Top 8 Biorxiv Papers Today in Immunology


2.022 Mikeys
#1. Rotavirus infection induces both interferon (IFN) and inflammatory resistance by re-programming intestinal IFN receptor signaling
Adrish Sen, Nima Namsa, Ningguo Feng, Harry B Greenberg
Rotaviruses (RV) cause acute severe diarrhea and are highly infectious in homologous host species. However, RV infection does not cause appreciable intestinal inflammation and homologous RV replication resists the antiviral effects of different interferon (IFN) types. In suckling mice, we found that homologous murine EW RV triggers sustained induction of IFNs, but not the amplification of interferon-stimulated genes (ISGs) or inflammatory transcripts. IFNs can trigger both apoptosis and inflammatory necroptotic cell death pathways. However, during RV infection intestinal epithelial cells (IECs) are severely impaired in the cleavage of different caspases regulating intrinsic and extrinsic cell death. Inhibition of caspase cleavage occurs in both RV-infected and -uninfected bystander IECs. In contrast, RV induces cleavage of receptor-interacting protein 1 (RIP1), a master regulator of cell death and survival decisions. Comparison of IFN-resistant (homologous) and -sensitive (heterologous) RV strains in mice demonstrates that...
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biorxivpreprint: Rotavirus infection induces both interferon (IFN) and inflammatory resistance by re-programming intestinal IFN receptor signaling https://t.co/6fho2wLcgS #bioRxiv
biorxiv_immuno: Rotavirus infection induces both interferon (IFN) and inflammatory resistance by re-programming intestinal IFN receptor signaling https://t.co/OV7RbApmgW #biorxiv_immuno
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Sample Sizes : [4, 3, 3, 3]
Authors: 4
Total Words: 23031
Unqiue Words: 4741

2.0 Mikeys
#2. A targeted multi-omic analysis approach measures protein expression and low abundance transcripts on the single cell level
Florian Mair, Jami R. Erickson, Valentin Voillet, Yannick Simoni, Timothy Bi, Aaron J. Tyznik, Jody Martin, Raphael Gottardo, Evan W. Newell, Martin Prlic
High throughput single-cell RNA sequencing (sc-RNAseq) has become a frequently used tool to assess immune cell function and heterogeneity. Recently, the combined measurement of RNA and protein expression by sequencing was developed, which is commonly known as CITE-Seq. Acquisition of protein expression data along with transcriptome data resolves some of the limitations inherent to only assessing transcript, but also nearly doubles the sequencing read depth required per single cell. Furthermore, there is still a paucity of analysis tools to visualize combined transcript-protein datasets. Here, we describe a novel targeted transcriptomics approach that combines analysis of over 400 genes with simultaneous measurement of over 40 proteins on more than 25,000 cells. This targeted approach requires only about 1/10 of the read depth compared to a whole transcriptome approach while retaining high sensitivity for low abundance transcripts. To analyze these multi-omic transcript-protein datasets, we adapted One-SENSE for intuitive...
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Mair and Erickson, A targeted multi-omic analysis approach measures protein expression and low abundance transcripts on the single cell level

Repository: Targeted_transcriptomics
User: MairFlo
Language: R
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Authors: 10
Total Words: 11473
Unqiue Words: 3616

1.998 Mikeys
#3. Oral tenofovir disoproxil fumarate/emtricitabine for HIV pre-exposure prophylaxis increases expression of type I/III interferon-stimulated factors in the gastrointestinal tract but not in the blood
Sean M. Hughes, Claire N. Levy, Fernanda Calienes, Joanne D. Stekler, Urvashi Pandey, Lucia Vojtech, Alicia R. Berard, Kenzie Birse, Laura Noel-Romas, Brian Richardson, Jackelyn Golden, Michael Cartwright, Ann C. Collier, Claire E. Stevens, Marcel E. Curlin, Timothy H. Holtz, Nelly Mugo, Elizabeth Irungu, Elly Katabira, Timothy Muwonge, Javier R Lama, Jared M. Baeten, Adam Burgener, Jairam R. Lingappa, M. Juliana McElrath, Romel Mackelprang, Ian McGowan, Ross D. Cranston, Mark J. Cameron, Florian Hladik
Tenofovir disoproxil fumarate and emtricitabine are used for HIV treatment and pre-exposure prophylaxis. Previously, we found that topical rectal application of tenofovir 1% gel caused many gene expression changes. Here, we measured RNA and protein expression in several clinical trials of oral administration in HIV-uninfected individuals (using microarrays, RNAseq, droplet digital PCR, mass spectrometry, and microscopy). We found tens to hundreds of differentially expressed genes in the gastrointestinal tract, but none in the blood or female reproductive tract. In rectal samples from one trial, most of the 13 upregulated genes were related to type I/III interferon signaling. Similar changes were seen at the protein level in the same trial and in the duodenum and rectum in another trial. We conclude that tenofovir disoproxil fumarate and emtricitabine have little effect on gene expression in the blood or female reproductive tract but increase type I/III interferon signaling in the gut. This effect may enhance their anti-viral...
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biorxivpreprint: Oral tenofovir disoproxil fumarate/emtricitabine for HIV pre-exposure prophylaxis increases expression of type I/III interferon-stimulated factors in the gastrointestinal tract but not in the blood https://t.co/V0rO8OhGNn #bioRxiv
biorxiv_immuno: Oral tenofovir disoproxil fumarate/emtricitabine for HIV pre-exposure prophylaxis increases expression of type I/III ... https://t.co/EzTQnNly1n #biorxiv_immuno
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Authors: 30
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1.996 Mikeys
#4. CD4+ Th immunogenicity of the Ascaris spp. secreted products
Friederike Ebner, Eliot Morrison, Miriam Bertazzon, Ankur Midha, Susanne Hartmann, Christian Freund, Miguel &Aacutelvaro-Benito
Ascaris spp. is a major health problem of humans and animals alike, and understanding the immunogenicity of its antigens is required for developing urgently needed vaccines. The parasite-secreted products represent the most relevant, yet highly complex (>250 proteins) antigens of Ascaris spp. as defining the pathogen-host interplay. We applied an in vitro antigen processing system coupled to quantitative proteomics to identify potential CD4+ Th cell epitopes in Ascaris suum-secreted products. This approach restricts the theoretical list of epitopes, based on affinity prediction, by a factor of ~1200. More importantly, selection of 2 candidate peptides based on experimental evidence demonstrated the presence of epitope-reactive T cells in Ascaris-specific T cell lines generated from healthy human individuals. Thus, this stringent work pipeline identifies a human haplotype-specific T cell epitope of a major human pathogen. The methodology described represents an easily adaptable platform for characterization of highly complex...
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Authors: 7
Total Words: 8348
Unqiue Words: 3003

1.992 Mikeys
#5. Differential pulmonary immunopathologic response of domestic sheep (Ovis aries) and bighorn sheep (Ovis canadensis) to Mycoplasma ovipneumoniae infection: a retrospective study
Paige C Grossman, David A Schneider, Donald P Knowles, Margaret A. Highland
Mycoplasma ovipneumoniae is a respiratory pathogen that can impact domestic sheep (Ovis aries; DS) and bighorn sheep (Ovis canadensis; BHS). Experimental and field data have indicated BHS are more susceptible than DS to developing polymicrobial pneumonia associated with Mycoplasma ovipneumoniae infection. We hypothesized that DS and BHS have a differential immunopathologic pulmonary response to M. ovipneumoniae infection. A retrospective study was performed using formalin-fixed, paraffin-embedded (FFPE) lung tissue from DS and BHS without and with M. ovipneumoniae detected in the lung tissue (n=8 per group). While each M. ovipneumoniae positive lung sample had microscopic changes typical of infection, including hyperplasia of intrapulmonary bronchus-associated lymphoid tissue (BALT) and respiratory epithelium, DS exhibited a more robust and well-organized BALT formation as compared to BHS. Immunohistochemistry was performed with antibodies reactive in FFPE tissues and specific for leukocyte and cytokine markers: T cell marker CD3,...
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1.992 Mikeys
#6. An atlas of infiltrated B-lymphocytes in breast cancer revealed by paired single-cell RNA-sequencing and antigen receptor profiling
qingtao hu, yu hong, pan qi, guangqing lu, xueying mai, sheng xu, xiaoying he, yu guo, linlin gao, zhiyi jing, jiawen wang, tao cai, yu zhang
While it has been well-recognized that T-cell mediated adaptive cellular immunity plays important roles in cancer immune response and tumor control, the roles of B lymphocytes in tumor development and therapy have only been proposed until recently, and are still mostly controversial. To gain mechanistic insights into the origin and dynamics of tumor infiltrated immune cells, especially B lymphocytes, we combine single-cell RNA-sequencing and antigen receptor lineage analysis to characterize a large number of triple-negative breast cancer (TNBC) infiltrated immune cells and present a comprehensive atlas of infiltrated B-lymphocytes in TNBC, the most aggressive breast cancer subtype. We demonstrate that TNBC infiltrated B cells showed more mature and memory B cell characteristics, as well as high clonality and extensive IgH class switching recombination and somatic hypermutations. The B cell signatures based on single-cell RNA-seq results are significantly associated with improved survival for TNBC patients and provide better...
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Authors: 13
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1.992 Mikeys
#7. Long term outcomes of Everolimus therapy in de novo liver transplantation: a systematic review and meta-analysis of randomized controlled trials
Khalid Ibrahim Bzeizi, Smith Richard, Ali AlBenmousa, Dama Madhukar, Aba AlKhail Faisal, Jalan Rajiv, Broering Dieter
Background: Risk of nephrotoxicity in liver transplant patients on calcineurin inhibitors (CnIs) is a concern. Several controlled trials reported benefit of Everolimus (EVR) in minimizing this risk when combined with a reduced CnIs dose. Objective: To systematically review the efficacy and safety of EVR, alone or with reduced CnI dose, as compared to CnI alone post liver transplantation. Methods: We searched MEDLINE, Scopus and the Cochrane Library for randomized controlled trials (RCTs) comparing EVR and CnI based regimens post liver transplanation. Assessment of studies and data extraction was undertaken independently. Results: Eight studies were selected describing 769 patients. Cockcroft-Gault GFR (CG-GFR) was significantly higher at one (p=0.05), 3 & 5 years (p=0.030) in patients receiving EVR as compared to those receiving CnI therapy. The composite end point of efficacy failure was similar between the two arms after 1, 3 & 5 years of study. Higher number of patients discontinued EVR due to adverse effects in one year,...
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Authors: 7
Total Words: 4379
Unqiue Words: 1292

1.99 Mikeys
#8. Microarray Gene Expression DatasetRe-Analysis Reveals Variability in InfluenzaInfection and Vaccination.
Lavida RK Rogers, Gustavo de los Campos, George Mias
Influenza, a communicable disease affects thousands of people worldwide. Young children, elderly, immunocompromised individuals and pregnant women are at higher risk for being infected by the influenza virus. Our study aims to highlight differentially expressed genes in influenza disease compared to influenza vaccination. We also investigate genetic variation due to the age and sex of samples. To accomplish our goals, we conducted a meta-analysis using publicly available microarray expression data. Our inclusion criteria included subjects with influenza, subjects who received the influenza vaccine and healthy controls. We curated 18 microarray datasets for a total of 3,481 samples (1,277 controls, 297 influenza infection, 1,907 influenza vaccination). We pre-processed the raw microarray expression data in R using packages available to pre-process Affymetrix and Illumina microarray platforms. We used a Box-Cox power transformation of the data prior to our down-stream analysis to identify differentially expressed genes. We used a...
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