A guide to antigen processing and presentation

Pishesha, Novalia; Harmand, Thibault J.; Ploegh, Hidde L.

doi:10.1038/s41577-022-00707-2

Cited by 354 publications

(222 citation statements)

References 158 publications

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“…Meanwhile, DAXX formed histone dependent interactions with a set of enigmatic proteins, including the proteoglycans (GPC1 and GPC5) (Filmus, 2001), and major histocompatibility complex I molecules (1A69/HLAA and beta-2-microglobulin/B2MG)(Pishesha et al, 2022), and the cargo receptor for selective autophagy SQSTM/p62 (Sánchez-Martín et al, 2019). These interactors suggest a role of DAXX in the membrane localization or extracellular secretion of histones (Chen et al, 2014; Silvestre-Roig et al, 2019), potentially utilized in the innate immune response to silence incoming viral genomes.…”

Section: Resultsmentioning

confidence: 99%

Section: Histone Chaperone Cooperation Is Built Through Histone Depen...mentioning

confidence: 99%

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DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network

Carraro

Hendriks

Hammond

et al. 2022

Preprint

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A multitude of histone chaperones are required to protect histones after their biosynthesis until DNA deposition. They cooperate through the formation of co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using explorative interactomics approaches, we characterize the organization of the histone H3-H4 chaperones network and define the interplay between histone chaperone systems. We identify and validate several novel histone dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX acts separately from the rest of the network, recruiting heterochromatin factors and promoting lysine 9 tri-methylation of new histone H3.3 prior to deposition onto DNA. With its functionality, DAXX provides a molecular mechanism for de novo heterochromatin assembly. Collectively, our findings provide a new framework for understanding how cells orchestrate histone supply and comply with chromatin dynamics throughout the cell cycle.

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Section: Resultsmentioning

confidence: 99%

Section: Histone Chaperone Cooperation Is Built Through Histone Depen...mentioning

confidence: 99%

DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network

Carraro

Hendriks

Hammond

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Immune Infiltrate Analysis. Six immune cell types, B cells, CD4+ T cells, CD8+ T cells [28], neutrophils, dendritic cells (DCs) [29], and macrophages [30], in the tumor micro-environment have been previously reported. We used the Tumor Immune Estimation Resource (TIMER), an established algorithm, to estimate the correlation between immune cells and gene expression.…”

Section: Cry2mentioning

confidence: 99%

Circadian Clock Genes Act as Diagnostic and Prognostic Biomarkers of Glioma: Clinic Implications for Chronotherapy

Chai

Liao

et al. 2022

BioMed Research International

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Gliomas are the most common primary intracranial tumors and closely related to circadian clock. Due to the high mortality and morbidity of gliomas, exploring novel diagnostic and early prognostic markers is necessary. Circadian clock genes (CCGs) play important roles in regulating the daily oscillation of biological processes and the development of tumor. Therefore, we explored the influences that the oscillations of circadian clock genes (CCGs) on diagnosis and prognosis of gliomas using bioinformatics. In this work, we systematically analyzed the rhythmic expression of CCGs in brain and found that some CCGs had strong rhythmic expression; the expression levels were significantly different between day and night. Four CCGs (ARNTL, NPAS2, CRY2, and DBP) with rhythmic expression were not only identified as differentially expressed genes but also had significant independent prognostic ability in the overall survival of glioma patients and were highly correlated with glioma prognosis in COX analysis. Besides, we found that CCG-based predictive model demonstrated higher predictive accuracy than that of the traditional grade-based model; this new prediction model can greatly improve the accuracy of glioma prognosis. Importantly, based on the four CCGs’ circadian oscillations, we revealed that patients sampled at night had higher predictive ability. This may help detect glioma as early as possible, leading to early cancer intervention. In addition, we explored the mechanism of CCGs affecting the prognosis of glioma. CCGs regulated the cell cycle, DNA damage, Wnt, mTOR, and MAPK signaling pathways. In addition, it also affects prognosis through gene coexpression and immune infiltration. Importantly, ARNTL can rhythmically modulated the cellular sensitivity to clinic drugs, temozolomide. The optimal point of temozolomide administration should be when ARNTL expression is highest, that is, the effect is better at night. In summary, our study provided a basis for optimizing clinical dosing regimens and chronotherapy for glioma. The four key CCGs can serve as potential diagnostic and prognostic biomarkers for glioma patients, and ARNTL also has obvious advantages in the direction of glioma chronotherapy.

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“…Virus phagocytosed by professional antigen-presenting cells (APCs) produces peptides that bind to MHC Class II, which are presented on the cell surface to CD4 + T cells. 13 …”

Section: Antiviral Immunitymentioning

confidence: 99%

T cells in SARS-CoV-2 infection and vaccination

Young¹

2022

Therapeutic Advances in Vaccines and Immunotherapy

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While antibodies garner the lion’s share of attention in SARS-CoV-2 immunity, cellular immunity (T cells) may be equally, if not more important, in controlling infection. Both CD8+ and CD4+ T cells are elicited earlier and are associated with milder disease, than antibodies, and T-cell activation appears to be necessary for control of infection. Variants of concern (VOCs) such as Omicron have escaped the neutralizing antibody responses after two mRNA vaccine doses, but T-cell immunity is largely intact. The breadth and patient-specific nature of the latter offers a formidable line of defense that can limit the severity of illness, and are likely to be responsible for most of the protection from natural infection or vaccination against VOCs which have evaded the antibody response. Comprehensive searches for T-cell epitopes, T-cell activation from infection and vaccination of specific patient groups, and elicitation of cellular immunity by various alternative vaccine modalities are here reviewed. Development of vaccines that specifically target T cells is called for, to meet the needs of patient groups for whom cellular immunity is weaker, such as the elderly and the immunosuppressed. While VOCs have not yet fully escaped T-cell immunity elicited by natural infection and vaccines, some early reports of partial escape suggest that future VOCs may achieve the dreaded result, dislodging a substantial proportion of cellular immunity, enough to cause a grave public health burden. A proactive, rather than reactive, solution which identifies and targets immutable sequences in SARS-CoV-2, not just those which are conserved, may be the only recourse humankind has to disarm these future VOCs before they disarm us.

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A guide to antigen processing and presentation

Cited by 354 publications

References 158 publications

DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network

DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network

Circadian Clock Genes Act as Diagnostic and Prognostic Biomarkers of Glioma: Clinic Implications for Chronotherapy

T cells in SARS-CoV-2 infection and vaccination

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