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Hypervariable T cell receptors (TCRs) play a key role in adaptive immunity, recognizing a vast diversity of pathogen-derived antigens. Our ability to extract clinically relevant information from large high-throughput sequencing of TCR repertoires (RepSeq) data is limited, because little is known about TCR-disease associations. We present Antigen-specific Lymphocyte Identification by Clustering of Expanded sequences (ALICE), a statistical approach that identifies TCR sequences actively involved in current immune responses from a single RepSeq sample and apply it to repertoires of patients with a variety of disorders-patients with autoimmune disease (ankylosing spondylitis [AS]), under cancer immunotherapy, or subject to an acute infection (live yellow fever [YF] vaccine). We validate the method with independent assays. ALICE requires no longitudinal data collection nor large cohorts, and it is directly applicable to most RepSeq datasets. Its results facilitate the identification of TCR variants associated with diseases and conditions, which can be used for diagnostics and rational vaccine design.
This article was published in the following journal.
Name: PLoS biology
Plant plasma membrane pattern recognition receptors are key to microbe sensing and activation of immunity to microbial invasion. Plants employ several types of such receptors that differ mainly in the...
Many different adjuvants are currently being developed for subunit vaccines against a number of pathogens and diseases. Rational design is increasingly used to develop novel vaccine adjuvants, which r...
The immune system is able to detect and eliminate nascent and developing tumors. Thus, T lymphocytes of the adaptive immunity recognize cancer cells by detecting tumor-associated antigens, whereas cer...
The extracellular matrix (ECM) is a complex network of proteins and proteoglycans secreted by keratinocytes, fibroblasts and immune cells. The function of the skin ECM has expanded from being a scaffo...
The immune system generates pathogen-tailored responses. The precise innate immune cell types and pathways that direct robust adaptive immune responses have not been fully characterized. By using fluo...
The purpose of this study is to investigate the mechanism of a successful immune response to hepatitis C virus (HCV) infection. Currently, it is believed that the immune system is involved...
The study concerns donors and patients receiving allogeneic stem cell haematopoietic transplantation. The aim of the study is to analyse HSC graft content in immune effector T (naive, memo...
Hypothesis: Treatment with raltegravir does not alter V(D)J recombination or immune responses to neoantigens. A process known as V(D)J recombination is essential for developing lymphocyte...
The aim of this study is the assessment B-cell immune responses in HIV-infected individuals.
Typhoid fever caused by Salmonella Typhi and Paratyphi causes over 21 million cases of febrile illness and 200,000 deaths are attributed to enteric fever each year. Typhoid fever is an ent...
55-kDa antigens found on HELPER-INDUCER T-LYMPHOCYTES and on a variety of other immune cell types. They are members of the immunoglobulin supergene family and are implicated as associative recognition elements in MAJOR HISTOCOMPATIBILITY COMPLEX class II-restricted immune responses. On T-lymphocytes they define the helper/inducer subset. T4 antigens also serve as INTERLEUKIN-15 receptors and bind to the HIV receptors, binding directly to the HIV ENVELOPE PROTEIN GP120.
55-kDa antigens found on HELPER-INDUCER T-LYMPHOCYTES and on a variety of other immune cell types. CD4 antigens are members of the immunoglobulin supergene family and are implicated as associative recognition elements in MAJOR HISTOCOMPATIBILITY COMPLEX class II-restricted immune responses. On T-lymphocytes they define the helper/inducer subset. CD4 antigens also serve as INTERLEUKIN-15 receptors and bind to the HIV receptors, binding directly to the HIV ENVELOPE PROTEIN GP120.
A conserved AMINO ACID SEQUENCE located in the intracellular domains of a family of transmembrane proteins involved in various IMMUNE RESPONSES. The CONSENSUS SEQUENCE of this motif is YXXL(or I)X(6-8)YXXL(or I) (where X denotes any amino acid). When phosphorylated ITAM motifs provide docking sites for PROTEIN TYROSINE KINASES of the Syk family thus forming signaling complexes which lead to activation of immune responses.
Collagen receptors are cell surface receptors that modulate signal transduction between cells and the EXTRACELLULAR MATRIX. They are found in many cell types and are involved in the maintenance and regulation of cell shape and behavior, including PLATELET ACTIVATION and aggregation, through many different signaling pathways and differences in their affinities for collagen isoforms. Collagen receptors include discoidin domain receptors, INTEGRINS, and glycoprotein VI.
A ubiquitously-expressed cysteine peptidase that exhibits carboxypeptidase activity. It is highly expressed in a variety of immune cell types and may play a role in inflammatory processes and immune responses.
Allergies Automimmune Disease Human Papillomavirus (HPV) Immunology Vaccine Immunology is the study of immunity and the defence mechanisms of the body. A greater understanding of immunology is needed to develop vaccines, understand ...
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...