Role of HLA class I and class II antigens in activation and differentiation of B cells

Biagiotti, R; Almerigogna, Fabio; Alessi, Anna; Tiri, A; Prete, G.; Ferrone, Soldano; Romagnani, Sergio

doi:10.1016/0008-8749(87)90196-1

Cited by 15 publications

(5 citation statements)

References 33 publications

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“…Among the genes upregulated in cluster 3 were genes encoding proteins that promote interactions between B cells and T cells, such as human leukocyte antigen (HLA)-DR/DQ, CD86, and CD74, the latter of which regulates antigen presentation by class II major histocompatibility complex (MHC). 28 , 29 , 30 In addition, we observed upregulation of genes encoding class I MHC ( HLA-A and HLA-C ) and several genes that are associated with cytotoxicity, including granzyme M ( GZMM ), cystatin 7 ( CST7 ), natural killer cell granule protein 7 ( NKG7 , a target gene of T-bet), and natural cytotoxicity triggering receptor 3 ( NCR3 ). While it is unlikely that atypical B cells in cluster 3 are cytotoxic, upregulation of these genes could affect cell-cell interactions or antigen presentation.…”

Section: Resultsmentioning

confidence: 97%

Atypical B cells consist of subsets with distinct functional profiles

Reyes,

Batugedara,

Dutta

et al. 2023

iScience

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Section: Resultsmentioning

confidence: 97%

Atypical B cells consist of subsets with distinct functional profiles

Reyes,

Batugedara,

Dutta

et al. 2023

iScience

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“…4 I). It is known that the relevant translational products make up the HLA class I ( HLA-A , HLA-B , HLA-C ) and class II ( HLA-DQ , HLA-DR ) complexes, which play important and distinctive roles in presenting processed peptide antigene ( Giudizi et al 1987 ; Choo 2007 ). The results indicated that not only direct protein interactions within each class of complex but also coregulation between the two complexes may be partially coded in genomic structure, although they are distant in the linear genome.…”

Section: Resultsmentioning

confidence: 99%

Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome

He¹,

Xue²,

Wang³

et al. 2023

Genome Res.

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The interactome networks in DNA, RNA, and protein levels are crucial for cellular functions, and the diverse variations of these networks are heavily involved in the establishment of different cell states. We developed a diffusion-based method, CTG (HiC To Geometry), to obtain reliable geometric information on the chromatin from Hi-C data. CTG produces a consistent and reproducible framework for the 3D genomic structure and allows for a reliable and quantitative understanding of the alteration of genomic structures under different cellular conditions. The genomic structure yielded by CTG serves as an architectural blueprint of the dynamic gene regulatory network, based on which cell-specific correspondence between gene-gene and corresponding protein-protein physical interactions, as well as transcription correlation, were revealed. It was also found that gene fusion events are significantly enriched between genes of short CTG distances and are thus close in 3D space. These findings indicate that 3D chromatin structure is at least partially correlated with downstream processes such as transcription, gene regulation, and regulatory networking through affecting protein-protein interactions.

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“…For example, close proximity is seen among HLA (Human Leukocyte Antigen) genes (Figure S9). It is known that the relavent translational products make up the HLA class I (HLA-A, HLA-B, HLA-C) and class II (HLA-DQ, HLA-DR) complexes, which play important and distinctive roles in presenting processed peptide antigene (Choo, 2007; Giudizi et al, 1987). The results indicated that not only direct protein interations within each class of complex, but also co-regualtion between the two complexes may be partially coded in genomic structure, although they are distant in the linear genome.…”

Section: Resultsmentioning

confidence: 99%

Computational Enhanced Hi-C data reveals the function of structural geometry in genomic regulation

Xue

Wang

et al. 2022

Preprint

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High-throughput chromosome conformation capture (Hi-C) technique profiles the genomic structure in a genome-wide fashion. The reproducibility and consistency of Hi-C data are essential in characterizing dynamics of genomic structures. We developed a diffusion-based method, CTG (Hi-C To Geometry), to deal with the technical bias induced by insufficient sampling in sequencing and obtain reliable gemeotric information of the chromatin. CTG properly quantifies dubiously weak or even undetected interactions and produces a consistent and reproducible framework for the 3D genomic structure. CTG allows for a reliable genome-wide insight on the alteration of genomic structures under different cellular conditions and reveals correlations between genomic-proximal genes at both transcriptional and translational levels. Cell-specific correspondence between gene-gene and corresponding protein-protein physical interactions, as well as that with the transcription correlation reveals the coordinated inter-molecular structural and regulatory information passage in the central dogma.

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Role of HLA class I and class II antigens in activation and differentiation of B cells

Cited by 15 publications

References 33 publications

Atypical B cells consist of subsets with distinct functional profiles

Atypical B cells consist of subsets with distinct functional profiles

Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome

Computational Enhanced Hi-C data reveals the function of structural geometry in genomic regulation

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