# NK cell–associated LncRNA signature predicts prognosis and immune landscape in hepatocellular carcinoma

**Authors:** Xiangyang Li, Jinze Li, Yuxuan Li, Yuhao Fan, Wei Tan, Fan Shi, Ya Zhu, Cheng Gong

PMC · DOI: 10.1007/s10238-026-02083-w · Clinical and Experimental Medicine · 2026-02-24

## TL;DR

This study creates a model using lncRNAs linked to NK cells to predict liver cancer outcomes and understand immune interactions.

## Contribution

A novel NK cell-associated lncRNA model is developed for HCC prognosis and immune landscape analysis.

## Key findings

- A four-lncRNA model robustly predicts HCC patient outcomes.
- NK cells synergize with CD8+ T cells in the HCC tumor microenvironment.
- New HCC molecular subgroups linked to immune profiles and drug sensitivity are identified.

## Abstract

The purpose of this investigation was to develop and validate a risk model based on natural killer (NK) cell-associated lncRNAs to predict outcomes in individuals with hepatocellular carcinoma (HCC). To further explore the role of NK cells in the HCC tumor microenvironment, we leveraged single-cell RNA sequencing data and the TCGA-LIHC dataset to identify NK cell-associated lncRNAs. Using Cox regression and LASSO techniques, we pinpointed four key lncRNAs as prognostic markers for the model. The model demonstrated robust predictive power across the training set, validation set, and entire dataset. Additionally, we identified a synergistic interaction between NK cells and other immune cells, particularly CD8 + T cells, in HCC. Moreover, we uncovered novel molecular subgroups of HCC and their associations with the immune microenvironment and drug sensitivity. To further validate these findings, we performed experimental validation of the expression and function of the model lncRNAs in HCC. These results suggest that the NK cell-associated lncRNA model not only serves as an effective prognostic tool for HCC patient outcomes but also offers potential molecular targets for immunotherapy and targeted therapies.

The online version contains supplementary material available at 10.1007/s10238-026-02083-w.

## Linked entities

- **Diseases:** hepatocellular carcinoma (MONDO:0007256), HCC (MONDO:0007256)

## Full-text entities

- **Genes:** IL2 (interleukin 2) [NCBI Gene 3558] {aka IL-2, TCGF, lymphokine}, CD274 (CD274 molecule) [NCBI Gene 29126] {aka ADMIO5, B7-H, B7H1, PD-L1, PDCD1L1, PDCD1LG1}, SNAI1 (snail family transcriptional repressor 1) [NCBI Gene 6615] {aka SLUGH2, SNA, SNAH, SNAIL, SNAIL1, dJ710H13.1}, CD80 (CD80 molecule) [NCBI Gene 941] {aka B7, B7-1, B7.1, BB1, CD28LG, CD28LG1}, NRAV (negative regulator of antiviral response) [NCBI Gene 100506668] {aka DYNLL1-AS1, DYNLL1AS1}, CD4 (CD4 molecule) [NCBI Gene 920] {aka CD4mut, IMD79, Leu-3, OKT4D, T4}, MYBL2 (MYB proto-oncogene like 2) [NCBI Gene 4605] {aka B-MYB, BMYB}, TNFSF18 (TNF superfamily member 18) [NCBI Gene 8995] {aka AITRL, GITRL, TL6, TNLG2A, hGITRL}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, LINC01139 (long intergenic non-protein coding RNA 1139) [NCBI Gene 339535] {aka LINK-A, LINKA}, TBP (TATA-box binding protein) [NCBI Gene 6908] {aka GTF2D, GTF2D1, HDL4, SCA17, TBP1, TFIID}, TNFSF9 (TNF superfamily member 9) [NCBI Gene 8744] {aka 4-1BB-L, CD137L, TNLG5A}, MAF (MAF bZIP transcription factor) [NCBI Gene 4094] {aka AYGRP, CCA4, CTRCT21, c-MAF}, NOTCH1 (notch receptor 1) [NCBI Gene 4851] {aka AOS5, AOVD1, TAN1, hN1}, TIPE2 (TNF alpha induced protein 8 like 2) [NCBI Gene 79626] {aka TNFAIP8L2}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, TAF1 (TATA-box binding protein associated factor 1) [NCBI Gene 6872] {aka BA2R, CCG1, CCGS, DYT3, DYT3/TAF1, KAT4}, CTLA4 (cytotoxic T-lymphocyte associated protein 4) [NCBI Gene 1493] {aka ALPS5, CD, CD152, CELIAC3, CTLA-4, GRD4}, F3 (coagulation factor III, tissue factor) [NCBI Gene 2152] {aka CD142, TF, TFA}, BCL3 (BCL3 transcription coactivator) [NCBI Gene 602] {aka BCL4, D19S37}, ETS1 (ETS proto-oncogene 1, transcription factor) [NCBI Gene 2113] {aka ETS-1, EWSR2, c-ets-1, p54}, CD44 (CD44 molecule (IN blood group)) [NCBI Gene 960] {aka CDW44, CSPG8, ECM-III, ECMR-III, H-CAM, HCELL}, BRD4 (bromodomain containing 4) [NCBI Gene 23476] {aka CAP, CDLS6, FSHRG4, HUNK1, HUNKI, MCAP}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, CD86 (CD86 molecule) [NCBI Gene 942] {aka B7-2, B7.2, B70, BU63, CD28LG2, CD86 v6}, KMT2A (lysine methyltransferase 2A) [NCBI Gene 4297] {aka ALL-1, ALL1, CXXC7, GAS7, HRX, HTRX}, CTNNB1 (catenin beta 1) [NCBI Gene 1499] {aka CTNNB, EVR7, MRD19, NEDSDV, armadillo}, E2F1 (E2F transcription factor 1) [NCBI Gene 1869] {aka E2F-1, RBAP1, RBBP3, RBP3}, ZMYND8 (zinc finger MYND-type containing 8) [NCBI Gene 23613] {aka PRKCBP1, PRO2893, RACK7}, CD28 (CD28 molecule) [NCBI Gene 940] {aka IMD123, Tp44}, PDCD1 (programmed cell death 1) [NCBI Gene 5133] {aka ADMIO4, AIMTBS, CD279, PD-1, PD1, SLEB2}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}
- **Diseases:** breast cancer (MESH:D001943), systemic lupus erythematosus (MESH:D008180), NK (MESH:D000077428), solid (MESH:D018250), HCC (MESH:D006528), hematological malignancies (MESH:D019337), pancreatic cancer (MESH:D010190), colon cancer (MESH:D015179), CDF (MESH:D012090), inflammatory (MESH:D007249), cirrhosis (MESH:D005355), Cancer (MESH:D009369)
- **Chemicals:** Pictilisib (MESH:C532162), Atezolizumab (MESH:C000594389), Ribociclib (MESH:C000589651), Trizol (MESH:C411644), 5-Fluorouracil (MESH:D005472), Fludarabine (MESH:C024352), glutamine (MESH:D005973), CO2 (MESH:D002245), Erlotinib (MESH:D000069347), Bevacizumab (MESH:D000068258), Oxaliplatin (MESH:D000077150), glycine (MESH:D005998), threonine (MESH:D013912), Gemcitabine (MESH:D000093542), EdU (MESH:C022811), SB216763 (MESH:C417521), Axitinib (MESH:D000077784), glycosaminoglycan (MESH:D006025), Entospletinib (MESH:C000589391), penicillin (MESH:D010406), AL354743.2 (-), bile acid (MESH:D001647), Carmustine (MESH:D002330), serine (MESH:D012694), Alpelisib (MESH:C585539), streptomycin (MESH:D013307), Dasatinib (MESH:D000069439), graphene oxide (MESH:C000628730), AT13148 (MESH:C000600307)
- **Species:** Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090]
- **Cell lines:** Hep3B — Homo sapiens (Human), Childhood hepatocellular carcinoma, Cancer cell line (CVCL_0326), MIHA — Homo sapiens (Human), Transformed cell line (CVCL_SA11), HepG2 — Homo sapiens (Human), Hepatoblastoma, Cancer cell line (CVCL_0027), HuH-7 — Homo sapiens (Human), Adult hepatocellular carcinoma, Cancer cell line (CVCL_0336)

## Full text

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## Figures

13 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12953435/full.md

## References

1 references — full list in the complete paper: https://tomesphere.com/paper/PMC12953435/full.md

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Source: https://tomesphere.com/paper/PMC12953435