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Integration of Bulk RNA Sequencing and Single-Cell Sequencing to Identify Prognostic Genes Associated With MCDRGs in Neuroblastoma.

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Title: Integration of Bulk RNA Sequencing and Single-Cell Sequencing to Identify Prognostic Genes Associated With MCDRGs in Neuroblastoma.
Authors: Lin J; Department of Pediatric Urology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.; Sichuan Provincial Children's Hospital (Sichuan Provincial Children's Medical Center), Meishan, Sichuan, China., Gao Z; Shenzhen Medical Academy of Research and Translation, Shenzhen, Guangdong, China.; Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China., Qin D; Department of Pediatric Urology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.; Sichuan Provincial Children's Hospital (Sichuan Provincial Children's Medical Center), Meishan, Sichuan, China., Huang H; Department of Pediatric Urology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.; Sichuan Provincial Children's Hospital (Sichuan Provincial Children's Medical Center), Meishan, Sichuan, China., Zhang Z; Department of Pediatric Urology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.; Sichuan Provincial Children's Hospital (Sichuan Provincial Children's Medical Center), Meishan, Sichuan, China., Liu F; Department of Pediatric Urology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.; Sichuan Provincial Children's Hospital (Sichuan Provincial Children's Medical Center), Meishan, Sichuan, China.
Source: FASEB journal : official publication of the Federation of American Societies for Experimental Biology [FASEB J] 2026 Aug 31; Vol. 40 (16), pp. e72175.
Publication Type: Journal Article
Language: English
Journal Info: Publisher: Federation of American Societies for Experimental Biology Country of Publication: United States NLM ID: 8804484 Publication Model: Print Cited Medium: Internet ISSN: 1530-6860 (Electronic) Linking ISSN: 08926638 NLM ISO Abbreviation: FASEB J Subsets: MEDLINE
Imprint Name(s): Publication: 2020- : [Bethesda, Md.] : Hoboken, NJ : Federation of American Societies for Experimental Biology ; Wiley
Original Publication: [Bethesda, Md.] : The Federation, [c1987-
MeSH Terms: Neuroblastoma*/genetics , Neuroblastoma*/pathology , Single-Cell Analysis*/methods , Sequence Analysis, RNA*/methods , Myeloid Cells*/metabolism , Myeloid Cells*/pathology , Biomarkers, Tumor*/genetics , Gene Expression Regulation, Neoplastic*, Tumor Microenvironment/genetics ; Cell Differentiation/genetics ; Humans ; Prognosis ; Single-Cell Gene Expression Analysis ; Transcriptome ; Gene Expression Profiling
Abstract: Neuroblastoma (NB) is a common pediatric tumor that exhibits significant clinical heterogeneity and substantial prognostic variability. However, there is still a lack of effective prognostic tools. It has been found that the differentiation of myeloid cells in the tumor microenvironment (TME) has a profound influence on tumor progression and immune regulation in neuroblastoma. But the correlation between NB and myeloid cell differentiation-related genes (MCDRGs) is still unclear. This study integrated bulk and single-cell RNA sequencing data to identify key prognostic genes associated with myeloid cell differentiation, construct and validate a risk prediction model, and thoroughly investigate the molecular mechanisms through which these genes regulate the TME and influence NB prognosis. Using bioinformatic approaches, we retrieved NB-related transcriptomic data from public databases, identified differentially expressed myeloid cell differentiation-related genes (MCDRGs), and constructed a prognostic risk model using Cox regression and machine-learning algorithms. Functional enrichment analysis, TME characterization, immune checkpoint profiling, drug sensitivity analysis, and somatic mutation analysis were performed between the high-risk group (HRG) and low-risk group (LRG). Single-cell RNA sequencing data were used to dissect the cell type-specific expression patterns of prognostic genes, which were further experimentally validated via reverse transcription quantitative polymerase chain reaction (RT-qPCR). Five key prognostic genes (FAXDC2, GP1BB, TRIB1, ETV2, and H4C12) were identified from 187 candidate genes, and a robust risk prediction model was constructed. Significant differences were observed between the HRG and LRG in terms of TME scores, immune cell infiltration, and immune checkpoint expression. Ribosome biogenesis and cell cycle-related pathways were enriched in the HRG, which displayed higher sensitivity to entinostat and sapitinib. Single-cell analysis further highlighted fibroblasts and myeloid cells as key cell subsets in which prognostic genes exhibited dynamic expression patterns. RT-qPCR further validated these gene expression trends. The prognostic model based on MCDRGs effectively predicts survival outcomes in patients with NB. This model systematically reveals the comprehensive mechanisms by which MCDRGs influence prognosis through regulating the TME, cell-cell interactions, and therapeutic responses. These findings provide a new theoretical basis and potential targets for precise risk stratification and individualized treatment strategies in NB.
(© 2026 Federation of American Societies for Experimental Biology.)
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Grant Information: KZ317 K Foundation of West China Second University Hospital, Sichuan University
Contributed Indexing: Keywords: Neuroblastoma; myeloid cell differentiation; prognostic genes; risk model
Substance Nomenclature: 0 (Biomarkers, Tumor)
Entry Date(s): Date Created: 20260814 Date Completed: 20260814 Latest Revision: 20260816
Update Code: 20260816
PubMed Central ID: PMC13475957
DOI: 10.1096/fj.202601255R
PMID: 42600038
Database: MEDLINE
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  Data: Integration of Bulk RNA Sequencing and Single-Cell Sequencing to Identify Prognostic Genes Associated With MCDRGs in Neuroblastoma.
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  Data: <searchLink fieldCode="AU" term="%22Lin+J%22">Lin J</searchLink>; Department of Pediatric Urology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.; Sichuan Provincial Children's Hospital (Sichuan Provincial Children's Medical Center), Meishan, Sichuan, China.<br /><searchLink fieldCode="AU" term="%22Gao+Z%22">Gao Z</searchLink>; Shenzhen Medical Academy of Research and Translation, Shenzhen, Guangdong, China.; Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China.<br /><searchLink fieldCode="AU" term="%22Qin+D%22">Qin D</searchLink>; Department of Pediatric Urology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.; Sichuan Provincial Children's Hospital (Sichuan Provincial Children's Medical Center), Meishan, Sichuan, China.<br /><searchLink fieldCode="AU" term="%22Huang+H%22">Huang H</searchLink>; Department of Pediatric Urology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.; Sichuan Provincial Children's Hospital (Sichuan Provincial Children's Medical Center), Meishan, Sichuan, China.<br /><searchLink fieldCode="AU" term="%22Zhang+Z%22">Zhang Z</searchLink>; Department of Pediatric Urology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.; Sichuan Provincial Children's Hospital (Sichuan Provincial Children's Medical Center), Meishan, Sichuan, China.<br /><searchLink fieldCode="AU" term="%22Liu+F%22">Liu F</searchLink>; Department of Pediatric Urology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.; Sichuan Provincial Children's Hospital (Sichuan Provincial Children's Medical Center), Meishan, Sichuan, China.
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  Data: <searchLink fieldCode="MM" term="%22Neuroblastoma%22">Neuroblastoma*</searchLink>/<searchLink fieldCode="MM" term="%22Neuroblastoma+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Neuroblastoma%22">Neuroblastoma*</searchLink>/<searchLink fieldCode="MM" term="%22Neuroblastoma+pathology%22">pathology</searchLink> <br /><searchLink fieldCode="MM" term="%22Single-Cell+Analysis%22">Single-Cell Analysis*</searchLink>/<searchLink fieldCode="MM" term="%22Single-Cell+Analysis+methods%22">methods</searchLink> <br /><searchLink fieldCode="MM" term="%22Sequence+Analysis%2C+RNA%22">Sequence Analysis, RNA*</searchLink>/<searchLink fieldCode="MM" term="%22Sequence+Analysis%2C+RNA+methods%22">methods</searchLink> <br /><searchLink fieldCode="MM" term="%22Myeloid+Cells%22">Myeloid Cells*</searchLink>/<searchLink fieldCode="MM" term="%22Myeloid+Cells+metabolism%22">metabolism</searchLink> <br /><searchLink fieldCode="MM" term="%22Myeloid+Cells%22">Myeloid Cells*</searchLink>/<searchLink fieldCode="MM" term="%22Myeloid+Cells+pathology%22">pathology</searchLink> <br /><searchLink fieldCode="MM" term="%22Biomarkers%2C+Tumor%22">Biomarkers, Tumor*</searchLink>/<searchLink fieldCode="MM" term="%22Biomarkers%2C+Tumor+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Gene+Expression+Regulation%2C+Neoplastic%22">Gene Expression Regulation, Neoplastic*</searchLink><br /><searchLink fieldCode="MH" term="%22Tumor+Microenvironment%22">Tumor Microenvironment</searchLink>/<searchLink fieldCode="MH" term="%22Tumor+Microenvironment+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Cell+Differentiation%22">Cell Differentiation</searchLink>/<searchLink fieldCode="MH" term="%22Cell+Differentiation+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Humans%22">Humans</searchLink> ; <searchLink fieldCode="MH" term="%22Prognosis%22">Prognosis</searchLink> ; <searchLink fieldCode="MH" term="%22Single-Cell+Gene+Expression+Analysis%22">Single-Cell Gene Expression Analysis</searchLink> ; <searchLink fieldCode="MH" term="%22Transcriptome%22">Transcriptome</searchLink> ; <searchLink fieldCode="MH" term="%22Gene+Expression+Profiling%22">Gene Expression Profiling</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Neuroblastoma (NB) is a common pediatric tumor that exhibits significant clinical heterogeneity and substantial prognostic variability. However, there is still a lack of effective prognostic tools. It has been found that the differentiation of myeloid cells in the tumor microenvironment (TME) has a profound influence on tumor progression and immune regulation in neuroblastoma. But the correlation between NB and myeloid cell differentiation-related genes (MCDRGs) is still unclear. This study integrated bulk and single-cell RNA sequencing data to identify key prognostic genes associated with myeloid cell differentiation, construct and validate a risk prediction model, and thoroughly investigate the molecular mechanisms through which these genes regulate the TME and influence NB prognosis. Using bioinformatic approaches, we retrieved NB-related transcriptomic data from public databases, identified differentially expressed myeloid cell differentiation-related genes (MCDRGs), and constructed a prognostic risk model using Cox regression and machine-learning algorithms. Functional enrichment analysis, TME characterization, immune checkpoint profiling, drug sensitivity analysis, and somatic mutation analysis were performed between the high-risk group (HRG) and low-risk group (LRG). Single-cell RNA sequencing data were used to dissect the cell type-specific expression patterns of prognostic genes, which were further experimentally validated via reverse transcription quantitative polymerase chain reaction (RT-qPCR). Five key prognostic genes (FAXDC2, GP1BB, TRIB1, ETV2, and H4C12) were identified from 187 candidate genes, and a robust risk prediction model was constructed. Significant differences were observed between the HRG and LRG in terms of TME scores, immune cell infiltration, and immune checkpoint expression. Ribosome biogenesis and cell cycle-related pathways were enriched in the HRG, which displayed higher sensitivity to entinostat and sapitinib. Single-cell analysis further highlighted fibroblasts and myeloid cells as key cell subsets in which prognostic genes exhibited dynamic expression patterns. RT-qPCR further validated these gene expression trends. The prognostic model based on MCDRGs effectively predicts survival outcomes in patients with NB. This model systematically reveals the comprehensive mechanisms by which MCDRGs influence prognosis through regulating the TME, cell-cell interactions, and therapeutic responses. These findings provide a new theoretical basis and potential targets for precise risk stratification and individualized treatment strategies in NB.<br /> (© 2026 Federation of American Societies for Experimental Biology.)
– Name: Ref
  Label: References
  Group: RefInfo
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  Group: Grant
  Data: KZ317 K Foundation of West China Second University Hospital, Sichuan University
– Name: SubjectMinor
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  Data: <i>Keywords: </i>Neuroblastoma; myeloid cell differentiation; prognostic genes; risk model
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  Data: 10.1096/fj.202601255R
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        Value: 10.1096/fj.202601255R
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      – Code: eng
        Text: English
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      Pagination:
        StartPage: e72175
    Subjects:
      – SubjectFull: Tumor Microenvironment genetics
        Type: general
      – SubjectFull: Cell Differentiation genetics
        Type: general
      – SubjectFull: Humans
        Type: general
      – SubjectFull: Prognosis
        Type: general
      – SubjectFull: Single-Cell Gene Expression Analysis
        Type: general
      – SubjectFull: Transcriptome
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      – SubjectFull: Gene Expression Profiling
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      – SubjectFull: Neuroblastoma genetics
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      – SubjectFull: Neuroblastoma pathology
        Type: general
      – SubjectFull: Single-Cell Analysis methods
        Type: general
      – SubjectFull: Sequence Analysis, RNA methods
        Type: general
      – SubjectFull: Myeloid Cells metabolism
        Type: general
      – SubjectFull: Myeloid Cells pathology
        Type: general
      – SubjectFull: Biomarkers, Tumor genetics
        Type: general
      – SubjectFull: Gene Expression Regulation, Neoplastic
        Type: general
    Titles:
      – TitleFull: Integration of Bulk RNA Sequencing and Single-Cell Sequencing to Identify Prognostic Genes Associated With MCDRGs in Neuroblastoma.
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              M: 08
              Text: 2026 Aug 31
              Type: published
              Y: 2026
          Identifiers:
            – Type: issn-electronic
              Value: 1530-6860
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              Value: 40
            – Type: issue
              Value: 16
          Titles:
            – TitleFull: FASEB journal : official publication of the Federation of American Societies for Experimental Biology
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