Evidence map›Paper›PMID 40600064›Full record

ArticleGenes & diseases2025

Haplotype-resolved assemblies of the MHC region in five widely used tumor cell lines.

Haozhe Yuan, Mengping Jiang, Xingyu Xu, Jialiang Zhu, Shulong Dong, Weida Meng, Dandan Zhang, Jiakang Ma, Yicheng Lin, Ziqiang Chen and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genes & diseases, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0cells of the map it votes in
0citing papers in PubMed
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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Haozhe YuanMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200032, China.
Mengping JiangMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200032, China.
Xingyu XuMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200032, China.
Jialiang ZhuMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200032, China.
Shulong DongMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200032, China.
Weida MengMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200032, China.
Dandan ZhangMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200032, China.
Jiakang MaMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200032, China.
Yicheng LinMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200032, China.
Ziqiang ChenMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200032, China.
Shaoyang SunMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
Wenqing QiuShanghai Xuhui Central Hospital, Shanghai 200032, China.
Yun LiuMOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200032, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The major histocompatibility complex (MHC) region plays a crucial role in immune function and is implicated in various diseases and cancer immunoediting. However, its high polymorphism poses challenges for accurate genetic profiling using conventional reference genomes. Here, we present high-quality, haplotype-resolved assemblies of the MHC region in five widely used tumor cell lines: A549, HeLa, HepG2, K562, and U2OS. Numerous oncological studies extensively employ these cell lines, ranging from basic molecular research to drug discovery and personalized medicine approaches. By integrating CRISPR-based targeted enrichment with 10 × Genomics linked-read and PacBio HiFi long-read sequencing, we constructed MHC haplotypes for each cell line, providing a valuable resource for the research community. Using these assembled haplotypes as references, we characterize the aneuploidy of the MHC region in these cell lines, offering insights into the genetic landscape of this critical immunological locus. Our work addresses the urgent need for accurate MHC profiling in these widely used cell line models, enabling more precise interpretation of existing and future genomic and epigenomic data. This resource is expected to significantly enhance our understanding of tumor biology, immune responses, and the development of targeted therapies.

Indexed as

Cell linesCRISPR-Cas9Haplotype-resolved assemblyMHCTargeted sequencing

Identifiers

PMID40600064
PMCPMC12212132

What Socratic holds

Textmetadata
LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.