scholarly journals Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hesham ElAbd ◽  
Frauke Degenhardt ◽  
Tomas Koudelka ◽  
Ann-Kristin Kamps ◽  
Andreas Tholey ◽  
...  
Keyword(s):  
Source Code ◽  
Adaptive Immune System ◽  
Human Leukocyte ◽  
Specific Identification ◽  
Leukocyte Antigen ◽  
Interactive Analysis ◽  
Adaptive Immune ◽  
Link Type ◽  
Online Tutorials

Abstract Background The human leukocyte antigen (HLA) proteins play a fundamental role in the adaptive immune system as they present peptides to T cells. Mass-spectrometry-based immunopeptidomics is a promising and powerful tool for characterizing the immunopeptidomic landscape of HLA proteins, that is the peptides presented on HLA proteins. Despite the growing interest in the technology, and the recent rise of immunopeptidomics-specific identification pipelines, there is still a gap in data-analysis and software tools that are specialized in analyzing and visualizing immunopeptidomics data. Results We present the IPTK library which is an open-source Python-based library for analyzing, visualizing, comparing, and integrating different omics layers with the identified peptides for an in-depth characterization of the immunopeptidome. Using different datasets, we illustrate the ability of the library to enrich the result of the identified peptidomes. Also, we demonstrate the utility of the library in developing other software and tools by developing an easy-to-use dashboard that can be used for the interactive analysis of the results. Conclusion IPTK provides a modular and extendable framework for analyzing and integrating immunopeptidomes with different omics layers. The library is deployed into PyPI at https://pypi.org/project/IPTKL/ and into Bioconda at https://anaconda.org/bioconda/iptkl, while the source code of the library and the dashboard, along with the online tutorials are available at https://github.com/ikmb/iptoolkit.

scholarly journals Hypothetical COVID-19 protection mechanism: hints from centenarians

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Franca Rosa Guerini ◽  
Matteo Cesari ◽  
Beatrice Arosio
Keyword(s):  
Adaptive Immune Response ◽  
Human Leukocyte ◽  
Human Longevity ◽  
Biological Mechanisms ◽  
Protection Mechanism ◽  
Leukocyte Antigen ◽  
Adaptive Immune ◽  
Life Threatening ◽  
Coronavirus Infection ◽  
Rule Out

AbstractThe risk of serious complications and the fatality rate due to COVID-19 pandemic have proven particularly higher in older persons, putting a further strain in healthcare system as we dramatically observed.COVID-19 is not exclusively gerophile (géro “old” and philia “love”) as young people can be infected, even if older people experience more severe symptoms and mortality due to their greater frailty. Indeed, frailty could complicate the course of COVID-19, much more than the number of years lived. As demonstration, there are centenarians showing remarkable capacity to recover after coronavirus infection.We hypothesize that centenarian’s portfolio could help in identifying protective biological mechanisms underlying the coronavirus infection.The human leukocyte antigen (HLA) is one of the major genetic regions associated with human longevity, due to its central role in the development of adaptive immune response and modulation of the individual’s response to life threatening diseases. The HLA locus seems to be crucial in influencing susceptibility and severity of COVID-19.In this hypothesis, we assume that the biological process in which HLA are involved may explain some aspects of coronavirus infection in centenarians, although we cannot rule out other biological mechanisms that these extraordinary persons are able to adopt to cope with the infection.

scholarly journals Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium

2020 ◽  
Vol 8 (5) ◽  
pp. 720 ◽  
Author(s):  
Meichen Pan ◽  
Matthew A. Nethery ◽  
Claudio Hidalgo-Cantabrana ◽  
Rodolphe Barrangou
Keyword(s):  
Genome Engineering ◽  
Rare Variants ◽  
Adaptive Immune System ◽  
Effector Proteins ◽  
Type I ◽  
Human Gut ◽  
Adaptive Immune ◽  
Naturally Occurring ◽  
History Of

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated cas) systems constitute the adaptive immune system in prokaryotes, which provides resistance against bacteriophages and invasive genetic elements. The landscape of applications in bacteria and eukaryotes relies on a few Cas effector proteins that have been characterized in detail. However, there is a lack of comprehensive studies on naturally occurring CRISPR-Cas systems in beneficial bacteria, such as human gut commensal Bifidobacterium species. In this study, we mined 954 publicly available Bifidobacterium genomes and identified CRIPSR-Cas systems in 57% of these strains. A total of five CRISPR-Cas subtypes were identified as follows: Type I-E, I-C, I-G, II-A, and II-C. Among the subtypes, Type I-C was the most abundant (23%). We further characterized the CRISPR RNA (crRNA), tracrRNA, and PAM sequences to provide a molecular basis for the development of new genome editing tools for a variety of applications. Moreover, we investigated the evolutionary history of certain Bifidobacterium strains through visualization of acquired spacer sequences and demonstrated how these hypervariable CRISPR regions can be used as genotyping markers. This extensive characterization will enable the repurposing of endogenous CRISPR-Cas systems in Bifidobacteria for genome engineering, transcriptional regulation, genotyping, and screening of rare variants.

Characterization of a novel human leukocyte antigen-DQB1 allele, DQB1*030504+

2006 ◽  
Vol 68 (2) ◽  
pp. 189-190 ◽  
Author(s):  
M. C. Visschedijk ◽  
P. van den Boomgaard ◽  
N. Kouprie ◽  
S. P. M. Lems ◽  
B. G. Hepkema
Keyword(s):  
Human Leukocyte Antigen ◽  
Human Leukocyte ◽  
Leukocyte Antigen ◽  
Dqb1 Allele

Identification and characterization of human leukocyte antigen class I ligands in renal cell carcinoma cells

2011 ◽  
Vol 5 (9-10) ◽  
pp. 569-569
Author(s):  
Barbara Seliger ◽  
Sven P. Dressler ◽  
Chiara Massa ◽  
Christian V. Recktenwald ◽  
Florian Altenberend ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Human Leukocyte Antigen ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Human Leukocyte Antigen Class ◽  
Human Leukocyte ◽  
Carcinoma Cells ◽  
Leukocyte Antigen ◽  
Identification And Characterization

Characterization of two new human leukocyte antigen alleles: HLA‐A *02:982 and HLA‐C*04:441

HLA ◽  
2021 ◽  
Author(s):  
Maria Loginova ◽  
Daria Smirnova ◽  
Svetlana Kutyavina ◽  
Konstanin Kashin ◽  
Igor Paramonov
Keyword(s):  
Human Leukocyte Antigen ◽  
Human Leukocyte ◽  
Leukocyte Antigen

Characterization of two new human leukocyte antigen class I alleles B*0829 and Cw*0736

2006 ◽  
Vol 68 (3) ◽  
pp. 267-268 ◽  
Author(s):  
A. Balas ◽  
M. Alonso-Nieto ◽  
F. García-Sánchez ◽  
J. L. Vicario
Keyword(s):  
Human Leukocyte Antigen ◽  
Human Leukocyte Antigen Class ◽  
Human Leukocyte ◽  
Class I ◽  
Leukocyte Antigen ◽  
Leukocyte Antigen Class I

scholarly journals HLA Immune Function Genes in Autism

2012 ◽  
Vol 2012 ◽  
pp. 1-13 ◽  
Author(s):  
Anthony R. Torres ◽  
Jonna B. Westover ◽  
Allen J. Rosenspire
Keyword(s):  
Immune Responses ◽  
Autoimmune Diseases ◽  
Human Leukocyte ◽  
Chromosome 6 ◽  
Genetic Studies ◽  
Leukocyte Antigen ◽  
Adaptive Immune ◽  
Hla Genes ◽  
Genetic Complexity ◽  
Antigen Presenting

The human leukocyte antigen (HLA) genes on chromosome 6 are instrumental in many innate and adaptive immune responses. The HLA genes/haplotypes can also be involved in immune dysfunction and autoimmune diseases. It is now becoming apparent that many of the non-antigen-presenting HLA genes make significant contributions to autoimmune diseases. Interestingly, it has been reported that autism subjects often have associations with HLA genes/haplotypes, suggesting an underlying dysregulation of the immune system mediated by HLA genes. Genetic studies have only succeeded in identifying autism-causing genes in a small number of subjects suggesting that the genome has not been adequately interrogated. Close examination of the HLA region in autism has been relatively ignored, largely due to extraordinary genetic complexity. It is our proposition that genetic polymorphisms in the HLA region, especially in the non-antigen-presenting regions, may be important in the etiology of autism in certain subjects.

scholarly journals Idiosyncratic Drug-Induced Liver Injury: Mechanistic and Clinical Challenges

2021 ◽  
Vol 22 (6) ◽  
pp. 2954
Author(s):  
Alison Jee ◽  
Samantha Christine Sernoskie ◽  
Jack Uetrecht
Keyword(s):  
Immune Response ◽  
Immune System ◽  
T Cell ◽  
Liver Injury ◽  
Clinical Manifestations ◽  
Adaptive Immune System ◽  
Human Leukocyte ◽  
Drug Induced ◽  
Drug Induced Liver Injury ◽  
Adaptive Immune

Idiosyncratic drug-induced liver injury (IDILI) remains a significant problem for patients and drug development. The idiosyncratic nature of IDILI makes mechanistic studies difficult, and little is known of its pathogenesis for certain. Circumstantial evidence suggests that most, but not all, IDILI is caused by reactive metabolites of drugs that are bioactivated by cytochromes P450 and other enzymes in the liver. Additionally, there is overwhelming evidence that most IDILI is mediated by the adaptive immune system; one example being the association of IDILI caused by specific drugs with specific human leukocyte antigen (HLA) haplotypes, and this may in part explain the idiosyncratic nature of these reactions. The T cell receptor repertoire likely also contributes to the idiosyncratic nature. Although most of the liver injury is likely mediated by the adaptive immune system, specifically cytotoxic CD8+ T cells, adaptive immune activation first requires an innate immune response to activate antigen presenting cells and produce cytokines required for T cell proliferation. This innate response is likely caused by either a reactive metabolite or some form of cell stress that is clinically silent but not idiosyncratic. If this is true it would make it possible to study the early steps in the immune response that in some patients can lead to IDILI. Other hypotheses have been proposed, such as mitochondrial injury, inhibition of the bile salt export pump, unfolded protein response, and oxidative stress although, in most cases, it is likely that they are also involved in the initiation of an immune response rather than representing a completely separate mechanism. Using the clinical manifestations of liver injury from a number of examples of IDILI-associated drugs, this review aims to summarize and illustrate these mechanistic hypotheses.

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