scholarly journals Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation

2021 ◽  
Author(s):  
Hye Kyung Lee ◽  
Ludwig Knabl ◽  
Ludwig Knabl ◽  
Manuel Wieser ◽  
Anna Mur ◽  
...  
Keyword(s):  
Immune Response ◽  
Hospitalized Patients ◽  
Single Amino Acid ◽  
Escape Mutation ◽  
Rna Seq ◽  
Single Amino Acid Change ◽  
Fast Spreading ◽  
Predominant Variant ◽  
Altered Immune Response ◽  
Immune Pathways

Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. B.1.1.7 (VOC-202012/01) has become the predominant variant in many countries and a new lineage (VOC-202102/02) harboring the E484K escape mutation in the B.1.1.7 background emerged in February 2021. This variant is of concern due to reduced neutralizing activity by vaccine-elicited antibodies. However, it is not known whether this single amino acid change leads to an altered immune response. Here, we investigate differences in the immune transcriptome in hospitalized patients infected with either B.1.1.7 (n=28) or B.1.1.7+E484K (n=12). RNA-seq conducted on PBMCs isolated within five days after the onset of COVID symptoms demonstrated elevated activation of specific immune pathways, including JAK-STAT signaling, in B.1.1.7+E484K patients as compared to B.1.1.7. Longitudinal transcriptome studies demonstrated a delayed dampening of interferon-activated pathways in B.1.1.7+E484K patients. Prior vaccination with BNT162b vaccine (n=8 one dose; n=1 two doses) reduced the transcriptome inflammatory response to B.1.1.7+E484K infection relative to unvaccinated patients. Lastly, the immune transcriptome of patients infected with additional variants (B.1.258, B.1.1.163 and B.1.7.7) displayed a reduced activation compared to patients infected with B.1.1.7. Acquisition of the E484K substitution in the B.1.1.7 background elicits an altered immune response, which could impact disease progression.

scholarly journals A single-nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor alters the development of host immunity

2020 ◽  
Vol 6 (6) ◽  
pp. eaaw6957 ◽  
Author(s):  
Munir Akkaya ◽  
Abhisheka Bansal ◽  
Patrick W. Sheehan ◽  
Mirna Pena ◽  
Alvaro Molina-Cruz ◽  
...  
Keyword(s):  
Immune Response ◽  
Single Nucleotide Polymorphism ◽  
Transcription Factor ◽  
Plasmodium Berghei ◽  
Malaria Parasite ◽  
Interferon Γ ◽  
Single Amino Acid ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Single Amino Acid Change

The acquisition of malaria immunity is both remarkably slow and unpredictable. At present, we know little about the malaria parasite genes that influence the host’s ability to mount a protective immune response. Here, we show that a single-nucleotide polymorphism (SNP) resulting in a single amino acid change (S to F) in an ApiAP2 transcription factor in the rodent malaria parasite Plasmodium berghei (Pb) NK65 allowed infected mice to mount a T helper cell 1 (TH1)–type immune response that controlled subsequent infections. As compared to PbNK65S, PbNK65F parasites differentially expressed 46 genes, most of which are predicted to play roles in immune evasion. PbNK65F infections resulted in an early interferon-γ response and a later expansion of germinal centers, resulting in high levels of infected red blood cell–specific TH1-type immunoglobulin G2b (IgG2b) and IgG2c antibodies. Thus, the Pb ApiAP2 transcription factor functions as a critical parasite virulence factor in malaria infections.

scholarly journals Impact of BNT162b First Vaccination on the Immune Transcriptome of Elderly Patients Infected with the B.1.351 SARS-CoV-2 Variant

2021 ◽  
Author(s):  
Ludwig Knabl ◽  
Hye Kyung Lee ◽  
Manuel Wieser ◽  
Anna Mur ◽  
August Zabernigg ◽  
...  
Keyword(s):  
Immune Response ◽  
Time Course ◽  
Escape Mutation ◽  
Rna Seq ◽  
Prevention Measures ◽  
Interferon Stimulated Genes ◽  
Immunological Protection ◽  
Innate Antiviral Immunity ◽  
Full Protection ◽  
Stat Pathway

Abstract Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. The B.1.351 variant carrying the escape mutation E484K in the receptor binding domain is of particular concern due to reduced immunological protection following vaccination. Protection can manifest as early as 10 days following immunization with full protection two weeks following the second dose, but the course is not well-characterized for variants. Here, we investigated the immune transcriptome of six elderly individuals (average age 82 yr.) from an old people’s home, who contracted B.1.351, with four having received the first dose of BNT162b eight to 11 days prior to the onset of COVID-19 symptoms. The patients were hospitalized and received dexamethasone treatment. Immune transcriptomes were established from PBMCs approximately 10 and 35 days after the onset of COVID-19 symptomology. RNA-seq revealed a more intensive immune response in vaccinated patients as compared to unvaccinated ones. Specifically, transcription factors linked to the JAK/STAT pathway, interferon stimulated genes, and genes associated with innate antiviral immunity and COVID-19-SARS-CoV-2 infection were highly enriched in vaccinated patients. This rendered the transcriptomes of the older vaccinated group significantly different than older unvaccinated individuals infected at the same institution and more similar to the immune response of younger unvaccinated individuals (ages 48-62) following B.1.351 infection. All individuals in this study whether vaccinated or not were hospitalized due to B.1.351 infection and one vaccinated patient died illustrating that although an enhanced immune response was documented infection it was insufficient to protect from disease. This highlights the need for maintaining physical distancing and prevention measures throughout the time course of vaccination in older adults.

scholarly journals The antibody repertoire of colorectal cancer

2017 ◽  
Author(s):  
Seong Won Cha ◽  
Stefano Bonissone ◽  
Seungjin Na ◽  
Pavel A. Pevzner ◽  
Vineet Bafna
Keyword(s):  
Immune Response ◽  
Single Amino Acid ◽  
De Bruijn Graph ◽  
Rna Seq ◽  
Protein Databases ◽  
Sequencing Errors ◽  
Database Construction ◽  
De Bruijn ◽  
Occurrence Pattern ◽  
Standard Protein

Immunotherapy is becoming increasingly important in the fight against cancers, utilizing and manipulating the body's immune response to treat tumors. Understanding the immune repertoire - the collection of immunological proteins - of treated and untreated cells is possible at the genomic, but technically difficult at the protein level. Standard protein databases do not include the highly divergent sequences of somatic rearranged immunoglobulin genes, and may lead to missed identifications in a mass spectrometry search. We introduce a novel proteogenomic approach, AbScan, to identify these highly variable antibody peptides, by developing a customized antibody database construction method using RNA-seq reads aligned to immunoglobulin (Ig) genes. AbScan starts by filtering transcript (RNA-seq) reads that match the template for Ig genes. The retained reads are used to construct a repertoire graph using the 'split' de Bruijn graph: a graph structure that improves upon the standard de Bruijn graph to capture the high diversity of Ig genes in a compact manner. AbScan corrects for sequencing errors, and converts the graph to a format suitable for searching with MS/MS search tools. We used AbScan to create an antibody database from 90 RNA-seq colorectal tumor samples. Next, we used proteogenomics analysis to search MS/MS spectra of matched colorectal samples from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) against the AbScan generated database. AbScan identified 1,940 distinct antibody peptides. Correlating with previously identified Single Amino-Acid Variants (SAAVs) in the tumor samples, we identified 163 pairs (antibody peptide, SAAV) with significant co-occurrence pattern in the 90 samples. The presence of co-expressed antibody and mutated peptides was correlated with survival time of the individuals. Our results suggest that AbScan (https://github.com/csw407/AbScan.git) is an effective tool for a proteomic exploration of the immune response in cancers.

scholarly journals Whole-Genome Expression Profiling Reveals That Inhibition of Host Innate Immune Response Pathways by Ebola Virus Can Be Reversed by a Single Amino Acid Change in the VP35 Protein

2008 ◽  
Vol 82 (11) ◽  
pp. 5348-5358 ◽  
Author(s):  
Amy L. Hartman ◽  
Ling Ling ◽  
Stuart T. Nichol ◽  
Martin L. Hibberd
Keyword(s):  
Immune Response ◽  
Amino Acid ◽  
Host Cell ◽  
Innate Immune Response ◽  
Ebola Virus ◽  
Innate Immune ◽  
Single Amino Acid ◽  
Cell Responses ◽  
Single Amino Acid Change ◽  
Whole Genome Expression

ABSTRACT Ebola hemorrhagic fever is a rapidly progressing acute febrile illness characterized by high virus replication, severe immunosuppression, and case fatalities of ca. 80%. Inhibition of phosphorylation of interferon regulatory factor 3 (IRF-3) by the Ebola VP35 protein may block the host innate immune response and play an important role in the severity of disease. We used two precisely defined reverse genetics-generated Ebola viruses to investigate global host cell responses resulting from the inhibition of IRF-3 phosphorylation. The two viruses encoded either wild-type (WT) VP35 protein (recEbo-VP35/WT) or VP35 with an arginine (R)-to-alanine (A) amino acid substitution at position 312 (recEbo-VP35/R312A) within a previously defined IRF-3 inhibitory domain. When sucrose-gradient purified virus was used for infection, host cell whole-genome expression profiling revealed striking differences in human liver cell responses to these viruses differing by a single amino acid. The inhibition of host innate immune responses by WT Ebola virus was so potent that little difference in interferon and antiviral gene expression could be discerned between cells infected with purified WT, inactivated virus, or mock-infected cells. However, infection with recEbo-VP35/R312A virus resulted in a strong innate immune response including increased expression of MDA-5, RIG-I, RANTES, MCP-1, ISG-15, ISG-54, ISG-56, ISG-60, STAT1, IRF-9, OAS, and Mx1. The clear gene expression differences were obscured if unpurified virus stocks were used to initiate infection, presumably due to soluble factors present in virus-infected cell supernatant preparations. Ebola virus VP35 protein clearly plays a pivotal role in the potent inhibition of the host innate immune responses, and the present study indicates that VP35 has a wider effect on host cell responses than previously shown. The ability to eliminate this inhibitory effect with a single amino acid change in VP35 demonstrates the critical role this protein must play in the severe aspects this highly fatal disease.

scholarly journals Impact of BNT162b first vaccination on the immune transcriptome of elderly patients infected with the B.1.351 SARS-CoV-2 variant

2021 ◽  
Author(s):  
Ludwig Knabl ◽  
Hye Kyung Lee ◽  
Manuel Wieser ◽  
Anna Mur ◽  
August Zabernigg ◽  
...  
Keyword(s):  
Immune Response ◽  
Escape Mutation ◽  
Severe Illness ◽  
Rna Seq ◽  
Interferon Stimulated Genes ◽  
Younger Age ◽  
Comparative Group ◽  
Innate Antiviral Immunity ◽  
The Impact

Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. The B.1.351 variant carrying the escape mutation E484K in the receptor binding domain (RBD) is of particular concern, with widespread escape from monoclonal antibody neutralization and a limited protection of patients having received the first dose of the BNT162b vaccine. It is known that completion of two serial immunizations is required for adequate protection; however, characterization of immune responses in individuals who have received only one dose has not been completely defined. There is also a paucity of information on the impact of vaccination on the immune transcriptome upon infection with SARS-CoV-2 variants. Here, we investigate the immune transcriptome of six elderly individuals (average age 82 yr.) from an old people's home, who contracted B.1.351, with four having received the first dose of BNT162b about two weeks prior to the onset of COVID-19 symptoms. The patients were hospitalized and received dexamethasone treatment. Immune transcriptomes were established from PBMCs approximately 10 days and 35 days after the onset of COVID-19 symptomology. RNA-seq revealed a more intensive immune response in vaccinated patients as compared to unvaccinated ones. Specifically, transcription factors linked to the JAK/STAT pathway, interferon stimulated genes (ISGs), and genes associated with innate antiviral immunity and COVID-19-SARS-CoV-2 infection are highly enriched in vaccinated patients. The transcriptomes of the older vaccinated group were more similar to a younger (age 48-62) comparative group than those of the older unvaccinated group. Our study demonstrates an enhanced immune transcriptome response in B.1.351 patients that had received their first vaccination within 11 days prior to developing COVID-19 illness as compared to unvaccinated patients from the same old-people's home. Our study also reveals that induction of immune-regulated genes in vaccinated individuals was insufficient to protect from disease. This highlights the continued risk for severe illness shortly after vaccination, before a protective immune response has been achieved and reinforces the need for vaccinated adults to continue physical distancing and prevention behaviors.

scholarly journals Integration of tumor inflammation, cell proliferation, and traditional biomarkers improves prediction of immunotherapy resistance and response

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sarabjot Pabla ◽  
R. J. Seager ◽  
Erik Van Roey ◽  
Shuang Gao ◽  
Carrie Hoefer ◽  
...  
Keyword(s):  
Immune Response ◽  
Cell Proliferation ◽  
Cell Activation ◽  
Response Rate ◽  
Checkpoint Inhibitors ◽  
Host Immune Response ◽  
Gene Signature ◽  
B Cell Activation ◽  
Rna Seq ◽  
Multiple Tumor

Abstract Background Contemporary to the rapidly evolving landscape of cancer immunotherapy is the equally changing understanding of immune tumor microenvironments (TMEs) which is crucial to the success of these therapies. Their reliance on a robust host immune response necessitates clinical grade measurements of immune TMEs at diagnosis. In this study, we describe a stable tumor immunogenic profile describing immune TMEs in multiple tumor types with ability to predict clinical benefit from immune checkpoint inhibitors (ICIs). Methods A tumor immunogenic signature (TIGS) was derived from targeted RNA-sequencing (RNA-seq) and gene expression analysis of 1323 clinical solid tumor cases spanning 35 histologies using unsupervised analysis. TIGS correlation with ICI response and survival was assessed in a retrospective cohort of NSCLC, melanoma and RCC tumor blocks, alone and combined with TMB, PD-L1 IHC and cell proliferation biomarkers. Results Unsupervised clustering of RNA-seq profiles uncovered a 161 gene signature where T cell and B cell activation, IFNg, chemokine, cytokine and interleukin pathways are over-represented. Mean expression of these genes produced three distinct TIGS score categories: strong (n = 384/1323; 29.02%), moderate (n = 354/1323; 26.76%), and weak (n = 585/1323; 44.22%). Strong TIGS tumors presented an improved ICI response rate of 37% (30/81); with highest response rate advantage occurring in NSCLC (ORR = 36.6%; 16/44; p = 0.051). Similarly, overall survival for strong TIGS tumors trended upward (median = 25 months; p = 0.19). Integrating the TIGS score categories with neoplastic influence quantified via cell proliferation showed highly proliferative and strong TIGS tumors correlate with significantly higher ICI ORR than poorly proliferative and weak TIGS tumors [14.28%; p = 0.0006]. Importantly, we noted that strong TIGS and highly [median = not achieved; p = 0.025] or moderately [median = 16.2 months; p = 0.025] proliferative tumors had significantly better survival compared to weak TIGS, highly proliferative tumors [median = 7.03 months]. Importantly, TIGS discriminates subpopulations of potential ICI responders that were considered negative for response by TMB and PD-L1. Conclusions TIGS is a comprehensive and informative measurement of immune TME that effectively characterizes host immune response to ICIs in multiple tumors. The results indicate that when combined with PD-L1, TMB and cell proliferation, TIGS provides greater context of both immune and neoplastic influences on the TME for implementation into clinical practice.

scholarly journals The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Julie M. Steinbrink ◽  
Rachel A. Myers ◽  
Kaiyuan Hua ◽  
Melissa D. Johnson ◽  
Jessica L. Seidelman ◽  
...  
Keyword(s):  
Immune Response ◽  
Bacterial Infection ◽  
Viral Infection ◽  
Fungal Infection ◽  
Host Response ◽  
Hospitalized Patients ◽  
Neutrophil Activation ◽  
Heme Biosynthesis ◽  
Transcriptional Analysis ◽  
Diagnostic Approaches

Abstract Background Candidemia is one of the most common nosocomial bloodstream infections in the United States, causing significant morbidity and mortality in hospitalized patients, but the breadth of the host response to Candida infections in human patients remains poorly defined. Methods In order to better define the host response to Candida infection at the transcriptional level, we performed RNA sequencing on serial peripheral blood samples from 48 hospitalized patients with blood cultures positive for Candida species and compared them to patients with other acute viral, bacterial, and non-infectious illnesses. Regularized multinomial regression was utilized to develop pathogen class-specific gene expression classifiers. Results Candidemia triggers a unique, robust, and conserved transcriptomic response in human hosts with 1641 genes differentially upregulated compared to healthy controls. Many of these genes corresponded to components of the immune response to fungal infection, heavily weighted toward neutrophil activation, heme biosynthesis, and T cell signaling. We developed pathogen class-specific classifiers from these unique signals capable of identifying and differentiating candidemia, viral, or bacterial infection across a variety of hosts with a high degree of accuracy (auROC 0.98 for candidemia, 0.99 for viral and bacterial infection). This classifier was validated on two separate human cohorts (auROC 0.88 for viral infection and 0.87 for bacterial infection in one cohort; auROC 0.97 in another cohort) and an in vitro model (auROC 0.94 for fungal infection, 0.96 for bacterial, and 0.90 for viral infection). Conclusions Transcriptional analysis of circulating leukocytes in patients with acute Candida infections defines novel aspects of the breadth of the human immune response during candidemia and suggests promising diagnostic approaches for simultaneously differentiating multiple types of clinical illnesses in at-risk, acutely ill patients.

scholarly journals Single amino acid changes in the mumps virus haemagglutinin–neuraminidase and polymerase proteins are associated with neuroattenuation

2009 ◽  
Vol 90 (7) ◽  
pp. 1741-1747 ◽  
Author(s):  
Tahir H. Malik ◽  
Candie Wolbert ◽  
Laura Nerret ◽  
Christian Sauder ◽  
Steven Rubin
Keyword(s):  
Amino Acid ◽  
Clinical Isolate ◽  
Amino Acid Change ◽  
Mumps Virus ◽  
Site Directed Mutagenesis ◽  
Single Amino Acid ◽  
Supporting Evidence ◽  
L Protein ◽  
Single Amino Acid Change

It has previously been shown that three amino acid changes, one each in the fusion (F; Ala/Thr-91→Thr), haemagglutinin–neuraminidase (HN; Ser-466→Asn) and polymerase (L; Ile-736→Val) proteins, are associated with attenuation of a neurovirulent clinical isolate of mumps virus (88-1961) following serial passage in vitro. Here, using full-length cDNA plasmid clones and site-directed mutagenesis, it was shown that the single amino acid change in the HN protein and to a lesser extent, the change in the L protein, resulted in neuroattenuation, as assessed in rats. The combination of both amino acid changes caused neuroattenuation of the virus to levels previously reported for the clinical isolate following attenuation in vitro. The amino acid change in the F protein, despite having a dramatic effect on protein function in vitro, was previously shown to not be involved in the observed neuroattenuation, highlighting the importance of conducting confirmatory in vivo studies. This report provides additional supporting evidence for the role of the HN protein as a virulence factor and, as far as is known, is the first report to associate an amino acid change in the L protein with mumps virus neuroattenuation.

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