sumrep: A Summary Statistic Framework for Immune Receptor Repertoire Comparison and Model Validation.

Abstract:

:The adaptive immune system generates an incredible diversity of antigen receptors for B and T cells to keep dangerous pathogens at bay. The DNA sequences coding for these receptors arise by a complex recombination process followed by a series of productivity-based filters, as well as affinity maturation for B cells, giving considerable diversity to the circulating pool of receptor sequences. Although these datasets hold considerable promise for medical and public health applications, the complex structure of the resulting adaptive immune receptor repertoire sequencing (AIRR-seq) datasets makes analysis difficult. In this paper we introduce sumrep, an R package that efficiently performs a wide variety of repertoire summaries and comparisons, and show how sumrep can be used to perform model validation. We find that summaries vary in their ability to differentiate between datasets, although many are able to distinguish between covariates such as donor, timepoint, and cell type for BCR and TCR repertoires. We show that deletion and insertion lengths resulting from V(D)J recombination tend to be more discriminative characterizations of a repertoire than summaries that describe the amino acid composition of the CDR3 region. We also find that state-of-the-art generative models excel at recapitulating gene usage and recombination statistics in a given experimental repertoire, but struggle to capture many physiochemical properties of real repertoires.

journal_name

Front Immunol

journal_title

Frontiers in immunology

authors

Olson BJ,Moghimi P,Schramm CA,Obraztsova A,Ralph D,Vander Heiden JA,Shugay M,Shepherd AJ,Lees W,Matsen FA 4th

doi

10.3389/fimmu.2019.02533

subject

Has Abstract

pub_date

2019-11-01 00:00:00

pages

2533

issn

1664-3224

journal_volume

10

pub_type

杂志文章
  • Targeting Head and Neck Cancer by Vaccination.

    abstract::Head and neck cancer (HNC) is a heterogeneous group of squamous cell cancers that affect the oral cavity, pharynx, and larynx. Worldwide, it is the sixth most common cancer but in parts of Southern and South-East Asia, HNC is one of the most common cancers. A significant proportion of HNC is driven by human papillomav...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2018.00830

    authors: Wang C,Dickie J,Sutavani RV,Pointer C,Thomas GJ,Savelyeva N

    更新日期:2018-04-23 00:00:00

  • Pulmonary Innate Immune Response Determines the Outcome of Inflammation During Pneumonia and Sepsis-Associated Acute Lung Injury.

    abstract::The lung is a primary organ for gas exchange in mammals that represents the largest epithelial surface in direct contact with the external environment. It also serves as a crucial immune organ, which harbors both innate and adaptive immune cells to induce a potent immune response. Due to its direct contact with the ou...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2020.01722

    authors: Kumar V

    更新日期:2020-08-04 00:00:00

  • The Immunomodulatory Potential of tolDCs Loaded with Heat Shock Proteins.

    abstract::Disease suppressive T cell regulation may depend on cognate interactions of regulatory T cells with self-antigens that are abundantly expressed in the inflamed tissues. Heat shock proteins (HSPs) are by their nature upregulated in stressed cells and therefore abundantly present as potential targets for such regulation...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2017.01690

    authors: van Eden W,Jansen MAA,de Wolf ACM,Ludwig IS,Leufkens P,Broere F

    更新日期:2017-11-30 00:00:00

  • Siplizumab, an Anti-CD2 Monoclonal Antibody, Induces a Unique Set of Immune Modulatory Effects Compared to Alemtuzumab and Rabbit Anti-Thymocyte Globulin In Vitro.

    abstract::Antibodies are commonly used in organ transplant induction therapy and to treat autoimmune disorders. The effects of some biologics on the human immune system remain incompletely characterized and a deeper understanding of their mechanisms of action may provide useful insights for their clinical application. The goal ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.592553

    authors: Binder C,Sellberg F,Cvetkovski F,Berglund E,Berglund D

    更新日期:2020-11-11 00:00:00

  • Development of CD4 T Cell Dependent Immunity Against N. brasiliensis Infection.

    abstract::Of all the microbial infections relevant to mammals the relationship between parasitic worms and what constitutes and regulates a host protective immune response is perhaps the most complex and evolved. Nippostrongylus brasiliensis is a tissue migrating parasitic roundworm of rodents that exemplifies many of the salie...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2013.00074

    authors: Harvie M,Camberis M,Le Gros G

    更新日期:2013-03-20 00:00:00

  • Interaction of the Factor H Family Proteins FHR-1 and FHR-5 With DNA and Dead Cells: Implications for the Regulation of Complement Activation and Opsonization.

    abstract::Complement plays an essential role in the opsonophagocytic clearance of apoptotic/necrotic cells. Dysregulation of this process may lead to inflammatory and autoimmune diseases. Factor H (FH), a major soluble complement inhibitor, binds to dead cells and inhibits excessive complement activation on their surface, preve...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.01297

    authors: Kárpáti É,Papp A,Schneider AE,Hajnal D,Cserhalmi M,Csincsi ÁI,Uzonyi B,Józsi M

    更新日期:2020-07-16 00:00:00

  • Immune Cell-Type Specific Ablation of Adapter Protein ADAP Differentially Modulates EAE.

    abstract::The cytosolic adhesion and degranulation-promoting adapter protein ADAP is expressed in various hematopoietic cells including T cells, NK cells, myeloid cells, and platelets but absent in mature B cells. The role of ADAP in T cell activation, proliferation and integrin activation is well-accepted. We previously demons...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2019.02343

    authors: Rudolph J,Meinke C,Voss M,Guttek K,Kliche S,Reinhold D,Schraven B,Reinhold A

    更新日期:2019-10-01 00:00:00

  • Ontogenic, Phenotypic, and Functional Characterization of XCR1(+) Dendritic Cells Leads to a Consistent Classification of Intestinal Dendritic Cells Based on the Expression of XCR1 and SIRPα.

    abstract::In the past, lack of lineage markers confounded the classification of dendritic cells (DC) in the intestine and impeded a full understanding of their location and function. We have recently shown that the chemokine receptor XCR1 is a lineage marker for cross-presenting DC in the spleen. Now, we provide evidence that i...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2014.00326

    authors: Becker M,Güttler S,Bachem A,Hartung E,Mora A,Jäkel A,Hutloff A,Henn V,Mages HW,Gurka S,Kroczek RA

    更新日期:2014-07-28 00:00:00

  • Precision Subtypes of T Cell-Mediated Rejection Identified by Molecular Profiles.

    abstract::Among kidney transplant recipients, the treatment of choice for acute T cell-mediated rejection (TCMR) with pulse steroids or antibody protocols has variable outcomes. Some rejection episodes are resistant to an initial steroid pulse, but respond to subsequent antibody protocols. The biological mechanisms causing the ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2015.00536

    authors: Kadota PO,Hajjiri Z,Finn PW,Perkins DL

    更新日期:2015-11-06 00:00:00

  • A System Dynamics Model to Predict the Human Monocyte Response to Endotoxins.

    abstract::System dynamics is a powerful tool that allows modeling of complex and highly networked systems such as those found in the human immune system. We have developed a model that reproduces how the exposure of human monocytes to lipopolysaccharides (LPSs) induces an inflammatory state characterized by high production of t...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2017.00915

    authors: Álvarez E,Toledano V,Morilla F,Hernández-Jiménez E,Cubillos-Zapata C,Varela-Serrano A,Casas-Martín J,Avendaño-Ortiz J,Aguirre LA,Arnalich F,Maroun-Eid C,Martín-Quirós A,Quintana Díaz M,López-Collazo E

    更新日期:2017-08-03 00:00:00

  • "Small" Intestinal Immunopathology Plays a "Big" Role in Lethal Cytokine Release Syndrome, and Its Modulation by Interferon-γ, IL-17A, and a Janus Kinase Inhibitor.

    abstract::Chimeric antigen receptor T cell (CART) therapy, administration of certain T cell-agonistic antibodies, immune check point inhibitors, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) and Toxic shock syndrome (TSS) caused by streptococcal as well as staphylococ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.01311

    authors: Kale SD,Mehrkens BN,Stegman MM,Kastelberg B,Carnes H,McNeill RJ,Rizzo A,Karyala SV,Coutermarsh-Ott S,Fretz JA,Sun Y,Koff JL,Rajagopalan G

    更新日期:2020-06-26 00:00:00

  • Histone H2A-Reactive B Cells Are Functionally Anergic in Healthy Mice With Potential to Provide Humoral Protection Against HIV-1.

    abstract::Peripheral tolerance is essential for silencing weakly autoreactive B cells that have escaped central tolerance, but it is unclear why these potentially pathogenic B cells are retained rather than being eliminated entirely. Release from peripheral tolerance restraint can occur under certain circumstances (i.e., strong...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.01565

    authors: Agazio A,Cimons J,Shotts KM,Guo K,Santiago ML,Pelanda R,Torres RM

    更新日期:2020-07-22 00:00:00

  • Hepatic-Specific Decrease in the Expression of Selenoenzymes and Factors Essential for Selenium Processing After Endotoxemia.

    abstract:Background:Selenium (Se) levels decrease in the circulation during acute inflammatory states and sepsis, and are inversely associated with morbidity and mortality. A more specific understanding of where selenoproteins and Se processing are compromised during insult is needed. We investigated the acute signaling respons...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.595282

    authors: Sherlock LG,Sjostrom K,Sian L,Delaney C,Tipple TE,Krebs NF,Nozik-Grayck E,Wright CJ

    更新日期:2020-11-05 00:00:00

  • CAR T Cell Therapy of Non-hematopoietic Malignancies: Detours on the Road to Clinical Success.

    abstract::Chimeric antigen receptor (CAR)-engineered T cells represent a breakthrough in personalized medicine. In this strategy, a patient's own T lymphocytes are genetically reprogrammed to encode a synthetic receptor that binds a tumor antigen, allowing T cells to recognize and kill antigen-expressing cancer cells. As a resu...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2018.02740

    authors: Long KB,Young RM,Boesteanu AC,Davis MM,Melenhorst JJ,Lacey SF,DeGaramo DA,Levine BL,Fraietta JA

    更新日期:2018-12-03 00:00:00

  • Vγ4 T Cells Inhibit the Pro-healing Functions of Dendritic Epidermal T Cells to Delay Skin Wound Closure Through IL-17A.

    abstract::Dendritic epidermal T cells (DETCs) and dermal Vγ4 T cells engage in wound re-epithelialization and skin inflammation. However, it remains unknown whether a functional link between Vγ4 T cell pro-inflammation and DETC pro-healing exists to affect the outcome of skin wound closure. Here, we revealed that Vγ4 T cell-der...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.00240

    authors: Li Y,Wang Y,Zhou L,Liu M,Liang G,Yan R,Jiang Y,Hao J,Zhang X,Hu X,Huang Y,Wang R,Yin Z,Wu J,Luo G,He W

    更新日期:2018-02-12 00:00:00

  • Peripheral Immune Cell Ratios and Clinical Outcomes in Seropositive Autoimmune Encephalitis: A Study by the Australian Autoimmune Encephalitis Consortium.

    abstract:Objective:To examine the utility of the peripheral blood neutrophil-to-lymphocyte ratio (NLR) and monocyte-to-lymphocyte ratio (MLR) as biomarkers of prognosis in seropositive autoimmune encephalitis (AE). Methods:In this multicenter study, we retrospectively analyzed 57 cases of seropositive AE with hospital admissio...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.597858

    authors: Broadley J,Wesselingh R,Seneviratne U,Kyndt C,Beech P,Buzzard K,Nesbitt C,D'Souza W,Brodtmann A,Kalincik T,Butzkueven H,O'Brien TJ,Monif M,Australian Autoimmune Encephalitis Consortium.

    更新日期:2021-01-14 00:00:00

  • Toward the Discovery of Host-Defense Peptides in Plants.

    abstract::Defense peptides protect multicellular eukaryotes from infections. In biomedical sciences, a dominant conceptual framework refers to defense peptides as host-defense peptides (HDPs), which are bifunctional peptides with both direct antimicrobial and immunomodulatory activities. No HDP has been reported in plants so fa...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.01825

    authors: Petre B

    更新日期:2020-08-21 00:00:00

  • Epigenetic Regulation of Interleukin 6 by Histone Acetylation in Macrophages and Its Role in Paraquat-Induced Pulmonary Fibrosis.

    abstract::Overexpression of interleukin 6 (IL-6) has been proposed to contribute to pulmonary fibrosis and other fibrotic diseases. However, the regulatory mechanisms and the role of IL-6 in fibrosis remain poorly understood. Epigenetics refers to alterations of gene expression without changes in the DNA sequence. Alternation o...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2016.00696

    authors: Hu L,Yu Y,Huang H,Fan H,Hu L,Yin C,Li K,Fulton DJ,Chen F

    更新日期:2017-01-30 00:00:00

  • Mast Cell Activation and Microtubule Organization Are Modulated by Miltefosine Through Protein Kinase C Inhibition.

    abstract::Mast cells play an effector role in innate immunity, allergy, and inflammation. Antigen-mediated activation of mast cells initiates signaling events leading to Ca2+ response and the release of inflammatory and allergic mediators from granules. Diseases associated with deregulated mast cell functions are hard to treat ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.01563

    authors: Rubíková Z,Sulimenko V,Paulenda T,Dráber P

    更新日期:2018-07-09 00:00:00

  • Tryptophan Metabolic Pathways Are Altered in Obesity and Are Associated With Systemic Inflammation.

    abstract::Background: Obesity is a condition with a complex pathophysiology characterized by both chronic low-grade inflammation and changes in the gut microbial ecosystem. These alterations can affect the metabolism of tryptophan (TRP), an essential amino acid and precursor of serotonin (5-HT), kynurenine (KYN), and indoles. T...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.00557

    authors: Cussotto S,Delgado I,Anesi A,Dexpert S,Aubert A,Beau C,Forestier D,Ledaguenel P,Magne E,Mattivi F,Capuron L

    更新日期:2020-04-15 00:00:00

  • Is the A-Chain the Engine That Drives the Diversity of C1q Functions? Revisiting Its Unique Structure.

    abstract::The immunopathological functions associated with human C1q are still growing in terms of novelty, diversity, and pathologic relevance. It is, therefore, not surprising that C1q is being recognized as an important molecular bridge between innate and adaptive immunity. The secret of this functional diversity, in turn, r...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.00162

    authors: Ghebrehiwet B,Kandov E,Kishore U,Peerschke EIB

    更新日期:2018-02-05 00:00:00

  • The Significance of Discordant Serology in Chagas Disease: Enhanced T-Cell Immunity to Trypanosoma cruzi in Serodiscordant Subjects.

    abstract:BACKGROUND:Subjects are considered infected with Trypanosoma cruzi when tested positive by at least two out of three serological tests, whereas a positive result in only one of up to three tests is termed "serodiscordant" (SD). Assessment of parasite-specific T-cell responses may help discriminate the uninfected from i...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2017.01141

    authors: Castro Eiro MD,Alvarez MG,Cooley G,Viotti RJ,Bertocchi GL,Lococo B,Albareda MC,De Rissio AM,Natale MA,Parodi C,Tarleton RL,Laucella SA

    更新日期:2017-09-15 00:00:00

  • Research Progress in Atopic March.

    abstract::The incidence of allergic diseases continues to rise. Cross-sectional and longitudinal studies have indicated that allergic diseases occur in a time-based order: from atopic dermatitis and food allergy in infancy to gradual development into allergic asthma and allergic rhinitis in childhood. This phenomenon is defined...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2020.01907

    authors: Yang L,Fu J,Zhou Y

    更新日期:2020-08-27 00:00:00

  • Single-Cell RNA-Sequencing Shift in the Interaction Pattern Between Glioma Stem Cells and Immune Cells During Tumorigenesis.

    abstract::Glioblastoma is one of the most common neoplasms in the central nervous system characterized by limited immune response and unlimited expansion capability. Cancer stem cells (GSCs), a small fraction of the tumor cells, possess a pivotal regulation capability in the tumor microenvironment with a superior proliferation ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.581209

    authors: Zhai Y,Li G,Li R,Chang Y,Feng Y,Wang D,Wu F,Zhang W

    更新日期:2020-10-08 00:00:00

  • IFN-I Mediates Dysfunction of Endothelial Progenitor Cells in Atherosclerosis of Systemic Lupus Erythematosus.

    abstract::Systemic lupus erythematosus (SLE) is a multi-system autoimmune disease including the cardiovascular system. Atherosclerosis is the most common cardiovascular complication of SLE and a significant risk factor for morbidity and mortality. Vascular damage/protection mechanism in SLE patients is out of balance, caused by...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2020.581385

    authors: Ding X,Xiang W,He X

    更新日期:2020-11-11 00:00:00

  • Combined p14ARF and Interferon-β Gene Transfer to the Human Melanoma Cell Line SK-MEL-147 Promotes Oncolysis and Immune Activation.

    abstract::Immune evasion is an important cancer hallmark and the understanding of its mechanisms has generated successful therapeutic approaches. Induction of immunogenic cell death (ICD) is expected to attract immune cell populations that promote innate and adaptive immune responses. Here, we present a critical advance for our...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.576658

    authors: Cerqueira OLD,Clavijo-Salomon MA,Cardoso EC,Citrangulo Tortelli Junior T,Mendonça SA,Barbuto JAM,Strauss BE

    更新日期:2020-10-22 00:00:00

  • Helminth Infections: Recognition and Modulation of the Immune Response by Innate Immune Cells.

    abstract::The survival of helminths in the host over long periods of time is the result of a process of adaptation or dynamic co-evolution between the host and the parasite. However, infection with helminth parasites causes damage to the host tissues producing the release of danger signals that induce the recruitment of various...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2018.00664

    authors: Motran CC,Silvane L,Chiapello LS,Theumer MG,Ambrosio LF,Volpini X,Celias DP,Cervi L

    更新日期:2018-04-04 00:00:00

  • Evaluating the Vaccine Potential of a Tetravalent Fusion Protein (rBmHAXT) Vaccine Antigen Against Lymphatic Filariasis in a Mouse Model.

    abstract::Lymphatic filariasis (LF) is a tropical parasitic infection of human transmitted by mosquitoes. Chronic infection results in severe physical disability in the infected patients. Although several potential vaccine antigens were identified by several groups, there are no licensed prophylactic vaccine to date against thi...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.01520

    authors: Chauhan N,Khatri V,Banerjee P,Kalyanasundaram R

    更新日期:2018-07-02 00:00:00

  • IgA and IgG1 Specific to Vi Polysaccharide of Salmonella Typhi Correlate With Protection Status in a Typhoid Fever Controlled Human Infection Model.

    abstract::Vaccination against Salmonella Typhi using the Vi capsular polysaccharide, a T-cell independent antigen, can protect from the development of typhoid fever. This implies that antibodies to Vi alone can protect in the absence of a T cell-mediated immune response; however, protective Vi antibodies have not been well-char...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,随机对照试验

    doi:10.3389/fimmu.2019.02582

    authors: Dahora LC,Jin C,Spreng RL,Feely F,Mathura R,Seaton KE,Zhang L,Hill J,Jones E,Alam SM,Dennison SM,Pollard AJ,Tomaras GD

    更新日期:2019-11-01 00:00:00

  • A Novel Siglec-4 Derived Spacer Improves the Functionality of CAR T Cells Against Membrane-Proximal Epitopes.

    abstract::A domain that is often neglected in the assessment of chimeric antigen receptor (CAR) functionality is the extracellular spacer module. However, several studies have elucidated that membrane proximal epitopes are best targeted through CARs comprising long spacers, while short spacer CARs exhibit highest activity on di...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.01704

    authors: Schäfer D,Henze J,Pfeifer R,Schleicher A,Brauner J,Mockel-Tenbrinck N,Barth C,Gudert D,Al Rawashdeh W,Johnston ICD,Hardt O

    更新日期:2020-08-07 00:00:00