HLA RNAseq reveals high allele-specific variability in mRNA expression

AbstractThe HLA gene complex is the most important, single genetic factor in susceptibility to most diseases with autoimmune or autoinflammatory origin and in transplantation matching. The majority of the studies have focused on the huge allelic variation in these genes; only a few studies have explored differences in expression levels of HLA alleles. To study the expression levels of HLA alleles more systematically we utilised two different RNA sequencing methods. Illumina RNAseq has a high sequencing accuracy and depth but is limited by the short read length, whereas Oxford Nanopore’s technology can sequence long templates, but has a poor accuracy. We studied allelic mRNA levels of HLA class I and II alleles from peripheral blood samples of 50 healthy individuals. The results demonstrate large differences in mRNA expression levels between HLA alleles. The method can be applied to quantitate the expression differences of HLA alleles in various tissues and to evaluate the role of this type of variation in transplantation matching and susceptibility to autoimmune diseases.Author SummaryEven though HLA is widely studied less is known of its allele-specific expression. Due to the pivotal role of HLA in infection response, autoimmunity, and transplantation biology its expression surely must play a part as well. In hematopoietic stem cell transplantation the challenge often is to find a suitable HLA-matched donor due to the high allelic variation. Classical HLA typing methods do not take into account HLA allele-specific expression. However, differential allelic expression levels could be crucial in finding permissive mismatches in order to save a patient’s life. Additionally, differential HLA expression levels can lead into beneficial impact in viral clearance but also undesirable effects in autoimmune diseases. To study HLA expression we developed a novel RNAseq-based method to systematically characterize allele-specific expression levels of classical HLA genes. We tested our method in a set of 50 healthy individuals and found differential expression levels between HLA alleles as well as interindividual variability at the gene level. Since NGS is already well adopted in HLA research the next step could be to determine HLA allele-specific expression in addition to HLA allelic variation and HLA-disease association studies in various cells, tissues, and diseases.

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HLA RNA Sequencing With Unique Molecular Identifiers Reveals High Allele-Specific Variability in mRNA Expression

Frontiers in Immunology ◽

10.3389/fimmu.2021.629059 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tiira Johansson ◽

Dawit A. Yohannes ◽

Satu Koskela ◽

Jukka Partanen ◽

Päivi Saavalainen

Keyword(s):

Mrna Expression ◽

Rna Sequencing ◽

Allelic Variation ◽

Hla Class I ◽

Sequencing Technology ◽

Hla Alleles ◽

Expression Levels ◽

Allele Specific ◽

Specific Mrna

The HLA gene complex is the most important single genetic factor in susceptibility to most diseases with autoimmune or autoinflammatory origin and in transplantation matching. Most studies have focused on the vast allelic variation in these genes; only a few studies have explored differences in the expression levels of HLA alleles. In this study, we quantified mRNA expression levels of HLA class I and II genes from peripheral blood samples of 50 healthy individuals. The gene- and allele-specific mRNA expression was assessed using unique molecular identifiers, which enabled PCR bias removal and calculation of the number of original mRNA transcripts. We identified differences in mRNA expression between different HLA genes and alleles. Our results suggest that HLA alleles are differentially expressed and these differences in expression levels are quantifiable using RNA sequencing technology. Our method provides novel insights into HLA research, and it can be applied to quantify expression differences of HLA alleles in various tissues and to evaluate the role of this type of variation in transplantation matching and susceptibility to autoimmune diseases.

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Allele-specific expression and total expression levels of imprinted genes during early mouse development: implications for imprinting mechanisms.

Genes & Development ◽

10.1101/gad.9.24.3097 ◽

1995 ◽

Vol 9 (24) ◽

pp. 3097-3108 ◽

Cited By ~ 113

Author(s):

P E Szabo ◽

J R Mann

Keyword(s):

Imprinted Genes ◽

Mouse Development ◽

Specific Expression ◽

Allele Specific Expression ◽

Expression Levels ◽

Allele Specific ◽

Early Mouse

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Allele specific expression and methylation in the bumblebee, Bombus terrestris

PeerJ ◽

10.7717/peerj.3798 ◽

2017 ◽

Vol 5 ◽

pp. e3798 ◽

Cited By ~ 9

Author(s):

Zoë Lonsdale ◽

Kate Lee ◽

Maria Kiriakidu ◽

Harindra Amarasinghe ◽

Despina Nathanael ◽

...

Keyword(s):

Bombus Terrestris ◽

Social Hymenoptera ◽

Specific Expression ◽

Allele Specific Expression ◽

Epigenetic Marker ◽

The Social ◽

Allele Specific ◽

Contradictory Evidence ◽

Allele Specific Methylation

The social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the role of methylation on allele specific expression in social insects. The aim of this paper is to investigate allele specific expression and monoallelic methylation in the bumblebee, Bombus terrestris. We found nineteen genes that were both monoallelically methylated and monoallelically expressed in a single bee. Fourteen of these genes express the hypermethylated allele, while the other five express the hypomethylated allele. We also searched for allele specific expression in twenty-nine published RNA-seq libraries. We found 555 loci with allele-specific expression. We discuss our results with reference to the functional role of methylation in gene expression in insects and in the as yet unquantified role of genetic cis effects in insect allele specific methylation and expression.

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Workshop: Inference of allele specific expression levels from RNA-Seq data

2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS) ◽

10.1109/iccabs.2012.6182666 ◽

2012 ◽

Cited By ~ 1

Author(s):

Sahar Al Seesi ◽

Ion Mandoiu

Keyword(s):

Rna Seq ◽

Specific Expression ◽

Allele Specific Expression ◽

Expression Levels ◽

Allele Specific

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RNA-Seq Reveals Allele-Specific Expression of Somatic Mutations in Neuroblastoma

10.21203/rs.3.rs-119906/v1 ◽

2020 ◽

Author(s):

Xiaoqing Li ◽

Lan Sun ◽

Qian Liu ◽

Lingli Tu ◽

Andres Stucky ◽

...

Keyword(s):

Somatic Mutations ◽

Driver Mutations ◽

Integrated Analysis ◽

Driver Gene ◽

Rna Seq ◽

Specific Expression ◽

Allele Specific Expression ◽

Expression Levels ◽

Allele Specific ◽

Novel Therapeutic Strategies

Abstract Neuroblastoma (NB) is one of the most common solid tumors in children, accounting for approximately 8% of all pediatric malignancies and 15% of childhood cancer deaths. Somatic mutations in several genes such as ALK have been associated with neuroblastoma progression and can facilitate the discovery of novel therapeutic strategies. However, differential expression of mutated and wild-type alleles on the transcriptome level is not well studied. In this study, we analyzed 219 whole-exome sequencing datasets (with somatic mutations detected by MuTect from paired normal and tumor samples) and prioritized mutations in eight candidate genes as potential driver mutations. Meanwhile, we analyzed 127 RNA-seq samples (of which 85 also had DNA-seq data available) for allele-specific expression levels of each mutation. Our integrated analysis of somatic mutations and allele-specific expression levels confirmed the presence of allele-specific expression of somatic mutations in neuroblastoma including MYCN, ALK and PTPN22. The allele-specific expression of mutations suggests that the same somatic mutation may have different effects on clinical outcomes of tumors. Our study also suggests possible involvement of ZNF44 as a candidate driver gene for neuroblastoma. In summary, this study demonstrates the value of examining allele-specific expression levels of somatic mutations through the analysis of RNA-Seq data to assess the effects of somatic mutations in different patients. Improved understanding of allele-specific expression of somatic mutations can facilitate development of personalized treatment for neuroblastoma in precision medicine.

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Allele specific expression and methylation in the bumblebee, Bombus terrestris

10.1101/022657 ◽

2015 ◽

Author(s):

Zoë N. Lonsdale ◽

Kate D. Lee ◽

Maria Kyriakidou ◽

Harindra E. Amarasinghe ◽

Despina Nathanael ◽

...

Keyword(s):

Bombus Terrestris ◽

Social Hymenoptera ◽

Specific Expression ◽

Allele Specific Expression ◽

Epigenetic Marker ◽

The Social ◽

Allele Specific ◽

Contradictory Evidence ◽

Allele Specific Methylation

ABSTRACTThe social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the role of methylation on allele specific expression in social insects. The aim of this paper is to investigate allele specific expression and monoallelic methylation in the bumblebee, Bombus terrestris. We found nineteen genes that were both monoallelically methylated and monoallelically expressed in a single bee. Fourteen of these genes express the hypermethylated allele, while the other five express the hypomethylated allele. We also searched for allele specific expression in twenty-nine published RNA-seq libraries. We found 555 loci with allele-specific expression. We discuss our results with reference to the functional role of methylation in gene expression in insects and in the, as yet unquantified, role of genetic cis effects in insect allele specific methylation and expression.

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263 Update on sle-hla association: contribution of allele-specific expression in addition to amino acid changes in hla alleles

10.1136/lupus-2017-000215.263 ◽

2017 ◽

Author(s):

SC Bae ◽

K Kim

Keyword(s):

Amino Acid ◽

Specific Expression ◽

Allele Specific Expression ◽

Hla Association ◽

Hla Alleles ◽

Allele Specific

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Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

Scientific Reports ◽

10.1038/s41598-021-83459-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Joseph Tomlinson ◽

Shawn W. Polson ◽

Jing Qiu ◽

Juniper A. Lake ◽

William Lee ◽

...

Keyword(s):

Broiler Chickens ◽

Nucleotide Polymorphisms ◽

Rna Seq ◽

Specific Expression ◽

Single Nucleotide ◽

Allele Specific Expression ◽

Detection Tool ◽

Commercial Broiler ◽

Significant Phenomenon ◽

Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

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