scholarly journals Spatially-resolved proteomics and transcriptomics: An emerging digital spatial profiling approach for tumor microenvironment

2021 ◽  
Vol 2 ◽  
pp. 1
Author(s):  
Nan Wang ◽  
Rongshui Wang ◽  
Xue Zhang ◽  
Xia Li ◽  
Yan Liang ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Epithelial Cells ◽  
Immune Cells ◽  
Principal Component ◽  
Tumor Stroma ◽  
Spatially Resolved ◽  
Research Areas ◽  
Spatial Profiling ◽  
Wide Range ◽  
Dsp Technology

Digital spatial profiling (DSP) is an emerging powerful technology for proteomics and transcriptomics analyses in a spatially resolved manner for formalin-fixed paraffin-embedded (FFPE) samples developed by nanoString Technologies. DSP applies several advanced technologies, including high-throughput readout technologies (digital optical barcodes by nCounter instruments or next generation sequencing (NGS)), programmable digital micromirror device (DMD) technology, and microfluidic sampling technologies into traditional immunohistochemistry (IHC) and RNA in situ hybridization (ISH) approaches, creating an innovative tool for discovery, translational research, and clinical uses. Since its launch in 2019, DSP has been rapidly adopted, especially in immuno-oncology and tumor microenvironment research areas, and has revealed valuable information that was inaccessible before. In this article, we report the successful setup and validation of the first DSP technology platform in China. Both DSP spatial protein and RNA profiling approaches were validated using FFPE colorectal cancer tissues. Regions of interest (ROIs) were selected in the areas enriched with tumor cells, stroma/immune cells, or normal epithelial cells, and multiplex spatial profiling of both proteins and RNAs were performed. DSP spatial profiling data were processed and normalized accordingly, validating the high quality and consistency of the data. Unsupervised hierarchical clustering as well as principal component analysis (PCA) grouped tumor, stroma/immune cells, and normal epithelial cells into distinct clusters, indicating that the DSP approach effectively captured the spatially resolved proteomics and transcriptomics profiles of different compartments within the tumor microenvironment. In summary, the results confirmed the expected sensitivity and robustness of the DSP approach in profiling both proteins and RNAs in a spatially resolved manner. As a novel technology in highly complex spatial analyses, DSP endows refined analytical power from the tumor microenvironment perspective with the potential of scaling up to more analyzable targets at relatively low cell input levels. We expect that the DSP technology will greatly advance a wide range of biomedical research, especially in immuno-oncology and tumor microenvironment research areas.

scholarly journals Single-Cell Profiling to Explore Immunological Heterogeneity of Tumor Microenvironment in Breast Cancer

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiao Yuan ◽  
Jinxi Wang ◽  
Yixuan Huang ◽  
Dangang Shangguan ◽  
Peng Zhang
Keyword(s):  
Breast Cancer ◽  
Tumor Microenvironment ◽  
Single Cell ◽  
Immune Cells ◽  
Critical Role ◽  
Therapy Resistance ◽  
Spatial Profiling ◽  
Wide Range ◽  
Single Cell Profiling ◽  
Immunological Heterogeneity

Immune infiltrates in the tumor microenvironment (TME) of breast cancer (BRCA) have been shown to play a critical role in tumorigenesis, progression, invasion, and therapy resistance, and thereby will affect the clinical outcomes of BRCA patients. However, a wide range of intratumoral heterogeneity shaped by the tumor cells and immune cells in the surrounding microenvironment is a major obstacle in understanding and treating BRCA. Recent progress in single-cell technologies such as single-cell RNA sequencing (scRNA-seq), mass cytometry, and digital spatial profiling has enabled the detailed characterization of intratumoral immune cells and vastly improved our understanding of less-defined cell subsets in the tumor immune environment. By measuring transcriptomes or proteomics at the single-cell level, it provides an unprecedented view of the cellular architecture consist of phenotypical and functional diversities of tumor-infiltrating immune cells. In this review, we focus on landmark studies of single-cell profiling of immunological heterogeneity in the TME, and discuss its clinical applications, translational outlook, and limitations in breast cancer studies.

scholarly journals HDAC9 deficiency promotes tumor progression by decreasing the CD8+ dendritic cell infiltration of the tumor microenvironment

2020 ◽  
Vol 8 (1) ◽  
pp. e000529 ◽  
Author(s):  
Yongling Ning ◽  
Jun Ding ◽  
Xiao Sun ◽  
Yewen Xie ◽  
Mingming Su ◽  
...  
Keyword(s):  
Lung Cancer ◽  
T Cell ◽  
Tumor Microenvironment ◽  
Tumor Progression ◽  
Immune Cells ◽  
Tumor Antigens ◽  
Tumor Stroma ◽  
Human Lung Cancer ◽  
Cell Counts

BackgroundThe tumor microenvironment (TME) contains a variety of immune cells, which play critical roles during the multistep development of tumors. Histone deacetylase 9 (HDAC9) has been reported to have either proinflammatory or anti-inflammatory effects, depending on the immune environment. In this study, we investigated whether HDAC9 in the tumor stroma regulated inflammation and antitumor immunity.MethodsHdac9 knockout mice were generated to analyze the HDAC9-associated inflammation and tumor progression. Immune cells and cytokines in TME or draining lymph nodes were quantified by flow cytometry and quantitative reverse transcription-PCR. The antigen presentation and CD8+ T cell priming by tumor-infiltrating dendritic cells (DCs) were evaluated in vitro and in vivo. HDAC9-associated inflammation was investigated in a mouse model with dextran sulfate sodium–induced colitis. Correlation of HDAC9 with CD8+ expression was assessed in tissue sections from patients with non-small cell lung cancer.ResultsHDAC9 deficiency promoted tumor progression by decreasing the CD8+ DC infiltration of the TME. Compared with wild-type mice, the tumor-infiltrating DCs of Hdac9-/- mice displayed impaired cross-presentation of tumor antigens and cross-priming of CD8+ T cells. Moreover, HDAC9 expression was significantly positively correlated with CD8+ cell counts in human lung cancer stroma samples.ConclusionsHDAC9 deficiency decreased inflammation and promoted tumor progression by decreasing CD8+ DC infiltration of the TME. HDAC9 expression in the tumor stroma may represent a promising biomarker to predict the therapeutic responses of patients receiving CD8+ T cell-dependent immune treatment regimens.

The CXCL12/CXCR4/ACKR3 Axis in the Tumor Microenvironment: Signaling, Crosstalk, and Therapeutic Targeting

2021 ◽  
Vol 61 (1) ◽  
pp. 541-563 ◽  
Author(s):  
Martine J. Smit ◽  
Géraldine Schlecht-Louf ◽  
Maria Neves ◽  
Jelle van den Bor ◽  
Petronila Penela ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Immune Cells ◽  
Chemokine Receptors ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Cancer Therapies ◽  
Signaling Crosstalk ◽  
Wide Range ◽  
Elevated Expression

Elevated expression of the chemokine receptors CXCR4 and ACKR3 and of their cognate ligand CXCL12 is detected in a wide range of tumors and the tumor microenvironment (TME). Yet, the molecular mechanisms by which the CXCL12/CXCR4/ACKR3 axis contributes to the pathogenesis are complex and not fully understood. To dissect the role of this axis in cancer, we discuss its ability to impinge on canonical and less conventional signaling networks in different cancer cell types; its bidirectional crosstalk, notably with receptor tyrosine kinase (RTK) and other factors present in the TME; and the infiltration of immune cells that supporttumor progression. We discuss current and emerging avenues that target the CXCL12/CXCR4/ACKR3 axis. Coordinately targeting both RTKs and CXCR4/ACKR3 and/or CXCL12 is an attractive approach to consider in multitargeted cancer therapies. In addition, inhibiting infiltrating immune cells or reactivating the immune system along with modulating the CXCL12/CXCR4/ACKR3 axis in the TME has therapeutic promise.

Recent Progress and Plans in Computer-Controlled High Resolution Electron Microscopy

1990 ◽  
Vol 48 (1) ◽  
pp. 154-155
Author(s):  
W.J. de Ruijter ◽  
Peter Rez ◽  
David J. Smith
Keyword(s):  
Electron Microscopy ◽  
Digital Processing ◽  
High Resolution Electron Microscopy ◽  
Objective Lens ◽  
Linear Filter ◽  
Contrast Transfer Function ◽  
Image Displacement ◽  
Spatially Resolved ◽  
Wide Range ◽  
On Line

Digital computers are becoming widely recognized as standard accessories for electron microscopy. Due to instrumental innovations the emphasis in digital processing is shifting from off-line manipulation of electron micrographs to on-line image acquisition, analysis and microscope control. An on-line computer leads to better utilization of the instrument and, moreover, the flexibility of software control creates the possibility of a wide range of novel experiments, for example, based on temporal and spatially resolved acquisition of images or microdiffraction patterns. The instrumental resolution in electron microscopy is often restricted by a combination of specimen movement, radiation damage and improper microscope adjustment (where the settings of focus, objective lens stigmatism and especially beam alignment are most critical). We are investigating the possibility of proper microscope alignment based on computer induced tilt of the electron beam. Image details corresponding to specimen spacings larger than ∼20Å are produced mainly through amplitude contrast; an analysis based on geometric optics indicates that beam tilt causes a simple image displacement. Higher resolution detail is characterized by wave propagation through the optical system of the microscope and we find that beam tilt results in a dispersive image displacement, i.e. the displacement varies with spacing. This approach is valid for weak phase objects (such as amorphous thin films), where transfer is simply described by a linear filter (phase contrast transfer function) and for crystalline materials, where imaging is described in terms of dynamical scattering and non-linear imaging theory. In both cases beam tilt introduces image artefacts.

JAK3-inhibition: Suppressing immune cells while preserving epithelial cells

2012 ◽  
Vol 60 (S 01) ◽  
Author(s):  
T Gossler ◽  
F Ricklefs ◽  
T Deuse ◽  
E Masuda ◽  
V Taylor ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Immune Cells

It is better an approximate answer to the right question than the exact answer to the wrong question : the case of the psychometric analysis of the ASQ:SE

2020 ◽  
Author(s):  
Luis Anunciacao ◽  
janet squires ◽  
J. Landeira-Fernandez
Keyword(s):  
Internal Structure ◽  
Statistical Methods ◽  
Principal Component ◽  
Psychological Theory ◽  
Published Data ◽  
Multivariate Statistical ◽  
Exact Answer ◽  
Wide Range ◽  
Ages And Stages Questionnaire ◽  
The Right

One of the main activities in psychometrics is to analyze the internal structure of a test. Multivariate statistical methods, including Exploratory Factor analysis (EFA) and Principal Component Analysis (PCA) are frequently used to do this, but the growth of Network Analysis (NA) places this method as a promising candidate. The results obtained by these methods are of valuable interest, as they not only produce evidence to explore if the test is measuring its intended construct, but also to deal with the substantive theory that motivated the test development. However, these different statistical methods come up with different answers, providing the basis for different analytical and theoretical strategies when one needs to choose a solution. In this study, we took advantage of a large volume of published data (n = 22,331) obtained by the Ages and Stages Questionnaire Social-Emotional (ASQ:SE), and formed a subset of 500 children to present and discuss alternative psychometric solutions to its internal structure, and also to its subjacent theory. The analyses were based on a polychoric matrix, the number of factors to retain followed several well-known rules of thumb, and a wide range of exploratory methods was fitted to the data, including EFA, PCA, and NA. The statistical outcomes were divergent, varying from 1 to 6 domains, allowing a flexible interpretation of the results. We argue that the use of statistical methods in the absence of a well-grounded psychological theory has limited applications, despite its appeal. All data and codes are available at https://osf.io/z6gwv/.

ROS-responsive nanomedicine: Towards targeting the breast tumor microenvironment

2020 ◽  
Vol 28 ◽  
Author(s):  
RamaRao Malla ◽  
Mohammad Amjad Kamal
Keyword(s):  
Reactive Oxygen Species ◽  
Gene Therapy ◽  
Drug Resistance ◽  
Molecular Imaging ◽  
Tumor Microenvironment ◽  
Immune Cells ◽  
Breast Tumor ◽  
Imaging Techniques ◽  
Oxygen Species ◽  
Massive Accumulation

: The breast tumor microenvironment (TME) promotes drug resistance through an elaborated interaction of TME components mediated by reactive oxygen species (ROS). Despite a massive accumulation of data concerning the targeting the ROS, but little is known about the ROS-responsive nanomedicine for targeting breast TME. This review submits the ROS landscape in breast TME, including ROS biology, ROS mediated carcinogenesis, reprogramming of stromal and immune cells of TME. We also discussed ROS-based precision strategies for imaging TME, including molecular imaging techniques with advanced probes, multiplexed methods, and multi-omic profiling strategies. ROS-responsive nanomedicine also describes various therapies, such as chemo-dynamic, photodynamic, photothermal, sono-dynamic, immune, and gene therapy for BC. We expound ROS-responsive primary delivery systems for chemotherapeutics, phytochemicals, and immunotherapeutics. This review also presents recent updates on nano-theranostics for simultaneous diagnosis and treatment of BCs. We assume that review on this advancing field will be beneficial to the development of ROS-based nanotheranostics for BC.

Metabolism in the Tumor Microenvironment: What is Known about Stromal and Immune Cells?

2018 ◽  
Vol 4 (1) ◽  
Author(s):  
Mª Carmen Ocana ◽  
Beatriz Martinez-Poveda ◽  
Ana R. Quesada ◽  
Miguel Angel Medina
Keyword(s):  
Tumor Microenvironment ◽  
Immune Cells

scholarly journals SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation

2021 ◽  
Vol 6 (58) ◽  
pp. eabg0833
Author(s):  
Bingyu Yan ◽  
Tilo Freiwald ◽  
Daniel Chauss ◽  
Luopin Wang ◽  
Erin West ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Clinical Manifestations ◽  
Lung Epithelial Cells ◽  
Complement Factor ◽  
Respiratory Epithelial Cells ◽  
Signature Genes ◽  
Wide Range ◽  
Lung Epithelial ◽  
Gene Transcripts ◽  
Respiratory Epithelial

Patients with coronavirus disease 2019 (COVID-19) present a wide range of acute clinical manifestations affecting the lungs, liver, kidneys and gut. Angiotensin converting enzyme (ACE) 2, the best-characterized entry receptor for the disease-causing virus SARS-CoV-2, is highly expressed in the aforementioned tissues. However, the pathways that underlie the disease are still poorly understood. Here, we unexpectedly found that the complement system was one of the intracellular pathways most highly induced by SARS-CoV-2 infection in lung epithelial cells. Infection of respiratory epithelial cells with SARS-CoV-2 generated activated complement component C3a and could be blocked by a cell-permeable inhibitor of complement factor B (CFBi), indicating the presence of an inducible cell-intrinsic C3 convertase in respiratory epithelial cells. Within cells of the bronchoalveolar lavage of patients, distinct signatures of complement activation in myeloid, lymphoid and epithelial cells tracked with disease severity. Genes induced by SARS-CoV-2 and the drugs that could normalize these genes both implicated the interferon-JAK1/2-STAT1 signaling system and NF-κB as the main drivers of their expression. Ruxolitinib, a JAK1/2 inhibitor, normalized interferon signature genes and all complement gene transcripts induced by SARS-CoV-2 in lung epithelial cell lines, but did not affect NF-κB-regulated genes. Ruxolitinib, alone or in combination with the antiviral remdesivir, inhibited C3a protein produced by infected cells. Together, we postulate that combination therapy with JAK inhibitors and drugs that normalize NF-κB-signaling could potentially have clinical application for severe COVID-19.

Prevention of Dextran Sulfate Sodium-induced Mouse Colitis by a Fungal Protein Ling Zhi-8 via Promoting the Barrier Function of Intestinal Epithelial Cells

2021 ◽  
Author(s):  
Yu-Huan Chen ◽  
Jenn-Yeu Shin ◽  
Hsiu-Mei Wei ◽  
Chi-Chen Lin ◽  
Linda Chia-Hui Yu ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Immune Cells ◽  
Ganoderma Lucidum ◽  
Dextran Sulfate ◽  
Dextran Sulfate Sodium ◽  
Intestinal Epithelial Cells ◽  
Intestinal Epithelial ◽  
Fungal Protein ◽  
Fungal Immunomodulatory Protein

A fungal immunomodulatory protein Ling Zhi-8 (LZ-8) isolated from Ganoderma lucidum (GL) regulates immune cells and inhibits tumor growth; however, the role of LZ-8 in intestinal epithelial cells (IECs) is...

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