image: (A) A detailed diagram illustrating the CRISPR-based targeted haplotype-resolved assembly of the MHC region. (B) The positions of two sets of sgRNAs targeting the MHC regions. The lines and boxes colored with semitransparent blue and red represent two sets of sgRNAs showing the targeting sites, respectively. The targeted region spans from 28.6 Mb to 33.4 Mb, while the violet, blue, and green colored boxes represent the regions encompassing HLA class I, class III, and class II genes, respectively. The amber boxes denote the genes used for quantitative real-time PCR analyses, listed according to their coordinates on the GRCh38 reference. (C) The relative enrichment of the targeted MHC region of the tumor cell lines was validated using quantitative real-time PCR. The fold enrichment was quantified relative to the HFE gene, located upstream of the targeted region, and normalized to cells treated without sgRNAs. The relative enrichment for RNF8, a gene outside the targeted MHC region, was tested as a negative control. Data were obtained from two independent experiments. (D) The sequencing coverage of the targeted MHC region of the A549 cell line based on data from the 10x Genomic linked-read and PacBio HiFi sequencing platforms. The beige area, encompassed by the two sets of sgRNAs (red and blue bars at the top), highlights the targeted MHC region. The dashed lines indicate a 50-fold enrichment for 10x Genomics linked-read data (green) and a 30-fold enrichment for PacBio HiFi data (orange).
Credit: Haozhe Yuan, Mengping Jiang, Xingyu Xu, Jialiang Zhu, Shulong Dong, Weida Meng, Dandan Zhang, Jiakang Ma, Yicheng Lin, Ziqiang Chen, Shaoyang Sun, Wenqing Qiu, Yun Liu
The major histocompatibility complex (MHC) region plays a crucial role in immune function; therefore, any genetic or epigenetic polymorphisms within the MHC locus may result in various diseases, as well as cancer immunoediting. Given its high polymorphism, accurately profiling the MHC region using conventional reference genomes is a challenge. Yet, generating complete, high-quality haplotype-resolved assemblies of the MHC region for commonly used cell lines is both a necessity and a valuable resource for the research community.
A recent study published in the Genes & Diseases journal by researchers from Shanghai Xuhui Central Hospital and Fudan University presents high-quality, haplotype-resolved assemblies of the MHC regions in five widely used tumor cell lines: A549 (lung adenocarcinoma), HeLa (cervical adenocarcinoma), HepG2 (hepatocellular carcinoma), K562 (chronic myelogenous leukemia), and U2OS (osteosarcoma).
The authors used CRISPR-based in-gel digestion for the targeted enrichment of the 4.3 Mb MHC region and qRT-PCR to validate its efficiency, which showed more than five-fold enrichment in all three loci within the targeted region (HLA-E, TCF-19, MICB) and no enrichment in the MHC-flanking locus.
The enriched molecules from each cell line were then subjected to 10x Genomics linked reads and PacBio CCS HiFi sequencing, and the sequencing reads aligned to the GRCh38 human reference genome. The A549 and U2OS cells showed the highest enrichment among the five investigated cell lines, while HepG2 cells had the lowest.
The assembled MHC haplotypes ranged from 4.1 Mb to 4.7 Mb in length and demonstrated good continuity when compared with the GRCh38 reference genome. Quality analysis of the assembly with QUAST, BUSCO, and Merqury showed that the assembled MHC haplotypes achieved approximately 90% completeness, with the A549 cell line exhibiting the highest assembly quality.
Furthermore, comprehensive analyses of the haplotype-resolved MHC assemblies for genetic variants identified a large number of single nucleotide polymorphisms, indels, and structural variants, with most located in regions surrounding three HLA class I genes (HLA-A, HLA-B, and HLA-C) and three HLA class II genes (HLA-DR, HLA-DQ, and HLA-DP). Using the assembled MHC haplotypes as references, the authors further characterized the aneuploidy of the MHC region in these cell lines, "offering insights into the genetic landscape of this critical immunological locus."
In conclusion, by integrating CRISPR-based targeted enrichment with 10x Genomics linked-read and PacBio HiFi long-read sequencing, the authors of this study constructed MHC haplotype-resolved assemblies for five commonly used tumor cell lines, which may enable more precise interpretation of existing and future genomic and epigenomic data.
Reference
Title of the original paper: Haplotype-resolved assemblies of the MHC region in five widely used tumor cell lines
Journal: Genes & Diseases
Genes & Diseases is a journal for molecular and translational medicine. The journal primarily focuses on publishing investigations on the molecular bases and experimental therapeutics of human diseases. Publication formats include full length research article, review article, short communication, correspondence, perspectives, commentary, views on news, and research watch.
DOI: https://doi.org/10.1016/j.gendis.2025.101603
# # # # # #
Genes & Diseases publishes rigorously peer-reviewed and high quality original articles and authoritative reviews that focus on the molecular bases of human diseases. Emphasis is placed on hypothesis-driven, mechanistic studies relevant to pathogenesis and/or experimental therapeutics of human diseases. The journal has worldwide authorship, and a broad scope in basic and translational biomedical research of molecular biology, molecular genetics, and cell biology, including but not limited to cell proliferation and apoptosis, signal transduction, stem cell biology, developmental biology, gene regulation and epigenetics, cancer biology, immunity and infection, neuroscience, disease-specific animal models, gene and cell-based therapies, and regenerative medicine.
Scopus CiteScore: 8.4 | Impact Factor: 9.4
# # # # # #
More information: https://www.keaipublishing.com/en/journals/genes-and-diseases/
Editorial Board: https://www.keaipublishing.com/en/journals/genes-and-diseases/editorial-board/
All issues and articles in press are available online in ScienceDirect (https://www.sciencedirect.com/journal/genes-and-diseases).
Submissions to Genes & Disease may be made using Editorial Manager (https://www.editorialmanager.com/gendis/default.aspx ).
Print ISSN: 2352-4820
eISSN: 2352-3042
CN: 50-1221/R
Contact Us: editor@genesndiseases.com
X (formerly Twitter): @GenesNDiseases (https://x.com/GenesNDiseases)
Journal
Genes & Diseases