Fusion RNA Profiling in Cancer: Investigating the Etiology of Fusion-Gene-Associated Cancers and Proposing an Approach to Study Connections Between Biological Samples.

Zhongqiu Xie, Huiling Yuan, Hui Li

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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. 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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1 · What the graph read from it

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4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Zhongqiu Xie *Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.

Huiling Yuan *Department of Breast Surgery, Dongguan People's Hospital, Southern Medical University, Dongguan, Guangdong, 523059, China.

Hui LiDepartment of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA. hl9r@virginia.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Gene fusions were thought to be unique features of neoplasia. However, more and more studies have identified fusion RNAs in normal physiology. Through RNA sequencing of human normal tissues from GTEx project, many chimeric RNAs were found. By analyzing the fusion transcriptome, we observed a close cluster between samples of the same or similar tissues, supporting the feasibility of using fusion RNA profiling to reveal connections between biological samples. To put the concept into use, we selected alveolar rhabdomyosarcoma (ARMS), a myogenic pediatric cancer whose exact cell of origin is not clear. PAX3-FOXO1 fusion RNA, which is considered a hallmark of ARMS, was found during normal muscle cell differentiation. We analyzed RNA sequencing from various time points during myogenesis and uncovered many chimeric fusion RNAs.

Indexed as

Gene Expression ProfilingGene FusionNeoplasmsOncogene Proteins, FusionRhabdomyosarcoma, AlveolarForkhead Box Protein O1Gene Expression Regulation, NeoplasticHumansMuscle DevelopmentPAX3 Transcription FactorSequence Analysis, RNATranscriptomeForkhead Box Protein O1Oncogene Proteins, FusionPAX3 Transcription FactorARMSBiological samplesFusion RNA profilingPAX3–FOXO1

Identifiers

PMID42400800

DOI10.1093/nar/gkz1223

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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 OpenQuestion graph.