ABSTRACT
Human leukocyte antigen (HLA) typing is of great importance in clinical applications such as organ transplantation, blood transfusion, disease diagnosis and treatment, and forensic analysis. In recent years, nanopore sequencing technology has emerged as a rapid and cost-effective option for HLA typing. However, due to the principles and data characteristics of nanopore sequencing, there was a scarcity of robust and generalizable bioinformatics tools for its downstream analysis, posing a significant challenge in deciphering the thousands of HLA alleles present in the human population. To address this challenge, we developed NanoHLA as a tool for high-resolution typing of HLA class I genes without error correction based on nanopore sequencing. The method integrated the concepts of HLA type coverage analysis and the data conversion techniques employed in Nano2NGS, which was characterized by applying nanopore sequencing data to NGS-liked data analysis pipelines. In validation with public nanopore sequencing datasets, NanoHLA showed an overall concordance rate of 84.34% for HLA-A, HLA-B, and HLA-C, and demonstrated superior performance in comparison to existing tools such as HLA-LA. NanoHLA provides tools and solutions for use in HLA typing related fields, and look forward to further expanding the application of nanopore sequencing technology in both research and clinical settings. The code is available at https://github.com/langjidong/NanoHLA .
Subject(s)
Alleles , Histocompatibility Testing , Nanopore Sequencing , Humans , Histocompatibility Testing/methods , Nanopore Sequencing/methods , Computational Biology/methods , High-Throughput Nucleotide Sequencing/methods , Software , Histocompatibility Antigens Class I/genetics , HLA Antigens/genetics , Sequence Analysis, DNA/methods , Genes, MHC Class I/geneticsABSTRACT
Background: Neoantigens, mutated tumour-specific antigens, are key targets of anti-tumour immunity during checkpoint inhibitor (CPI) treatment. Their identification is fundamental to designing neoantigen-directed therapy. Non-canonical neoantigens arising from the untranslated regions (UTR) of the genome are an overlooked source of immunogenic neoantigens. Here, we describe the landscape of UTR-derived neoantigens and release a computational tool, PrimeCUTR, to predict UTR neoantigens generated by start-gain and stop-loss mutations. Methods: We applied PrimeCUTR to a whole genome sequencing dataset of pre-treatment tumour samples from CPI-treated patients (n = 341). Cancer immunopeptidomic datasets were interrogated to identify MHC class I presentation of UTR neoantigens. Results: Start-gain neoantigens were predicted in 72.7% of patients, while stop-loss mutations were found in 19.3% of patients. While UTR neoantigens only accounted 2.6% of total predicted neoantigen burden, they contributed 12.4% of neoantigens with high dissimilarity to self-proteome. More start-gain neoantigens were found in CPI responders, but this relationship was not significant when correcting for tumour mutational burden. While most UTR neoantigens are private, we identified two recurrent start-gain mutations in melanoma. Using immunopeptidomic datasets, we identify two distinct MHC class I-presented UTR neoantigens: one from a recurrent start-gain mutation in melanoma, and one private to Jurkat cells. Conclusion: PrimeCUTR is a novel tool which complements existing neoantigen discovery approaches and has potential to increase the detection yield of neoantigens in personalised therapeutics, particularly for neoantigens with high dissimilarity to self. Further studies are warranted to confirm the expression and immunogenicity of UTR neoantigens.
Subject(s)
Melanoma , Humans , Antigens, Neoplasm/genetics , Genes, MHC Class I , Mutation , ImmunotherapyABSTRACT
The novel HLA-B*13:191 allele was detected during the HLA typing for kidney transplantation.
Subject(s)
HLA-B Antigens , Kidney Transplantation , Humans , Alleles , HLA-B Antigens/genetics , Genes, MHC Class I , High-Throughput Nucleotide SequencingABSTRACT
HLA-C*06:376N differs from HLA-C*06:02:01:01 by seven nucleotide changes in exon 2, intron 2, and exon 3.
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Humans , HLA-C Antigens/genetics , Alleles , Sequence Analysis, DNA , China , High-Throughput Nucleotide SequencingABSTRACT
HLA-C*07:04:29 differs from HLA-C*07:04:01:01 by a single substitution in exon 4.
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Humans , Alleles , China , High-Throughput Nucleotide Sequencing , HLA-C Antigens/genetics , East Asian PeopleABSTRACT
A novel HLA-C*07 allele, now officially designated HLA-C*07:02:150, was identified by next-generation sequencing.
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Humans , HLA-C Antigens/genetics , Alleles , High-Throughput Nucleotide SequencingABSTRACT
HLA-B*58:02:04 differs from HLA-B*58:02:01 by one synonymous nucleotide in codon 215 in exon 4.
Subject(s)
Genes, MHC Class I , HLA-B Antigens , Humans , Alleles , HLA-B Antigens/genetics , Codon , High-Throughput Nucleotide SequencingABSTRACT
The HLA-B*40:538 allele differs from HLA-B*40:01:02:01 at position 905 CâT in exon 5.
Subject(s)
Genes, MHC Class I , High-Throughput Nucleotide Sequencing , Humans , Alleles , Exons/genetics , HLA-B Antigens/geneticsABSTRACT
The novel allele HLA-C*07:02:147 differs from HLA-C*07:02:01:01 by one synonymous nucleotide substitution in exon 2.
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Humans , HLA-C Antigens/genetics , Alleles , Exons/genetics , NucleotidesABSTRACT
HLA-C*03:94:02 differs from HLA-C*03:94:01 by a single nucleotide substitution in exon 2 (codon 17 GGA->GGG).
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Humans , HLA-C Antigens/genetics , Alleles , High-Throughput Nucleotide Sequencing , ChinaABSTRACT
Novel HLA-B*55:01:31, HLA-C*07:1113 alleles and confirmatory HLA-C*12:392 allele were detected during the HLA typing process.
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Humans , Alleles , HLA-C Antigens/genetics , HLA-B Antigens/genetics , Histocompatibility TestingABSTRACT
Two nucleotide substitutions in intronic regions give rise to the novel alleles: HLA-B*35:01:01:39 and -B*35:03:01:32.
Subject(s)
Genes, MHC Class I , HLA-B Antigens , Humans , Alleles , HLA-B Antigens/genetics , Introns , High-Throughput Nucleotide SequencingABSTRACT
HLA-B*46:01:42 differs from HLA-B*46:01:01:01 by one nucleotide in exon 5.
Subject(s)
Genes, MHC Class I , Nucleotides , Humans , Alleles , HLA-B Antigens/genetics , China , Sequence Analysis, DNAABSTRACT
The novel HLA-C*14:159 allele was detected during the routine HLA typing for kidney transplantation.
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Humans , HLA-C Antigens/genetics , Alleles , High-Throughput Nucleotide Sequencing , Histocompatibility TestingABSTRACT
HLA-C*17:01:01:29 differs from the HLA-C*17:01:01:05 allele by one nucleotide substitution in the 3'UTR.
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Humans , HLA-C Antigens/genetics , Greece , Alleles , 3' Untranslated RegionsABSTRACT
HLA-C*04:01:01:174 differs from the HLA-C*04:01:01:06 allele by one nucleotide substitution in the intron 5.
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Humans , HLA-C Antigens/genetics , Greece , Alleles , IntronsABSTRACT
HLA-C*01:02:01:70 differs from the HLA-C*01:02:01:01 allele by one nucleotide substitution in the intron 4.
Subject(s)
Genes, MHC Class I , HLA-C Antigens , Humans , HLA-C Antigens/genetics , Greece , Alleles , IntronsABSTRACT
Antigen presentation to CD8+ T cells by MHC class I molecules is essential for host defense against viral infections. Various mechanisms have evolved in multiple viruses to escape immune surveillance and defense to support viral proliferation in host cells. Through in vitro SARS-CoV-2 infection studies and analysis of COVID-19 patient samples, we found that SARS-CoV-2 suppresses the induction of the MHC class I pathway by inhibiting the expression and function of NLRC5, a major transcriptional regulator of MHC class I genes. In this review, we discuss the molecular mechanisms for suppression of the MHC class I pathway and clinical implications for COVID-19.
Subject(s)
COVID-19 , Genes, MHC Class I , Humans , Trans-Activators/genetics , SARS-CoV-2/genetics , COVID-19/genetics , Histocompatibility Antigens Class I , Intracellular Signaling Peptides and Proteins/geneticsABSTRACT
HLA-B*58:01:40 differs from HLA-B*58:01:01 by a single nucleotide change in exon 3, 507 C- > T (codon 145.3 CGC- > CGT).
Subject(s)
Asian People , Genes, MHC Class I , Humans , Alleles , Asian People/genetics , HLA-B Antigens/genetics , ChinaABSTRACT
HLA-B*41:02:01:11 and -C*08:266 were detected in a solid organ recipient during the HLA typing process.