breast Cancer Patients ◽  
The Common

Fatal metastasis occurs when circulating tumor cells (CTCs) disperse through the blood to initiate a new tumor at specific sites distant from the primary tumor. CTCs have been classically defined as nucleated cells positive for epithelial cell adhesion molecule and select cytokeratins (EpCAM/CK/DAPI), while negative for the common lymphocyte marker CD45. The enumeration of CTCs allows an estimation of the overall metastatic burden in breast cancer patients, but challenges regarding CTC heterogeneity and metastatic propensities persist, and their decryption could improve therapies. CTCs from metastatic breast cancer (mBC) patients were captured using the RareCyteTM Cytefinder II platform. The Lin− and Lin+ (CD45+) cell populations isolated from the blood of three of these mBC patients were analyzed by single-cell transcriptomic methods, which identified a variety of immune cell populations and a cluster of cells with a distinct gene expression signature, which includes both cells expressing EpCAM/CK (“classic” CTCs) and cells possessing an array of genes not previously associated with CTCs. This study put forward notions that the identification of these genes and their interactions will promote novel areas of analysis by dissecting properties underlying CTC survival, proliferation, and interaction with circulatory immune cells. It improves upon capabilities to measure and interfere with CTCs for impactful therapeutic interventions.

scholarly journals Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF

2019 ◽  
Author(s):  
Meenakshi Venkatasubramanian ◽  
Kashish Chetal ◽  
Gowtham Atluri ◽  
Nathan Salomonis
Keyword(s):  
Single Cell ◽  
Gene Selection ◽  
Cell Types ◽  
Large Datasets ◽  
Detection Methods ◽  
Cell Populations ◽  
List Type ◽  
Hybrid Clustering ◽  
Benchmark Datasets ◽  
Unique Cell

ABSTRACTThe rapid proliferation of single-cell RNA-Sequencing (scRNA-Seq) technologies has spurred the development of diverse computational approaches to detect transcriptionally coherent populations. While the complexity of the algorithms for detecting heterogeneity have increased, most existing algorithms require significant user-tuning, are heavily reliant on dimensionality reduction techniques and are not scalable to ultra-large datasets. We previously described a multi-step algorithm, Iterative Clustering and Guide-gene selection (ICGS), which applies intra-gene correlation and hybrid clustering to uniquely resolve novel transcriptionally coherent cell populations from an intuitive graphical user interface. Here, we describe a new iteration of ICGS that outperforms state-of-the-art scRNA-Seq detection workflows when applied to well-established benchmarks. This approach combines multiple complementary subtype detection methods (HOPACH, sparse-NMF, cluster “fitness”, SVM) to resolve rare and common cell-states, while minimizing differences due to donor or batch effects. Using data from the Human Cell Atlas, we show that the PageRank algorithm effectively down samples ultra-large scRNA-Seq datasets, without losing extremely rare or transcriptionally similar distinct cell-types and while recovering novel transcriptionally unique cell populations. We believe this new approach holds tremendous promise in reproducibly resolving hidden cell populations in complex datasets.HighlightsICGS2 outperforms alternative approaches in small and ultra-large benchmark datasetsIntegrates multiple solutions for cell-type detection with supervised refinementScales effectively to resolve rare cell-states from ultra-large datasets using PageRank sampling with a low memory footprintIntegrated into AltAnalyze to enable sophisticated and automated downstream analysis

scholarly journals Exploring the Innate Immunological Response of an Alternative Nonhuman Primate Model of Infectious Disease; the Common Marmoset

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
M. Nelson ◽  
M. Loveday
Keyword(s):  
Infectious Disease ◽  
Immune Response ◽  
Nonhuman Primate ◽  
Immune Cell ◽  
Common Marmoset ◽  
Cell Types ◽  
Nonhuman Primate Model ◽  
Primate Model ◽  
The Common ◽  
Activation Status

The common marmoset (Callithrix jacchus) is increasingly being utilised as a nonhuman primate model for human disease, ranging from autoimmune to infectious disease. In order to fully exploit these models, meaningful comparison to the human host response is necessary. Commercially available reagents, primarily targeted to human cells, were utilised to assess the phenotype and activation status of key immune cell types and cytokines in naive and infected animals. Single cell suspensions of blood, spleen, and lung were examined. Generally, the phenotype of cells was comparable between humans and marmosets, with approximately 63% of all lymphocytes in the blood of marmosets being T cells, 25% B-cells, and 12% NK cells. The percentage of neutrophils in marmoset blood were more similar to human values than mouse values. Comparison of the activation status of cells following experimental systemic or inhalational infection exhibited different trends in different tissues, most obvious in cell types active in the innate immune response. This work significantly enhances the ability to understand the immune response in these animals and fortifies their use as models of infectious disease.

scholarly journals Integrative transcriptomic analysis of SLE reveals IFN-driven cross-talk between immune cells

2020 ◽  
Author(s):  
Bharat Panwar ◽  
Benjamin J. Schmiedel ◽  
Shu Liang ◽  
Brandie White ◽  
Enrique Rodriguez ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Autoimmune Disease ◽  
Cross Talk ◽  
Immune Cell ◽  
Cell Types ◽  
Cell Populations ◽  
Multiple Cell ◽  
Classical Monocytes ◽  
Multiple Immune Cell

ABSTRACTThe systemic lupus erythematosus (SLE) is an incurable autoimmune disease disproportionately affecting women and may lead to damage in multiple different organs. The marked heterogeneity in its clinical manifestations is a major obstacle in finding targeted treatments and involvement of multiple immune cell types further increases this complexity. Thus, identifying molecular subtypes that best correlate with disease heterogeneity and severity as well as deducing molecular cross-talk among major immune cell types that lead to disease progression are critical steps in the development of more informed therapies for SLE. Here we profile and analyze gene expression of six major circulating immune cell types from patients with well-characterized SLE (classical monocytes (n=64), T cells (n=24), neutrophils (n=24), B cells (n=20), conventional (n=20) and plasmacytoid (n=22) dendritic cells) and from healthy control subjects. Our results show that the interferon (IFN) response signature was the major molecular feature that classified SLE patients into two distinct groups: IFN-signature negative (IFNneg) and positive (IFNpos). We show that the gene expression signature of IFN response was consistent (i) across all immune cell types, (ii) all single cells profiled from three IFNpos donors using single-cell RNA-seq, and (iii) longitudinal samples of the same patient. For a better understanding of molecular differences of IFNpos versus IFNneg patients, we combined differential gene expression analysis with differential Weighted Gene Co-expression Network Analysis (WGCNA), which revealed a relatively small list of genes from classical monocytes including two known immune modulators, one the target of an approved therapeutic for SLE (TNFSF13B/BAFF: belimumab) and one itself a therapeutic for Rheumatoid Arthritis (IL1RN: anakinra). For a more integrative understanding of the cross-talk among different cell types and to identify potentially novel gene or pathway connections, we also developed a novel gene co-expression analysis method for joint analysis of multiple cell types named integrated WGNCA (iWGCNA). This method revealed an interesting cross-talk between T and B cells highlighted by a significant enrichment in the expression of known markers of T follicular helper cells (Tfh), which also correlate with disease severity in the context of IFNpos patients. Interestingly, higher expression of BAFF from all myeloid cells also shows a strong correlation with enrichment in the expression of genes in T cells that may mark circulating Tfh cells or related memory cell populations. These cell types have been shown to promote B cell class-switching and antibody production, which are well-characterized in SLE patients. In summary, we generated a large-scale gene expression dataset from sorted immune cell populations and present a novel computational approach to analyze such data in an integrative fashion in the context of an autoimmune disease. Our results reveal the power of a hypothesis-free and data-driven approach to discover drug targets and reveal novel cross-talk among multiple immune cell types specific to a subset of SLE patients. This approach is immediately useful for studying autoimmune diseases and is applicable in other contexts where gene expression profiling is possible from multiple cell types within the same tissue compartment.

scholarly journals Single-cell atlas of a non-human primate reveals new pathogenic mechanisms of COVID-19

2020 ◽  
Author(s):  
Lei Han ◽  
Xiaoyu Wei ◽  
Chuanyu Liu ◽  
Giacomo Volpe ◽  
Zhifeng Wang ◽  
...  
Keyword(s):  
Single Cell ◽  
Viral Entry ◽  
Immune Cell ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
List Type ◽  
Innate Immune Responses ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Substantial Heterogeneity

ABSTRACTStopping COVID-19 is a priority worldwide. Understanding which cell types are targeted by SARS-CoV-2 virus, whether interspecies differences exist, and how variations in cell state influence viral entry is fundamental for accelerating therapeutic and preventative approaches. In this endeavor, we profiled the transcriptome of nine tissues from a Macaca fascicularis monkey at single-cell resolution. The distribution of SARS-CoV-2 facilitators, ACE2 and TMRPSS2, in different cell subtypes showed substantial heterogeneity across lung, kidney, and liver. Through co-expression analysis, we identified immunomodulatory proteins such as IDO2 and ANPEP as potential SARS-CoV-2 targets responsible for immune cell exhaustion. Furthermore, single-cell chromatin accessibility analysis of the kidney unveiled a plausible link between IL6-mediated innate immune responses aiming to protect tissue and enhanced ACE2 expression that could promote viral entry. Our work constitutes a unique resource for understanding the physiology and pathophysiology of two phylogenetically close species, which might guide in the development of therapeutic approaches in humans.Bullet pointsWe generated a single-cell transcriptome atlas of 9 monkey tissues to study COVID-19.ACE2+TMPRSS2+ epithelial cells of lung, kidney and liver are targets for SARS-CoV-2.ACE2 correlation analysis shows IDO2 and ANPEP as potential therapeutic opportunities.We unveil a link between IL6, STAT transcription factors and boosted SARS-CoV-2 entry.

scholarly journals ASigNTF: Agnostic Signature using NTF – a universal agnostic strategy to estimate cell-types abundance from transcriptomic datasets

2021 ◽  
Author(s):  
Paul Fogel ◽  
Galina Boldina ◽  
Corinne Rocher ◽  
Charles Bettembourg ◽  
George Luta ◽  
...  
Keyword(s):  
Biological Material ◽  
Ad Hoc ◽  
Immune Cell ◽  
Cell Types ◽  
Data Driven ◽  
Molecular Signatures ◽  
Tensor Factorization ◽  
Rna Seq ◽  
Data Driven Approach

AbstractBackgroundMolecular signatures for deconvolution of immune cell types have been proposed, based on a methodology that relies on the biological classification of the cell types being studied. When working with less known biological material, a data-driven approach is needed to uncover the underlying classes and construct ad hoc signatures.ResultsWe introduce a new approach, ASigNTF: Agnostic Signature using Non-negative Tensor Factorization, to perform the deconvolution of cell types from transcriptomics data (RNAseq and microarray). ASigNTF, which is based on two complementary statistical/mathematical tools: non-negative tensor factorization (for dimensionality reduction) and the Herfindahl-Hirschman index (for signature selection), can be applied to any type of tissue as long as transcriptomic data on isolated cells is available. As a direct result of the new method, we propose two new signatures for the deconvolution of immune cell types, one consisting of a relatively small set of 415 genes, which is more compatible with microarray platforms, and a larger set of 915 genes. Using external datasets, our two signatures outperform the CIBERSORT LM22 signature in deconvolution of RNA-seq data. Our signature with 415 genes allows to recognize a larger number of cell types compared to the ABIS microarray signature.ConclusionsThe paper proposes a new method, ASigNTF; applies the method, and also provides a software implementation that allows to identify molecular signatures for deconvolution of complex tissues and specifically up to 16 immune cell types from micro-array or RNA-seq data.HighlightsSeveral signatures of immune cell types have been proposed, which follow a methodology deeply rooted in the known biological classification of the investigated cell types.When working with less known biological material, a more agnostic, data-driven approach is required to uncover the underlying classes and construct ad hoc signatures.We present ASigNTF, a new agnostic approach to cell type classification and signature selection supported by an application software.We discuss the results of benchmarking our proposed signatures, ABIS-seq and CIBERSORT on external datasets.

scholarly journals Dissociation, cellular isolation, and initial molecular characterization of neonatal and pediatric human lung tissues

2018 ◽  
Vol 315 (4) ◽  
pp. L576-L583 ◽  
Author(s):  
Gautam Bandyopadhyay ◽  
Heidie L. Huyck ◽  
Ravi S. Misra ◽  
Soumyaroop Bhattacharya ◽  
Qian Wang ◽  
...  
Keyword(s):  
Cell Adhesion ◽  
Adhesion Molecule ◽  
Cell Adhesion Molecule ◽  
Immune Cell ◽  
Human Lung ◽  
Tyrosine Phosphatase ◽  
Expression Patterns ◽  
Cell Types ◽  
Cell Populations ◽  
Isolated Cells

Human lung morphogenesis begins by embryonic life and continues after birth into early childhood to form a complex organ with numerous morphologically and functionally distinct cell types. Pulmonary organogenesis involves dynamic changes in cell proliferation, differentiation, and migration of specialized cells derived from diverse embryonic lineages. Studying the molecular and cellular processes underlying formation of the fully functional lung requires isolating distinct pulmonary cell populations during development. We now report novel methods to isolate four major pulmonary cell populations from pediatric human lung simultaneously. Cells were dissociated by protease digestion of neonatal and pediatric lung and isolated on the basis of unique cell membrane protein expression patterns. Epithelial, endothelial, nonendothelial mesenchymal, and immune cells were enriched by fluorescence-activated cell sorting. Dead cells and erythrocytes were excluded by 7-aminoactinomycin D uptake and glycophorin-A (CD235a) expression, respectively. Leukocytes were identified by membrane CD45 (protein tyrosine phosphatase, receptor type C), endothelial cells by platelet endothelial cell adhesion molecule-1 (CD31) and vascular endothelial cadherin (CD144), and both were isolated. Thereafter, epithelial cell adhesion molecule (CD326)-expressing cells were isolated from the endothelial- and immune cell-depleted population to enrich epithelial cells. Cells lacking these membrane markers were collected as “nonendothelial mesenchymal” cells. Quantitative RT-PCR and RNA sequencing analyses of population specific transcriptomes demonstrate the purity of the subpopulations of isolated cells. The method efficiently isolates major human lung cell populations that we announce are now available through the National Heart, Lung, and Blood Institute Lung Molecular Atlas Program (LungMAP) for their further study.

scholarly journals Family psychoeducation for people living with schizophrenia and their families

2018 ◽  
Vol 24 (1) ◽  
pp. 9-19 ◽  
Author(s):  
Carol Harvey
Keyword(s):  
Practice Change ◽  
Information Support ◽  
List Type ◽  
Family Psychoeducation ◽  
Problem Solving Skills ◽  
Family Service ◽  
Psychotherapeutic Interventions ◽  
The Family ◽  
The Common ◽  
Relapse Rates

SUMMARYMost people with schizophrenia have frequent contact with their families. Therefore, the family should be involved in their relative's treatment and care wherever possible, so that they can contribute to that person's recovery and the family's own needs for information, support and treatment can be addressed. Family psychoeducation refers to a group of structured psychotherapeutic interventions that involve the person with schizophrenia and their family as partners in care. Trained practitioners adopt a collaborative approach to information sharing and provide training in coping, communication and problem-solving skills. This article describes the common principles and techniques of family psychoeducation (FPE), along with the substantial evidence for its benefits for families, especially reduced relapse rates for the person with schizophrenia. Despite recommendations in clinical practice guidelines, FPE is not widely available throughout the world. The current challenge is to address this through systemic approaches to practice change and tiered approaches to family service delivery.LEARNING OBJECTIVES•Appreciate the needs of families and recognise how these may be addressed by family psychoeducation•Understand the evidence for family psychoeducation•Delineate the key elements of family psychoeducation and consider how it may be applied in practiceDECLARATION OF INTERESTNone.

scholarly journals Psychiatric assessment of adults in care proceedings

2019 ◽  
Vol 26 (1) ◽  
pp. 16-25
Author(s):  
Rajan Nathan ◽  
Ruth Scarisbrick ◽  
Gaynor Brown
Keyword(s):  
Critical Role ◽  
Legal Framework ◽  
Learning Objectives ◽  
Family Court ◽  
List Type ◽  
Assessment Framework ◽  
England And Wales ◽  
The Family ◽  
The Common ◽  
Key Aspects

SUMMARYPsychiatric assessments of adults involved in care proceedings can play a critical role in assisting the family court to resolve proceedings justly. To properly carry out this role, the psychiatric expert should have an up-to-date understanding of the wider context within which they are working. This article outlines the legal framework of care proceedings in England and Wales and summarises the key aspects of the process. The duties of the expert and how the expert is engaged are explained. Finally, guidance is presented on how the expert should approach questions that are commonly raised in these proceedings.LEARNING OBJECTIVESAfter reading this article you will be able to: •appreciate the legal framework relevant to care proceedings in England and Wales•recognise the circumstances in which expert psychiatric evidence relating to adults in care proceedings is commissioned•understand the common questions posed to expert psychiatrists undertaking assessments of adults in care proceedings and develop an assessment framework.

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