Regulatory noncoding RNAs and the major histocompatibility complex

Chitnis, Nilesh; Shieh, Mengkai; Monos, Dimitri

doi:10.1016/j.humimm.2020.06.005

Cited by 7 publications

(7 citation statements)

References 115 publications

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“…The results of the current study are consistent with this, indicating that serum IL-10 was significantly lower in the missed abortion group. Furthermore, a number of studies have demonstrated that lncRNAs are associated with the regulation of Th1/Th2 balance and inflammation at the maternal-fetal interface ( 43 , 44 ). Ou et al ( 45 ) recently reported that MALAT1 promotes the production of proinflammatory cytokines via activation of the NF-kB pathway, and exacerbates hypertension symptoms in the RUPP-induced rat model.…”

Section: Discussionmentioning

confidence: 99%

The expression and clinical significance of three lncRNAs in patients with a missed abortion

et al. 2020

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Missed abortions are common complications that occur in early pregnancy, and impaired trophoblast functions have been indicated to be associated with their pathogenesis. The long noncoding RNAs (lncRNAs) Metastasis Associated Lung Adenocarcinoma Transcript 1 ( MALAT1) , HOX Transcript Antisense RNA ( HOTAIR) and Maternally expressed gene 3 ( MEG3) have been demonstrated to serve a crucial regulatory role in the mobility of trophoblast cells and embryo implantation. However, the expression profile and role of each of these three lncRNAs in patients with a missed abortion remain unclear. The expression of MALAT1 , HOTAIR , and MEG3 in decidual and villous tissues from 26 patient exhibiting a missed abortion and 26 healthy controls was detected using reverse-transcription quantitative PCR. Serum TNF-α, IL-1β, IL-6 and IL-10 levels were measured using ELISA, and serum estradiol and progesterone levels were measured with electrochemiluminescence immunoassays. Additionally, the correlations between lncRNA expression and the levels of cytokines and hormones were further analyzed. MALAT1 , HOTAIR and MEG3 expression was significantly higher in villous tissues of patients exhibiting a missed abortion compared with healthy controls. MALAT1 expression was higher in decidual tissues of patients exhibiting a missed abortion compared with healthy controls. Serum IL-10 levels were significantly lower in patients exhibiting a missed abortion compared with healthy controls. Serum estradiol and progesterone levels were significantly lower in the group of patients exhibiting a missed abortion compared with the control group. Furthermore, MALAT1 expression in villous tissue was inversely related to serum progesterone levels. The results of the current study suggest that MALAT1 may be associated with the pathogenesis of missed abortions.

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Section: Discussionmentioning

confidence: 99%

The expression and clinical significance of three lncRNAs in patients with a missed abortion

et al. 2020

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“…The full significance of polymorphisms in the non-coding regions of MHC and KIR genes is far from being thoroughly understood, but recent studies revealed a key role of long noncoding RNAs (lncRNA) and microRNAs (miRNA), which are transcription products originating from non-coding DNA segments, in the regulation of MHC and KIR expression. 67,68 Disruption of these regulatory noncoding RNAs may be associated with susceptibility for infectious diseases, cancer, pregnancy failure and transplantation outcome. 67,[69][70][71] Approximately 17%-21% of all the classical HLA class I alleles that are deposited in the IPD (release 3.48.0, 2022-04) are characterized at a 4-field resolution, whereas the majority of the alleles reach 2-and 3-field resolution (Table 3).…”

Section: Genomic Amplicon Sequencing Might Reach 4-field Resolutionmentioning

confidence: 99%

“…67,68 Disruption of these regulatory noncoding RNAs may be associated with susceptibility for infectious diseases, cancer, pregnancy failure and transplantation outcome. 67,[69][70][71] Approximately 17%-21% of all the classical HLA class I alleles that are deposited in the IPD (release 3.48.0, 2022-04) are characterized at a 4-field resolution, whereas the majority of the alleles reach 2-and 3-field resolution (Table 3). For MHC-A and -B sequences derived from rhesus and cynomolgus macaques, a higher fraction of 4-field resolution is documented in the IPD-MHC (release 3.8.0.0, 2021-12), ranging from 27% to 67% (Table 3).…”

Section: Genomic Amplicon Sequencing Might Reach 4-field Resolutionmentioning

confidence: 99%

“…Although those polymorphisms might not directly affect the structure of the molecule, the variation in non‐coding segments could influence expression levels and alternative splicing. The full significance of polymorphisms in the non‐coding regions of MHC and KIR genes is far from being thoroughly understood, but recent studies revealed a key role of long noncoding RNAs (lncRNA) and microRNAs (miRNA), which are transcription products originating from non‐coding DNA segments, in the regulation of MHC and KIR expression 67,68 . Disruption of these regulatory noncoding RNAs may be associated with susceptibility for infectious diseases, cancer, pregnancy failure and transplantation outcome 67,69–71 …”

Section: Transcriptomic and Genomic Characterization Of Mhc And Kir F...mentioning

confidence: 99%

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HLA/MHC and KIR characterization in humans and non‐human primates using Oxford Nanopore Technologies and Pacific Biosciences sequencing platforms

Bruijnesteijn

2023

HLA

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The gene products of the HLA/MHC and KIR multigene families are important modulators of the immune system and are associated with health and disease. Characterization of the genes encoding these receptors has been integrated into different biomedical applications, including transplantation and reproduction biology, immune therapies and in fundamental research into disease susceptibility or resistance. Conventional short‐read sequencing strategies have shown their value in high throughput typing, but are insufficient to uncover the entire complexity of the highly polymorphic HLA/MHC and KIR gene systems. The implementation of single‐molecule and real‐time sequencing platforms, offered by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), revolutionized the fields of genomics and transcriptomics. Using fundamentally distinct principles, these platforms generate long‐read data that can unwire the plasticity of the HLA/MHC and KIR genes, including high‐resolution characterization of genes, alleles, phased haplotypes, transcription levels and epigenetics modification patterns. These insights might have profound clinical relevance, such as improved matching of donors and patients in clinical transplantation, but could also lift disease association studies to a higher level. Even more, a comprehensive characterization may refine animal models in preclinical studies. In this review, the different HLA/MHC and KIR characterization approaches using PacBio and ONT platforms are described and discussed.

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“…In humans, ncRNAs are involved in MHC regulation [ 135 ]. An RNA called lncRNA inducing MHC-I and immunogenicity of tumour (LIMIT) was activated (using CRISPR) [ 136 ] and found to indirectly cause MHC-I transcription, so was claimed to have a cancer immunogenic function.…”

Section: The Non-coding Rna Biology Of Transmissible Cancersmentioning

confidence: 99%

Between the Devil and the Deep Blue Sea: Non-Coding RNAs Associated with Transmissible Cancers in Tasmanian Devil, Domestic Dog and Bivalves

Lister

Milton

Hanrahan

et al. 2021

ncRNA

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Currently there are nine known examples of transmissible cancers in nature. They have been observed in domestic dog, Tasmanian devil, and six bivalve species. These tumours can overcome host immune defences and spread to other members of the same species. Non-coding RNAs (ncRNAs) are known to play roles in tumorigenesis and immune system evasion. Despite their potential importance in transmissible cancers, there have been no studies on ncRNA function in this context to date. Here, we present possible applications of the CRISPR/Cas system to study the RNA biology of transmissible cancers. Specifically, we explore how ncRNAs may play a role in the immortality and immune evasion ability of these tumours.

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Regulatory noncoding RNAs and the major histocompatibility complex

Cited by 7 publications

References 115 publications

The expression and clinical significance of three lncRNAs in patients with a missed abortion

The expression and clinical significance of three lncRNAs in patients with a missed abortion

HLA/MHC and KIR characterization in humans and non‐human primates using Oxford Nanopore Technologies and Pacific Biosciences sequencing platforms

Between the Devil and the Deep Blue Sea: Non-Coding RNAs Associated with Transmissible Cancers in Tasmanian Devil, Domestic Dog and Bivalves

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