Narrow Repertoire Research Articles

Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides.

In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome this deficiency in chemical diversity included conservative modifications to the sugar-phosphate backbone or the pendant base groups and resulted in enhanced in vivo performance. More importantly, later work involving other modifications led to the realization of new functional characteristics beyond initial intended therapeutic and diagnostic prospects. These results have inspired the exploration of increasingly exotic chemistries highly divergent from the canonical nucleic acid chemical structure that possess unnatural physiochemical properties. In this review, the authors highlight recent developments in modified oligonucleotides and the thrust towards designing novel nucleic acid-based ligands and catalysts with specifically engineered functions inaccessible to natural oligonucleotides.

In Defence of the Familiar: Understanding Conservatism in Concert Selection Amongst Classical Music Audiences

Since the establishment of a classical music canon in the 19th century, classical music culture has historically been focused on a stable set of masterpieces by genius composers predominantly from the classical and romantic periods. A small number of composers continue to dominate programming to this day. Many classical music organisations are keen to programme music beyond this narrow repertoire and to showcase new or unfamiliar works. The need to sell tickets, however, is often an obstacle, with organisations far more confident in the ability of big hits to attract large crowds. This article explores the experiences and opinions of classical music concertgoers in relation to familiar and unfamiliar music, providing a number of reasons as to why audiences may choose to hear well-known pieces rather than new works. This paper reports on one strand of a qualitative study with 42 individuals who booked tickets for one of two concert series consisting of core and populist repertoire, respectively. Semi-structured interviews were carried out to explore the reasons for their choices and their experiences of attending live concerts. These interviews showed that most participants did indeed have a clear preference for hearing music that was familiar to them, and only frequent attenders relished the challenge of unknown music. Participants felt that listening to familiar music was usually a more enjoyable experience than hearing something new. They rarely spoke of becoming bored with over-familiar music, perhaps because the live concert experience brings a sense of freshness to even the most familiar work.

Autism spectrum disorders and oral health status: review of the literature.

Autism Spectrum Disorder (ASD) is characterised by impairments in communication and social relationships and by a narrow, repetitive and stereotyped repertoire of activities, behaviours and interests. The aim of this work is to evaluate how these characteristics have an impact on oral health. A search was conducted through MEDLINE/PubMed and Web of Science in order to evaluate the oral health status of children with ASD and the correlation between ASD and dental caries, periodontal disease, dental injuries, oral microbiota, as well as the different strategies, approach and treatments in ASD patients. Forty-six articles were selected. Children with ASD are at higher risk of caries, alteration of the periodontal status, alterations of the oral microbiota and increased risk of traumatic injuries. Since ASD is a haeterogeneous disease with a wide range of expressions in individuals, adapted and specific strategies are needed. ASD children represent a challenge for the dental community.

Landscape Analysis of Escape Variants Identifies SARS-CoV-2 Spike Mutations that Attenuate Monoclonal and Serum Antibody Neutralization

Although neutralizing antibodies against the SARS-CoV-2 spike (S) protein are a goal of most COVID-19 vaccines and being developed as therapeutics, escape mutations could compromise such countermeasures. To define the immune-mediated mutational landscape in S protein, we used a VSV-eGFP-SARS-CoV-2-S chimeric virus and 19 neutralizing monoclonal antibodies (mAbs) against the receptor binding domain (RBD) to generate 48 escape mutants. These variants were mapped onto the RBD structure and evaluated for cross-resistance by convalescent human plasma. Although each mAb had unique resistance profiles, many shared residues within an epitope, as several variants were resistant to multiple mAbs. Remarkably, we identified mutants that escaped neutralization by convalescent human sera, suggesting that some humans induce a narrow repertoire of neutralizing antibodies. By comparing the antibody-mediated mutational landscape in S protein with sequence variation in circulating SARS-CoV-2 strains, we identified single amino acid substitutions that could attenuate neutralizing immune responses in some humans.Conflict of Interest: M.S.D. is a consultant for Inbios, Vir Biotechnology, NGM Biopharmaceuticals, and on the Scientific Advisory Board of Moderna and Immunome. The Diamond laboratory has received unrelated funding support in sponsored research agreements from Moderna, Vir Biotechnology, and Emergent BioSolutions. The Ellebedy laboratory has received unrelated funding support in sponsored research agreements from Emergent BioSolutions and funding support in sponsored research agreement from Abbvie to further develop 2B04 and 2H04 as therapeutic mAbs. A.H.E. and Washington University have filed a patent application that includes the SARS-CoV-2 antibodies 2B04 and 2H04 for potential commercial development. S.P.J.W. and Z.H.L have filed a disclosure with Washington University for VSV-SARS-CoV-2 mutants to characterize antibody panels. S. P. J. W has received unrelated funding support in sponsored research agreements with Vir Biotechnology and Abbvie. Ethical Approval: The protocols were approved by the Institutional Animal Care and Use Committee at the Washington University School of Medicine (Assurance number A3381-01).

Sociologies of Personal Relationships and the Challenge of Climate Change

The substantive concerns and theoretical insights of sociologies of family, intimate and personal life ought to place this body of work in closer dialogue with environmental sociology over the ‘big issue’ of climate change. However, its research active practitioners typically have a narrower repertoire of engagement with global issues and those who are outside the topic area often miss the value of its contributions. This article discusses common ground between this specialist area and sociologies of environmental issues in unpacking processes of social change through empirically grounded theoretical work. This includes the renewed theoretical emphasis on relationality, empirically based critique of the ‘individualisation thesis’, uses of ‘practice’ to transcend ‘micro’–‘macro’ and ‘social’–‘natural’ divisions, and interest in I/we boundary shifts. More fully recognising the potential of this overlapping territory may help leverage more effective sociological responses to the global challenge of climate change.

Intra-Tumoral CD8+ T-Cells in Follicular Lymphoma Contain Large Clonal Expansions That Are Amenable to Dual-Checkpoint Blockade

Introduction. Intra-tumoral T-cell infiltration is associated with R-CHOP responsiveness in aggressive B-cell lymphoma (Keane, Lancet Haem 2015). These patients also have a broad (i.e. diverse) intra-tumoral T-cell receptor (TCR) repertoire with a ~20% superior survival compared to those with a narrow (i.e. clonal) repertoire after R-CHOP therapy. Here, the major contributor to the TCR clonal expansion were CD8+ T cells (Keane, CCR 2017). Paradoxically, our recent results in Follicular Lymphoma (FL) (Tobin, JCO in press) found that clonal T-cell expansions were markedly enriched in those patients that experienced progression of disease within 24 months (POD24). Given that FL is a histological subtype associated with a tumor microenvironment distinct from DLBCL including numerous CD4+ T-follicular helper cells (TFH), we now expand upon these findings by comparing TCR repertoires across histological subtypes. We then established whether the TCR repertoire in FL is related to differential TCR clonal expansions between different T-cell subsets and immune checkpoints. Finally, the overlap between tissue and blood TCR repertoires was investigated. Methods. Firstly, unbiased, high-throughput TCRβ sequencing (ImmunoSEQ, Adaptive Biotechnologies) was compared in 164 FFPE tissues (12 healthy nodes, 40 FL, 88 DLBCL, and as a comparator tumor known to be sensitive to checkpoint blockade and to have a high neoantigen burden, 24 melanoma tissues). Next, to determine the contribution of individual T-cell subsets to overall clonality, a further 21 fresh de-aggregated/cryopreserved FL tumor samples were FACS sorted into four T-cell groupings: CD8+ cytotoxic T-lymphocytes (CTLs), CD4+ TFH, CD4+ regulatory T-cells (TREGs) and 'other' (non-TFH/TREG) CD4+ T-cells. Flow cytometry quantified the expression of the checkpoints LAG3, TIM3 and PD1. Then, 5 FL paired tissue/blood samples were tested for shared TCR clones. Results. FL exhibited strikingly reduced TCR repertoire clonality (higher diversity) compared to DLBCL, melanoma and healthy lymph nodes (Fig 1A). Analysis of de-aggregated sorted nodal T-cells revealed a more complex TCR repertoire. The outcome measure was median clonality index (CIx ranging from '0' or minimal, to '1' or maximal clonality). Large T-cell clones in FL (CIx=0.12) predominantly resided within the CTL subset (34% all T-cells). By contrast, there was marked T-cell diversity in TFH (CIx=0.04; 27% all T-cells), TREG (CIx=0.02; 7% all T-cells) and 'other' CD4+ T-cells (CIx=0.02; 32% all T-cells) (Fig 1B). The CTL population had a bimodal expression for PD1 (+51%/-49%), a marker in FL that has been shown to remain functionally active unless co-expressed with LAG3 and/or TIM3 (Yang, Oncotarget 2017). These dual-checkpoint expressing CTLs have reduced capacity to produce cytokines or lytic granules (i.e. they are 'exhausted'). Notably, 54% of the PD1+ CTLs co-expressed either LAG3 or TIM3. Put together, these results are consistent with expanded CTL clones that are frequently functionally exhausted. In contrast, TFH, TREG and 'other' CD4+ T-cells had a low expression of LAG3 and TIM3, although PD1 was frequently found (as expected, particularly in the TFH cells). Finally, in paired tissue/blood samples, there was weak overlap between the circulating and intra-tumoral TCR repertoire in CTLs and TFH T-cells. Conclusion. Although FL has a markedly less clonal TCR repertoire compared to DLBCL, melanoma and even healthy nodes, this result is misleading. Detailed analysis on sorted intra-tumoral T-cell subsets in FL revealed large clonal expansions in CTLs, with approximately half of these classified as functionally exhausted (dual-positive for PD1 and LAG3 and/or TIM3), a state potentially amenable to reversal by dual-checkpoint blockade. The explanation for TCR repertoire diversity lies in CD4+ T-cells (representing approximately two-thirds of T-cells, including the large TFH subset). T-cells in blood did not reflect FL tissue T-cell clones, further highlighting the need for sorted intra-tumoral nodal tissues to accurately assess TCR repertoires in FL. Further characterization of the neo-antigenic targets that CTL clones potentially recognize is required. These results have implications for therapeutic vaccine design and selective recruitment of patients for immune checkpoint blockade. Disclosures Keane: MSD: Consultancy; Gilead: Consultancy; Celgene: Consultancy; Roche: Consultancy, Other: Travel Grant; BMS: Research Funding. Gandhi:Roche: Honoraria, Other: Travel Support; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Merck: Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria; Bristol Myers Squibb: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Gilead: Honoraria, Research Funding.

In vitro-generated MART-1-specific CD8 T cells display a broader T-cell receptor repertoire than exvivo naïve and tumor-infiltrating lymphocytes.

The differentiation of human hematopoietic stem cells into CD8 T cells can be achieved invitro with the OP9-DL4 system. We considered that in the absence of medullary thymic epithelial cells, which serve to restrict the breath of the T-cell receptor (TCR) repertoire by expressing tissue-restricted antigens, a distinct repertoire would be generated invitro. To test this notion, we compared the TCR-Vα/Vβ (TRAV/TRBV) gene usage of major histocompatibility complex-restricted antigen (MART-1)-specific T cells generated invitro to that from exvivo naïve T cells and tumor-infiltrating lymphocytes (TILs) using high-throughput DNA sequencing. In contrast to naïve T cells and TILs, which showed the expected narrow TRAV repertoire, invitro-generated MART-1-specific T cells used almost all TRAV gene families and displayed unique CDR3 lengths. Our work demonstrates that the OP9-DL4 system supports the creation of a broad antigen-specific TCR repertoire, suggesting that T cells generated invitro may undergo a different set of selection events that otherwise constrains the TCR repertoire of thymus-derived T cells.

Update on influenza monitoring and vaccine development

Influenza causes substantial morbidity and mortality annually. Vaccination is the most practical means available to control this burden. Global virological surveillance, coordinated by the World Health Organization, is conducted year-round to monitor antigenic and genetic changes to the virus that may affect vaccine performance. However, recently vaccine effectiveness estimates have been low for at least one of the 4 components of the vaccine. Currently-available influenza vaccines suffer several problems. First, current influenza vaccines do not provide long-term protection because they target a surface protein of the virus which undergoes frequent antigenic change, thus requiring annual reformulation. Second, vaccines take many months to manufacture, so an updated formulation contains representative viruses that circulated at least 9 months prior. Third, vaccine may induce a narrow repertoire of antibodies that fail to protect against the broad range of circulating wild-type viruses. Fourth, most vaccines are developed using embryonated hen’s eggs, but rapidly acquire egg-adaptation mutations that alter antigenicity; the antibodies produced may be focused towards egg-grown not wild-type viruses providing limited protection. Finally, repeated, annual vaccination may exacerbate antibody focusing. This presentation will discuss current efforts to overcome these limitations and improve vaccine effectiveness.

Food selectivity in a diverse sample of young children with and without intellectual disabilities

Children with developmental concerns are more likely to be referred to feeding clinics for food selectivity than typically developing (TD) children. However, there is limited research on food selectivity in children with intellectual disabilities (ID). Fifty-nine TD children and 56 children with ID ages 3–8 years participated in the Children's Mealtime Study to compare food selectivity, conceptualized as food refusal and narrow food repertoire, among TD children and children with ID. Parents completed a 119-item food frequency questionnaire. Food refusal rate was calculated as the number of foods the child refused of those offered. Food repertoire, comprising the number of unique foods eaten, was determined from a 3-day food record. Compared to TD children, among children with ID the food refusal rate was significantly higher (28.5% vs. 15.7%) and mean food repertoire significantly narrower (20.7 vs. 24.2 unique foods) (p < 0.01). Approximately 10% of children with ID and approximately 4% of TD children reported eating no fruit on any of the three days of food intake recording, and approximately 10% of children with ID compared to approximately 2% of TD children reported no vegetable intake on any of the three days. In further analyses, we examined the two measures of food selectivity among children with both ID and probable autism spectrum disorder (ASD) (by the Autism Spectrum Rating Scale) compared to children with ID only and to TD children. Food selectivity appeared to be primarily attributable to those children who also had a probable diagnosis of ASD. These findings support the need for screening for food selectivity of children with ID, particularly those who also have ASD. Children who exhibit food selectivity should be referred for further evaluation and intervention.

Propaganda on shellac, vinyl and plastic: The politics of record production during the Cultural Revolution in China (1966–76)

Abstract When the People’s Republic of China was founded in 1949, Shanghai’s recording industry was nationalized and turned into a propaganda enterprise. For the next decades, the China Record Factory became China’s sole recording company. This article investigates the politics of record production and the development and organization of China’s recording industry. Censorship and control reached its peak during the Cultural Revolution; almost simultaneously the distribution of revolutionary sounds increased via a new record format: flexible plastic records. While revolutionary enthusiasm hit the factories, the goal of spreading the voice of Mao Zedong motivated record production until the late 1960s. Afterwards, however, the narrow record repertoire, ever-changing political slogans and campaigns resulted in a behaviour of avoiding risk that affected the entire industry and severely hampered record distribution and propaganda especially in the provinces.

Broadening CD4+ and CD8+ T Cell Responses against Hepatitis C Virus by Vaccination with NS3 Overlapping Peptide Panels in Cross-Priming Liposomes.

Despite the introduction of effective drugs to treat patients with chronic hepatitis C virus (HCV) infection, a vaccine would be the only means to substantially reduce the worldwide disease burden. An incomplete understanding of how HCV interacts with its human host and evades immune surveillance has hampered vaccine development. It is generally accepted that in infected individuals, a narrow repertoire of exhausted T cells is a hallmark of persistent infection, whereas broad, vigorous CD4+ and CD8+ T cell responses are associated with control of acute hepatitis C. We employed a vaccine approach based on a mixture of peptides (pepmix) spanning the entire sequence of HCV nonstructural protein 3 (NS3) in cross-priming cationic liposomes (CAF09) to facilitate a versatile presentation of all possible T cell epitopes, regardless of the HLA background of the vaccine recipient. Here, we demonstrate that vaccination of mice with NS3 pepmix broadens the repertoire of epitope-specific T cells compared to the corresponding recombinant protein (rNS3). Moreover, vaccination with rNS3 induced only CD4+ T cells, whereas the NS3 pepmix induced a far more vigorous CD4+ T cell response and was as potent a CD8+ T cell inducer as an adenovirus-vectored vaccine expressing NS3. Importantly, the cellular responses are dominated by multifunctional T cells, such as gamma interferon-positive (IFN-γ+) tumor necrosis factor alpha-positive (TNF-α+) coproducers, and displayed cytotoxic capacity in mice. In conclusion, we present a novel vaccine approach against HCV, inducing a broadened T cell response targeting both immunodominant and potential subdominant epitopes, which may be key elements to counter T cell exhaustion and prevent chronicity.IMPORTANCE With at least 700,000 annual deaths, development of a vaccine against hepatitis C virus (HCV) has high priority, but the tremendous ability of the virus to dodge the human immune system poses great challenges. Furthermore, many chronic infections, including HCV infection, have a remarkable ability to drive initially strong CD4+ and CD8+ T cell responses against dominant epitopes toward an exhausted, dysfunctional state. Thus, new and innovative vaccine approaches to control HCV should be evaluated. Here, we report on a novel peptide-based nanoparticle vaccine strategy (NS3 pepmix) aimed at generating T cell immunity against potential subdominant T cell epitopes that are not efficiently targeted by vaccination with full-length recombinant protein (rNS3) or infection with HCV. As proof of concept, we found that NS3 pepmix excels in broadening the repertoire of epitope-specific, multifunctional, and cytotoxic CD4+ and CD8+ T cells compared to vaccination with rNS3, which generated only CD4+ T cell responses.

Tentacle structure in freshwater bryozoans.

Tentacles are the main food-gathering organs of bryozoans. The most common design is a hollow tube of extracellular matrix (ECM), covered with ten columns of epithelial cells on the outside, and a coelothelium on the inside. Nerves follow the ECM, going between the bases of some epidermal cells. The tentacle musculature includes two bundles formed by myoepithelial cells of the coelothelium. The tentacles of freshwater (phylactolaemate) bryozoans, however, differ somewhat in structure from those of marine bryozoans. Here, we describe the tentacles of three species of phylactolaemates, comparing them to gymnolaemates and stenolaemates. Phylactolaemate tentacles tend to be longer, and with more voluminous coeloms. The composition of the frontal cell row and the number of frontal nerves is variable in freshwater bryozoans, but constant in marine groups. Abfrontal cells form a continuous row in Phylactolaemata, but occur intermittently in other two classes. Phylactolaemata lack the microvillar cuticle reported in Gymnolaemata. Abfrontal sensory tufts are always composed of pairs of mono- and/or biciliated cells. This arrangement differs from individual abfrontal ciliary cells of other bryozoans: monociliated in Stenolaemata and monociliated and multiciliated ones in Gymnolaemata. In all three groups, however, ciliated abfrontal cells probably serve as mechanoreceptors. We confirm previously described phylactolemate traits: an unusual arrangement of two-layered coelothelium lining the lateral sides of the tentacle and oral slits in the intertentacular membrane. As previously reported, tentacle movements involved in feeding differ between bryozoan groups, with phylactolaemates tending to have slower movements than both gymnolaemates and stenolaemates, and a narrower behavioral repertoire than gymnolaemates. The morphological and ultrastructural differences between the freshwater species we studied and marine bryozoans may be related to these functional differences. Muscle organization, tentacle and coelom size, and degree of confluence between tentacle and lophophore coeloms probably account for much of the observed behavioral variability.

T cells from hemophilia A subjects recognize the same HLA-restricted FVIII epitope with a narrow TCR repertoire

AbstractFactor VIII (FVIII)–neutralizing antibodies (“inhibitors”) are a serious problem in hemophilia A (HA). The aim of this study was to characterize HLA-restricted T-cell responses from a severe HA subject with a persistent inhibitor and from 2 previously studied mild HA inhibitor subjects. Major histocompatibility complex II tetramers corresponding to both of the severe HA subject's HLA-DRA-DRB1 alleles were loaded with peptides spanning FVIII-A2, C1, and C2 domains. Interestingly, only 1 epitope was identified, in peptide FVIII2194-2213, and it was identical to the HLA-DRA*01-DRB1*01:01-restricted epitope recognized by the mild HA subjects. Multiple T-cell clones and polyclonal lines having different avidities for the peptide-loaded tetramer were isolated from all subjects. Only high- and medium-avidity T cells proliferated and secreted cytokines when stimulated with FVIII2194-2213. T-cell receptor β (TCRB) gene sequencing of 15 T-cell clones from the severe HA subject revealed that all high-avidity clones expressed the same TCRB gene. High-throughput immunosequencing of high-, medium-, and low-avidity cells sorted from a severe HA polyclonal line revealed that 94% of the high-avidity cells expressed the same TCRB gene as the high-avidity clones. TCRB sequencing of clones and lines from the mild HA subjects also identified a limited TCRB gene repertoire. These results suggest a limited number of epitopes in FVIII drive inhibitor responses and that the T-cell repertoires of FVIII-responsive T cells can be quite narrow. The limited diversity of both epitopes and TCRB gene usage suggests that targeting of specific epitopes and/or T-cell clones may be a promising approach to achieve tolerance to FVIII.

The T Cell Receptor (TCR) Repertoire Is a Key Determinant of the Tumour Microenvironment (TME) in Diffuse Large B Cell Lymphoma (DLBCL)

Background: We have recently demonstrated that an 'immune score' is strongly and independently prognostic in de novo DLBCL treated with R-CHOP immuno-chemotherapy. The score quantifies the relative composition of immune effectors (T cells) and checkpoints (e.g. PD-1 axis molecules and M2 macrophages), as a measure of net anti-tumoral immunity within the TME. It is also known that a diverse TCR repertoire is a hallmark of a robust anti-HIV T cell immune response; conversely in metastatic melanoma treated with anti-PD-1 checkpoint blockade, narrow more clonal TCR repertoires are associated with favorable response. The relationship between the intra-tumoral TCR repertoire and the TME in DLBCL following R-CHOP immuno-chemotherapy is unknown.MethodsHigh-throughput unbiased TCR β chain sequencing was performed on 116 nodal tissues (101 de novo DLBCL patients treated with R-CHOP with long-term follow-up including 8 EBV+DLBCL; and 15 age/gender matched healthy lymph nodes). Outcomes included measurement of productive uniques (a measure of the number of functional T cells with a distinct TCR rearrangement or 'richness'); entropy (a measure of TCR 'diversity'), 'clonality' (a measure of clonal expansions) and the 'maximal frequency' of the most highly expressed clone within tumor biopsies. Results were compared to digital quantification (by nanoString) of key immune effector and checkpoint genes within the TME, the immune score, malignant cell-of-origin (COO), R-IPI and patient survival.Results:First we compared the TCR repertoire in lymphomatous and healthy nodes. There was a marked increase in clonality, reduced diversity and high maximal frequency within DLBCL nodes relative to healthy nodal tissue (both p<0.0001), consistent with an abnormally narrow TCR repertoire of antigen-specific T cells. Next, we tested the relationship between TCR and the TME. Notably, there was modest (r=0.3-0.7) but highly significant (all p<0.001) positive correlations between both richness and diversity (but not clonality) with CD3/CD4/CD8 T cells, and a range of immune checkpoints including PD-L1, PD-L2, LAG-3, CSF-1 and TIM-3. These findings are strongly suggestive of an adaptive immune response, in which malignant B cells influence (i.e. 'adapt') the TME in an attempt to counter an effective anti-lymphoma T-cell response that is in part influenced by the breadth of the TCR repertoire. Then we investigated the TCR repertoire in the context of prognosis and overall survival (OS) following R-CHOP. There were no correlations between COO or R-IPI with any TCR parameter. However, the presence of a high maximal frequency in the tumour biopsy was associated with significantly inferior 5 year OS of 59% compared to 81% in patients without a high maximal frequency (p=0.03, Figure 1). As expected, the immune score stratified patients into highly disparate outcomes: high-score 5-year overall survival 96% versus 42% for low-score (p<0.0001). Interestingly, there were significant differences in the TCR repertoire between the two groups. There was a significant increase for both richness and diversity in high immune score lymphoma patients (p=0.015 and p=0.018 respectively). In keeping, clonality was not increased in high-immune score patients. The only samples associated with increased T cell clonality were those patients with very high levels of intratumoral EBV, potentially reflecting the latent viral antigens expressed by this lymphoma. In the group of patients with poor prognosis (5 year OS 59%), defined by high maximal frequency, the immune score stratified two groups with very different outcomes (5 year OS 90% vs. 30%, p=0.003).Conclusions:These findings indicate the TCR repertoire as a key parameter of the TME that the malignant B cell attempts to narrow. A broad TCR repertoire is associated with a good prognostic immune score (i.e. increased T cells relative to PD-1 axis molecules and M2 macrophages checkpoints) after R-CHOP immunoÐchemotherapy, whereas a more clonal T cell response is associated with significantly inferior outcome. [Display omitted] DisclosuresHamm:Adaptive Biotech: Employment.

The common equine class I molecule Eqca-1*00101 (ELA-A3.1) is characterized by narrow peptide binding and T cell epitope repertoires.

Here we describe a detailed quantitative peptide-binding motif for the common equine leukocyte antigen (ELA) class I allele Eqca-1*00101, present in roughly 25% of Thoroughbred horses. We determined a preliminary binding motif by sequencing endogenously bound ligands. Subsequently, a positional scanning combinatorial library (PSCL) was used to further characterize binding specificity and derive a quantitative motif involving aspartic acid in position 2 and hydrophobic residues at the C-terminus. Using this motif, we selected and tested 9- and 10-mer peptides derived from the equine herpesvirus type 1 (EHV-1) proteome for their capacity to bind Eqca-1*00101. PSCL predictions were very efficient, with an receiver operating characteristic (ROC) curve performance of 0.877, and 87 peptides derived from 40 different EHV-1 proteins were identified with affinities of 500nM or higher. Quantitative analysis revealed that Eqca-1*00101 has a narrow peptide-binding repertoire, in comparison to those of most human, non-human primate, and mouse class I alleles. Peripheral blood mononuclear cells from six EHV-1-infected, or vaccinated but uninfected, Eqca-1*00101-positive horses were used in IFN-γ enzyme-linked immunospot (ELISPOT) assays. When we screened the 87 Eqca-1*00101-binding peptides for T cell reactivity, only one Eqca-1*00101 epitope, derived from the intermediate-early protein ICP4, was identified. Thus, despite its common occurrence in several horse breeds, Eqca-1*00101 is associated with a narrow binding repertoire and a similarly narrow T cell response to an important equine viral pathogen. Intriguingly, these features are shared with other human and macaque major histocompatibility complex (MHC) molecules with a similar specificity for D in position 2 or 3 in their main anchor motif.

How Do Cooks Actually Cook Vegetables? A Field Experiment With Low-Income Households.

Vegetables in the diet contribute to disease prevention. However, low-income households underconsume fresh vegetables, perhaps because of cost and of unavailability at nearby stores. A third reason may lurk behind those barriers: cooks' unfamiliarity with various and appealing ways to prepare vegetables. To illuminate that possibility and to suggest interventions that could be designed more effectively to boost vegetable consumption, this study took the novel step of providing ample, if temporary, supplies of a fresh vegetable to random sets of clients of food pantries. A week later, telephone interviews obtained details about preparations of meals and snacks that household cooks had made with their unexpected bounty. Among the experiment's 10 vegetables, some were used twice as often as others. Even more striking, cooks practiced a narrow repertoire of preparation methods, dominated by boiling and steaming, across most of the vegetables. Fats and salt were often added to boiled and steamed preparations. Implications are drawn to suggest kinds of recipes-pairings of vegetables and of vegetables with underused means of preparation-that could expand cooks' repertoires and add variety in flavors, appearances of dishes, meal textures, and aromas.

αβ T cell receptors as predictors of health and disease.

The diversity of antigen receptors and the specificity it underlies are the hallmarks of the cellular arm of the adaptive immune system. T and B lymphocytes are indeed truly unique in their ability to generate receptors capable of recognizing virtually any pathogen. It has been known for several decades that T lymphocytes recognize short peptides derived from degraded proteins presented by major histocompatibility complex (MHC) molecules at the cell surface. Interaction between peptide-MHC (pMHC) and the T cell receptor (TCR) is central to both thymic selection and peripheral antigen recognition. It is widely assumed that TCR diversity is required, or at least highly desirable, to provide sufficient immune coverage. However, a number of immune responses are associated with the selection of predictable, narrow, or skewed repertoires and public TCR chains. Here, we summarize the current knowledge on the formation of the TCR repertoire and its maintenance in health and disease. We also outline the various molecular mechanisms that govern the composition of the pre-selection, naive and antigen-specific TCR repertoires. Finally, we suggest that with the development of high-throughput sequencing, common TCR ‘signatures' raised against specific antigens could provide important diagnostic biomarkers and surrogate predictors of disease onset, progression and outcome.

The influence of prior knowledge and viewing repertoire on learning from video

Video is increasingly used as an instructional tool. It is therefore becoming more important to improve learning of students from video. We investigated whether student learning effects are influenced through an instruction about other viewing behaviours, and whether these learning effects depend on their prior knowledge. In a controlled environment, 115 students watched a number of instructional videos about the technical equipment needed in a course on digital photography. Every second student was instructed about other possible viewing behaviours. A pre-post-retention test was carried out to calculate learning effects. The differences with respect to the learning effects of students who received an awareness instruction on an alternative viewing strategy were not significantly different. The differences as observed in our earlier experiment however could not be reproduced. Students with a broad viewing repertoire showed higher learning effects than students with a narrow repertoire. Furthermore, students with a strategic viewing approach also showed higher learning effects. Certain conditions have to be met: the technical and didactical quality of the video must be good, the integration in a learning task must be apparent, students must be aware of their viewing behaviour, and teachers must be aware of their students’ viewing behaviour in order to enrich the viewing repertoire of students when they have at least some basic knowledge e.g. after several lessons on the topics at hand. In future research, this study should be replicated using more complex video episodes than the instruction videos we used in our experiments that were only on the factual knowledge level of the taxonomy of Bloom. Moreover, replication of this study with a larger sample size could yield a significant improvement in learning effects. This is plausible because students need an amount of prior knowledge beyond a certain threshold value in order to be able to expand their knowledge network in their long term memory. Finally, additional media player functionality, facilitating effective student learning from video, can be described based on the results of this study.

An extensive antigenic footprint underpins immunodominant TCR adaptability against a hypervariable viral determinant.

Mutations in T cell epitopes are implicated in hepatitis C virus (HCV) persistence and can impinge on vaccine development. We recently demonstrated a narrow bias in the human TCR repertoire targeted at an immunodominant, but highly mutable, HLA-B*0801-restricted epitope ((1395)HSKKKCDEL(1403) [HSK]). To investigate if the narrow TCR repertoire facilitates CTL escape, structural and biophysical studies were undertaken, alongside comprehensive functional analysis of T cells targeted at the natural variants of HLA-B*0801-HSK in different HCV genotypes and quasispecies. Interestingly, within the TCR-HLA-B*0801-HSK complex, the TCR contacts all available surface-exposed residues of the HSK determinant. This broad epitope coverage facilitates cross-genotypic reactivity and recognition of common mutations reported in HCV quasispecies, albeit to a varying degree. Certain mutations did abrogate T cell reactivity; however, natural variants comprising these mutations are reportedly rare and transient in nature, presumably due to fitness costs. Overall, despite a narrow bias, the TCR accommodated frequent mutations by acting like a blanket over the hypervariable epitope, thereby providing effective viral immunity. Our findings simultaneously advance the understanding of anti-HCV immunity and indicate the potential for cross-genotype HCV vaccines.

A narrow repertoire of transcriptional modules responsive to pyogenic bacteria is impaired in patients carrying loss-of-function mutations in MYD88 or IRAK4.

Loss of function in the kinase IRAK-4 or the adapter MyD88 in humans interrupts a pathway critical for pathogen sensing and ignition of inflammation. Yet patients with loss of function mutations are surprisingly only susceptible to a limited range of pathogens. We employed a systems approach to investigate transcriptome responses following in vitro exposure of patients’ blood to Toll-like receptor and interleukin-1 receptor agonists, and whole pathogens. Responses to purified agonists were globally abolished but variable residual responses were present following exposure to whole pathogens. Further dissection of the latter responses identified a narrow repertoire of immune transcriptional programs affected by loss of MyD88 or IRAK-4 function. This work introduces the use of a systems approach for the global assessment of innate immune responses, and the characterization of human primary immunodeficiencies.