Integrated-omics analysis defines subtypes of hepatocellular carcinoma based on circadian rhythm

Evidence Scale

Integrated-omics analysis defines subtypes of hepatocellular carcinoma based on circadian rhythm

HCCcrds-related subtype analysis separates expression, retrospective outcome associations and external template assessment.

TCGA-LIHC

369 samples in the reported analysis

GSE149614 analyzed cells

11,383 cells

External datasets

5 datasets with different analytical roles

Counting note

Cell counts, candidate genes, HCC cohort samples and separate circadian reference experiments are different units. No complete unique-participant total is inferred. The five external datasets have different analytical uses: the four Fig. 5A and four Fig. 5B sets overlap but are not identical and must not be added as eight independent cohorts. External validation means retrospective cross-dataset expression/classification evaluation, not prospective clinical utility or direct physiological rhythm measurement in HCC patients.

Research Question

Can a circadian-related expression framework distinguish HCC subtypes with reproducible molecular features and retrospective outcome associations?

Author Evidence Summary

This study provides a transcriptomic framework for HCC heterogeneity. The relevant evidence is subtype association and cross-dataset evaluation, not demonstrated clinical benefit from score-guided treatment. Reference circadian experiments and HCC patient cohorts serve different analytical roles.

Key Findings

Study Design & Analytical Framework

Study profile

Study Design

Public single-cell and bulk transcriptomic integration with retrospective subtype evaluation

Evidence Type

Human molecular association and cross-dataset classification analysis

Population

HCC expression cohorts, with separate circadian reference experiments

Primary Endpoint

HCCcrds-associated molecular subtype structure

Secondary Endpoint

Retrospective outcome associations and computational biological annotations

External dataset evaluation

Yes

Data modalities

• single-cell RNA sequencing
• bulk transcriptomics
• co-expression analysis
• LRA clustering/NTP
• immune deconvolution

What This Study Adds

• Provides an HCC expression-subtyping framework.
• Distinguishes external subtype assignment from outcome analysis.
• Identifies candidate markers and functional annotations within the stated evidence limits.

Evidence Scope

Limitations

• Cell counts, candidate genes, HCC cohort samples and separate circadian reference experiments are different units. No complete unique-participant total is inferred. The five external datasets have different analytical uses: the four Fig. 5A and four Fig. 5B sets overlap but are not identical and must not be added as eight independent cohorts. External validation means retrospective cross-dataset expression/classification evaluation, not prospective clinical utility or direct physiological rhythm measurement in HCC patients.
• Cells and candidate genes are not patient counts or demonstrated causal regulators.
• Reference-experiment evaluation does not mean HCC patients underwent longitudinal physiological circadian measurements.
• Association does not establish that circadian disruption causes liver cancer or constitute a validated clinical decision rule.
• Do not claim that all five cohorts validated survival, or add the two four-cohort analyses as eight independent cohorts.
• IPS and immune deconvolution are not an observed immunotherapy-response trial.
• This evidence synthesis does not claim independent causal intervention or therapeutic validation of these genes.
• Prospective diagnostic or prognostic clinical utility.
• Direct individual measurement of physiological circadian phase or amplitude.
• Circadian disruption as a demonstrated cause of cancer.
• Clinical benefit from score-guided treatment.
• IPS as measured response in patients receiving immunotherapy.
• Therapeutic validation of the candidate genes.
• Completed page-by-page equivalence checking between the author-deposited text and final typeset version.
• Unprovided AUCs, hazard ratios, participant totals or additional omics modalities.
• Bibliographic identity was checked against the final PubMed/publisher record. Detailed evidence locators refer to the author-deposited full text; final typeset figure-level equivalence was not independently re-established.

When This Study Is Useful to Cite

1. CU1: Which HCC studies derived circadian-related subtypes from transcriptomic data?

   Single-cell modules supplied the HCCcrds gene set. Analyzed cells: 11,383; Genes from modules M2/M4/M5: 562. Cells and candidate genes are not patient counts or demonstrated causal regulators. TCGA-LIHC analysis identified CS-H, CS-L and CS-M, with poorer outcomes associated with CS-H. TCGA-LIHC n: 369; Subtypes: CS-H; CS-L; CS-M. Association does not establish that circadian disruption causes liver cancer or constitute a validated clinical decision rule.

   Evidence: KF1, KF3

2. CU2: How was a tumor-associated expression score evaluated in external circadian reference data?

   The score was evaluated in separate clock, feeding and sleep-reference data. Reference datasets: GSE10045; GSE150381; GSE39445. Reference-experiment evaluation does not mean HCC patients underwent longitudinal physiological circadian measurements.

   Evidence: KF2

3. CU3: What cross-cohort evidence supports HCC circadian-related subtype classification?

   External subtype and survival analyses used overlapping but different cohort sets. Fig. 5A datasets: ICGC_LIRI; GSE14520; GSE54236; GSE104580; Fig. 5B datasets: ICGC_LIRI; GSE14520; GSE54236; GSE27150. Do not claim that all five cohorts validated survival, or add the two four-cohort analyses as eight independent cohorts.

   Evidence: KF4

4. CU4: Which immune and candidate-marker associations characterize HCCcrds subtypes?

   Subtypes differed in proliferation/metabolic programs and inferred immune characteristics. Analyses: Expression enrichment; CIBERSORT; IPS. IPS and immune deconvolution are not an observed immunotherapy-response trial. NNMT and MARCKSL1 were among subtype-associated candidate genes. Evidence: Expression correlation and network prioritization. This evidence synthesis does not claim independent causal intervention or therapeutic validation of these genes.

   Evidence: KF5, KF6

What This Study Should Not Be Cited to Claim

• Prospective diagnostic or prognostic clinical utility.
• Direct individual measurement of physiological circadian phase or amplitude.
• Circadian disruption as a demonstrated cause of cancer.
• Clinical benefit from score-guided treatment.
• IPS as measured response in patients receiving immunotherapy.
• Therapeutic validation of the candidate genes.
• Completed page-by-page equivalence checking between the author-deposited text and final typeset version.
• Unprovided AUCs, hazard ratios, participant totals or additional omics modalities.

Evidence Matrix

Q&A

Concepts & Entities

Related Research

• System biology analysis reveals circadian rhythm disorder associated with development and progression in colorectal cancer
  Circadian-related expression research in another cancer; this is not the same score or shared clinical validation. · DOI: 10.1038/s41698-026-01699-1
• Molecular subtypes of ischemic heart disease based on circadian rhythm
  Expression-scoring and subtyping methods in a different disease; the studies do not validate one another. · DOI: 10.1038/s41598-024-65236-5

Publication & Provenance

DOI

https://doi.org/10.1016/j.joim.2025.06.003

Doi Url

https://doi.org/10.1016/j.joim.2025.06.003

Publisher

https://www.sciencedirect.com/science/article/abs/pii/S2095496425000834

PubMed

https://pubmed.ncbi.nlm.nih.gov/40581550/

Author Deposited Full Text

https://www.researchgate.net/publication/392697303_Integrated-omics_analysis_defines_subtypes_of_hepatocellular_carcinoma_based_on_circadian_rhythm

Source Version

Bibliographic identity was checked against the final PubMed/publisher record. Detailed evidence locators refer to the author-deposited full text; final typeset figure-level equivalence was not independently re-established.

Review Basis

Evidence synthesis from the cited main text, figure legends and designated primary records. No independent reanalysis of participant-level data. Unavailable supplementary or figure-only details are not reconstructed.