SIMarker: Cellular similarity detection and its application to diagnosis and prognosis of liver cancer.
Comput Biol Med
; 171: 108113, 2024 Mar.
Article
en En
| MEDLINE
| ID: mdl-38368754
ABSTRACT
BACKGROUND:
The emergence of single-cell technology offers a unique opportunity to explore cellular similarity and heterogeneity between precancerous diseases and solid tumors. However, there is lacking a systematic study for identifying and characterizing similarities at single-cell resolution.METHODS:
We developed SIMarker, a computational framework to detect cellular similarities between precancerous diseases and solid tumors based on gene expression at single-cell resolution. Taking hepatocellular carcinoma (HCC) as a case study, we quantified the cellular and molecular connections between HCC and cirrhosis. Core analysis modules of SIMarker is publicly available at https//github.com/xmuhuanglab/SIMarker ("SIM" means "similarity" and "Marker" means "biomarkers).RESULTS:
We found PGA5+ hepatocytes in HCC showed cirrhosis-like characteristics, including similar transcriptional programs and gene regulatory networks. Consequently, the genes constituting the gene expression program of these cirrhosis-like subpopulations were designated as cirrhosis-like signatures (CLS). Strikingly, our utilization of CLS enabled the development of diagnosis and prognosis biomarkers based on within-sample relative expression orderings of gene pairs. These biomarkers achieved high precision and concordance compared with previous studies.CONCLUSIONS:
Our work provides a systematic method to investigate the clinical translational significance of cellular similarities between HCC and cirrhosis, which opens avenues for identifying similar paradigms in other categories of cancers and diseases.Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Lesiones Precancerosas
/
Carcinoma Hepatocelular
/
Neoplasias Hepáticas
Límite:
Humans
Idioma:
En
Revista:
Comput Biol Med
Año:
2024
Tipo del documento:
Article