scholarly journals Rhesus Macaque CODEX Multiplexed Immunohistochemistry Panel for Studying Immune Responses During Ebola Infection

2021 ◽  
Vol 12 ◽  
Author(s):  
Sizun Jiang ◽  
Nilanjan Mukherjee ◽  
Richard S. Bennett ◽  
Han Chen ◽  
James Logue ◽  
...  
Keyword(s):  
Immune Responses ◽  
Ebola Virus ◽  
Immune Cell ◽  
Rhesus Macaques ◽  
Cell Types ◽  
Tissue Imaging ◽  
Host Immune Responses ◽  
Spatially Resolved ◽  
Ebov Infection ◽  
Ffpe Tissues

Non-human primate (NHP) animal models are an integral part of the drug research and development process. For some biothreat pathogens, animal model challenge studies may offer the only possibility to evaluate medical countermeasure efficacy. A thorough understanding of host immune responses in such NHP models is therefore vital. However, applying antibody-based immune characterization techniques to NHP models requires extensive reagent development for species compatibility. In the case of studies involving high consequence pathogens, further optimization for use of inactivated samples may be required. Here, we describe the first optimized CO-Detection by indEXing (CODEX) multiplexed tissue imaging antibody panel for deep profiling of spatially resolved single-cell immune responses in rhesus macaques. This 21-marker panel is composed of a set of 18 antibodies that stratify major immune cell types along with a set three Ebola virus (EBOV)-specific antibodies. We validated these two sets of markers using immunohistochemistry and CODEX in fully inactivated Formalin-Fixed Paraffin-Embedded (FFPE) tissues from mock and EBOV challenged macaques respectively and provide an efficient framework for orthogonal validation of multiple antibody clones using CODEX multiplexed tissue imaging. We also provide the antibody clones and oligonucleotide tag sequences as a valuable resource for other researchers to recreate this reagent set for future studies of tissue immune responses to EBOV infection and other diseases.

scholarly journals Jointly leveraging spatial transcriptomics and deep learning models for pathology image annotation improves cell type identification over either approach alone.

2021 ◽  
Author(s):  
Asif Zubair ◽  
Richard H. Chapple ◽  
Sivaraman Natarajan ◽  
William C. Wright ◽  
Min Pan ◽  
...  
Keyword(s):  
Immune Cell ◽  
Image Annotation ◽  
Cell Types ◽  
Tissue Cell ◽  
Cell Type ◽  
Spatially Resolved ◽  
Transcriptomics Data ◽  
Diagnostic Applications ◽  
The Many ◽  
Level Performance

The disorganization of cell types within tissues underlies many human diseases and has been studied for over a century using the conventional tools of pathology, including tissue-marking dyes such as the H&E stain. Recently, spatial transcriptomics technologies were developed that can measure spatially resolved gene expression directly in pathology-stained tissues sections, revealing cell types and their dysfunction in unprecedented detail. In parallel, artificial intelligence (AI) has approached pathologist-level performance in computationally annotating H&E images of tissue sections. However, spatial transcriptomics technologies are limited in their ability to separate transcriptionally similar cell types and AI-based pathology has performed less impressively outside their training datasets. Here, we describe a methodology that can computationally integrate AI-annotated pathology images with spatial transcriptomics data to markedly improve inferences of tissue cell type composition made over either class of data alone. We show that this methodology can identify regions of clinically relevant tumor immune cell infiltration, which is predictive of response to immunotherapy and was missed by an initial pathologist's manual annotation. Thus, combining spatial transcriptomics and AI-based image annotation has the potential to exceed pathologist-level performance in clinical diagnostic applications and to improve the many applications of spatial transcriptomics that rely on accurate cell type annotations.

scholarly journals Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level

2021 ◽  
Author(s):  
Yanxiang Deng ◽  
Marek Bartosovic ◽  
Sai Ma ◽  
Di Zhang ◽  
Yang Liu ◽  
...  
Keyword(s):  
Immune Cell ◽  
System Development ◽  
Local Environment ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Cellular Level ◽  
Human Tonsil ◽  
Spatially Resolved ◽  
Fate Decision ◽  
Genome Scale

Cellular function in tissue is dependent upon the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping, but it remains elusive to capture spatial epigenetic information of tissue at cellular level and genome scale. Here we report on spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissue section via next-generation sequencing by combining in situ Tn5 transposition chemistry and microfluidic deterministic barcoding. Spatial chromatin accessibility profiling of mouse embryos delineated tissue region-specific epigenetic landscapes and identified gene regulators implicated in the central nerve system development. Mapping the accessible genome in human tonsil tissue with 20μm pixel size revealed spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology takes spatial biology to a new realm by enabling spatially resolved epigenomics to improve our understanding of cell identity, state, and fate decision in relation to epigenetic underpinnings in development and disease.

scholarly journals Genetically barcoded SIV reveals the emergence of escape mutations in multiple viral lineages during immune escape

2019 ◽  
Vol 117 (1) ◽  
pp. 494-502
Author(s):  
Taina T. Immonen ◽  
Celine Camus ◽  
Carolyn Reid ◽  
Christine M. Fennessey ◽  
Gregory Q. Del Prete ◽  
...  
Keyword(s):  
Immune Responses ◽  
Immune Escape ◽  
Rhesus Macaques ◽  
Quantitative Measure ◽  
Population Level ◽  
Therapeutic Interventions ◽  
Viral Escape ◽  
Virus Population ◽  
Host Immune Responses ◽  
Immune Pressure

The rapidity of replication coupled with a high mutation rate enables HIV to evade selective pressures imposed by host immune responses. Investigating the ability of HIV to escape different selection forces has generally relied on population-level measures, such as the time to detectable escape mutations in plasma and the rate these mutations subsequently take over the virus population. Here we employed a barcoded synthetic swarm of simian immunodeficiency virus (SIV) in rhesus macaques to investigate the generation and selection of escape mutations within individual viral lineages at the Mamu-A*01-restricted Tat-SL8 epitope. We observed the persistence of more than 1,000 different barcode lineages following selection after acquiring escape mutations. Furthermore, the increased resolution into the virus population afforded by barcode analysis revealed changes in the population structure of the viral quasispecies as it adapted to immune pressure. The high frequency of emergence of escape mutations in parallel viral lineages at the Tat-SL8 epitope highlights the challenge posed by viral escape for the development of T cell-based vaccines. Importantly, the level of viral replication required for generating escape mutations in individual lineages can be directly estimated using the barcoded virus, thereby identifying the level of efficacy required for a successful vaccine to limit escape. Overall, assessing the survival of barcoded viral lineages during selection provides a direct and quantitative measure of the stringency of the underlying genetic bottleneck, making it possible to predict the ability of the virus to escape selective forces induced by host immune responses as well as during therapeutic interventions.

scholarly journals Neutralization of rhesus cytomegalovirus IL-10 reduces horizontal transmission and alters long-term immunity

2019 ◽  
Vol 116 (26) ◽  
pp. 13036-13041 ◽  
Author(s):  
Jesse D. Deere ◽  
W. L. William Chang ◽  
Andradi Villalobos ◽  
Kimberli A. Schmidt ◽  
Ashlesha Deshpande ◽  
...  
Keyword(s):  
Immune Responses ◽  
Persistent Infection ◽  
Vaccine Development ◽  
Rhesus Macaques ◽  
Horizontal Transmission ◽  
Severe Disease ◽  
Interleukin 10 ◽  
Primate Model ◽  
Host Immune Responses ◽  
Rhesus Cytomegalovirus

Human cytomegalovirus (HCMV) causes severe disease in infants and immunocompromised people. There is no approved HCMV vaccine, and vaccine development strategies are complicated by evidence of both persistent infection and reinfection of people with prior immunity. The greatest emphasis has been placed on reducing transmission to seronegative pregnant women to prevent vertical transmission and its potentially severe sequelae. Increasing evidence suggests that the earliest host–HCMV interactions establish conditions for viral persistence, including evasion of host immune responses to the virus. Using a nonhuman primate model of HCMV infection, we show that rhesus macaques immunized against viral interleukin-10 (IL-10) manifest delayed rhesus cytomegalovirus (RhCMV) acquisition and altered immune responses to the infection when it does occur. Among animals with the greatest antiviral IL-10–neutralizing activity, the timing of RhCMV seroconversion was delayed by an average of 12 weeks. After acquisition, such animals displayed an antibody response to the new infection, which peaked as expected after 2 weeks but then declined rapidly. In contrast, surprisingly, vaccination with glycoprotein B (gB) protein had no discernible impact on these outcomes. Our results demonstrate that viral IL-10 is a key regulator of successful host immune responses to RhCMV. Viral IL-10 is, therefore, an important target for vaccine strategies against cytomegalovirus (CMV). Furthermore, given the immunoregulatory function of viral IL-10, targeting this protein may prove synergistic with other vaccine therapies and targets. Our study also provides additional evidence that the earliest host–CMV interactions can have a significant impact on the nature of persistent infection.

scholarly journals Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level

2021 ◽  
Author(s):  
Rong Fan ◽  
Yanxiang Deng ◽  
Marek Bartosovic ◽  
Sai Ma ◽  
Di Zhang ◽  
...  
Keyword(s):  
Immune Cell ◽  
System Development ◽  
Local Environment ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Cellular Level ◽  
Human Tonsil ◽  
Spatially Resolved ◽  
Fate Decision ◽  
Genome Scale

Abstract Cellular function in tissue is dependent upon the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping, but it remains elusive to capture spatial epigenetic information of tissue at cellular level and genome scale. Here we report on spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissue section via next-generation sequencing by combining in situ Tn5 transposition chemistry and microfluidic deterministic barcoding. Spatial chromatin accessibility profiling of mouse embryos delineated tissue region-specific epigenetic landscapes and identified gene regulators implicated in the central nerve system development. Mapping the accessible genome in human tonsil tissue with 20μm pixel size revealed spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology takes spatial biology to a new realm by enabling spatially resolved epigenomics to improve our understanding of cell identity, state, and fate decision in relation to epigenetic underpinnings in development and disease.

scholarly journals Chimpanzee adenoviral vector prime-boost regimen elicits potent immune responses against Ebola virus in mice and rhesus macaques

2019 ◽  
Vol 8 (1) ◽  
pp. 1086-1097 ◽  
Author(s):  
Xi Yang ◽  
Xiang Wang ◽  
Yufeng Song ◽  
Ping Zhou ◽  
Dapeng Li ◽  
...  
Keyword(s):  
Immune Responses ◽  
Adenoviral Vector ◽  
Ebola Virus ◽  
Rhesus Macaques ◽  
Boost Regimen

scholarly journals Development of a Well-Characterized Rhesus Macaque Model of Ebola Virus Disease for Support of Product Development

2021 ◽  
Vol 9 (3) ◽  
pp. 489
Author(s):  
Kendra J. Alfson ◽  
Yenny Goez-Gazi ◽  
Michal Gazi ◽  
Hilary Staples ◽  
Marc Mattix ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Ebola Virus ◽  
Virus Disease ◽  
Rna Virus ◽  
Rhesus Macaques ◽  
Systemic Disease ◽  
Clinical Pathology ◽  
Macaque Model ◽  
Progression Of Disease ◽  
Ebov Infection

Ebola virus (EBOV) is a negative-sense RNA virus that can infect humans and nonhuman primates with severe health consequences. Development of countermeasures requires a thorough understanding of the interaction between host and pathogen, and the course of disease. The goal of this study was to further characterize EBOV disease in a uniformly lethal rhesus macaque model, in order to support development of a well-characterized model following rigorous quality standards. Rhesus macaques were intramuscularly exposed to EBOV and one group was euthanized at predetermined time points to characterize progression of disease. A second group was not scheduled for euthanasia in order to analyze survival, changes in physiology, clinical pathology, terminal pathology, and telemetry kinetics. On day 3, sporadic viremia was observed and pathological evidence was noted in lymph nodes. By day 5, viremia was detected in all EBOV exposed animals and pathological evidence was noted in the liver, spleen, and gastrointestinal tissues. These data support the notion that EBOV infection in rhesus macaques is a rapid systemic disease similar to infection in humans, under a compressed time scale. Biomarkers that correlated with disease progression at the earliest stages of infection were observed thereby identifying potential “trigger-to-treat” for use in therapeutic studies.

scholarly journals A Catalogus Immune Muris of the mouse immune responses to diverse pathogens

2021 ◽  
Vol 12 (9) ◽  
Author(s):  
Céline Barlier ◽  
Diego Barriales ◽  
Alexey Samosyuk ◽  
Sascha Jung ◽  
Srikanth Ravichandran ◽  
...  
Keyword(s):  
Immune Response ◽  
Immune Responses ◽  
Biomedical Applications ◽  
Immune Cell ◽  
Cell Types ◽  
Computational Method ◽  
Functional Responses ◽  
Macrophage Cell ◽  
Functional States

AbstractImmunomodulation strategies are crucial for several biomedical applications. However, the immune system is highly heterogeneous and its functional responses to infections remains elusive. Indeed, the characterization of immune response particularities to different pathogens is needed to identify immunomodulatory candidates. To address this issue, we compiled a comprehensive map of functional immune cell states of mouse in response to 12 pathogens. To create this atlas, we developed a single-cell-based computational method that partitions heterogeneous cell types into functionally distinct states and simultaneously identifies modules of functionally relevant genes characterizing them. We identified 295 functional states using 114 datasets of six immune cell types, creating a Catalogus Immune Muris. As a result, we found common as well as pathogen-specific functional states and experimentally characterized the function of an unknown macrophage cell state that modulates the response to Salmonella Typhimurium infection. Thus, we expect our Catalogus Immune Muris to be an important resource for studies aiming at discovering new immunomodulatory candidates.

scholarly journals The Crossroads of Glycoscience, Infection, and Immunology

2021 ◽  
Vol 12 ◽  
Author(s):  
Tanya R. McKitrick ◽  
Margaret E. Ackerman ◽  
Robert M. Anthony ◽  
Clay S. Bennett ◽  
Michael Demetriou ◽  
...  
Keyword(s):  
Immune Responses ◽  
Host Response ◽  
Immune Cell ◽  
Microbial Infection ◽  
Surface Receptors ◽  
Host Interactions ◽  
Host Immune Responses ◽  
Immune Mediators ◽  
Immune Mediated ◽  
And Function

Advances in experimental capabilities in the glycosciences offer expanding opportunities for discovery in the broad areas of immunology and microbiology. These two disciplines overlap when microbial infection stimulates host immune responses and glycan structures are central in the processes that occur during all such encounters. Microbial glycans mediate host-pathogen interactions by acting as surface receptors or ligands, functioning as virulence factors, impeding host immune responses, or playing other roles in the struggle between host and microbe. In the context of the host, glycosylation drives cell–cell interactions that initiate and regulate the host response and modulates the effects of antibodies and soluble immune mediators. This perspective reports on a workshop organized jointly by the National Institute of Allergy and Infectious Diseases and the National Institute of Dental and Craniofacial Research in May 2020. The conference addressed the use of emerging glycoscience tools and resources to advance investigation of glycans and their roles in microbe-host interactions, immune-mediated diseases, and immune cell recognition and function. Future discoveries in these areas will increase fundamental scientific understanding and have the potential to improve diagnosis and treatment of infections and immune dysregulation.

scholarly journals Aging-Related Cellular, Structural and Functional Changes in the Lymph Nodes: A Significant Component of Immunosenescence? An Overview

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3148
Author(s):  
Marta Cakala-Jakimowicz ◽  
Paulina Kolodziej-Wojnar ◽  
Monika Puzianowska-Kuznicka
Keyword(s):  
Immune System ◽  
Immune Responses ◽  
Lymph Nodes ◽  
Immune Cell ◽  
Humoral Response ◽  
The Elderly ◽  
Cell Types ◽  
Functional Changes ◽  
B Cell Homeostasis

Aging affects all tissues and organs. Aging of the immune system results in the severe disruption of its functions, leading to an increased susceptibility to infections, an increase in autoimmune disorders and cancer incidence, and a decreased response to vaccines. Lymph nodes are precisely organized structures of the peripheral lymphoid organs and are the key sites coordinating innate and long-term adaptive immune responses to external antigens and vaccines. They are also involved in immune tolerance. The aging of lymph nodes results in decreased cell transport to and within the nodes, a disturbance in the structure and organization of nodal zones, incorrect location of individual immune cell types and impaired intercellular interactions, as well as changes in the production of adequate amounts of chemokines and cytokines necessary for immune cell proliferation, survival and function, impaired naïve T- and B-cell homeostasis, and a diminished long-term humoral response. Understanding the causes of these stromal and lymphoid microenvironment changes in the lymph nodes that cause the aging-related dysfunction of the immune system can help to improve long-term immune responses and the effectiveness of vaccines in the elderly.

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