Table 2.

Methods to identify lncRNA-associated proteins in cancer.

Method	Description	Strengths	Limitations	Applications in Cancer (Examples)	Key References
RNA pull-down	Biotinylated probes hybridize to lncRNA, isolating associated proteins for MS.	Direct isolation, high specificity.	It requires high RNA abundance and has potential for non-specific binding.	Lung: LncRNA BC promotes lung adenocarcinoma by modulating IMPAD1 splicing. Gastric: NEAT1/miR-17-5p/TGFβR2 axis drives GC angiogenesis. Colorectal: lncRNA FENDRR suppresses colorectal cancer by binding GSTP1 and promoting FBX8-mediated ubiquitination.	[61]; [51] [62]
ChIRP-MS	Probes hybridize to chromatin-bound lncRNAs, capturing associated proteins.	Identifies chromatin-associated partners; works for low-abundance lncRNAs.	Limited to nuclear lncRNAs; probe design critical.	Breast: MaTAR25 modulates Tensin1, influencing breast cancer progression. Gastric: m6A-modified TP53TG1 suppresses gastric cancer progression by modulating CIP2A stability. Liver: LncRNA CRLM1 cooperates with hnRNPK to inhibit apoptosis and promote metastasis in colorectal cancer.	[63] [64]
RAP-MS	Identifies key lncRNA-protein interactions that govern RNA stability, localization, and function.	Yields high-confidence, direct RNA-protein interactions via UV crosslinking and stringent purification.	Requires high RNA abundance and may miss transient or weak interactions.	Liver: lncRNA lincNMR modulates nucleotide metabolism via the YBX1-RRM2 axis in liver cancer.	[65]
HyPR-MS	Enables multiplexed discovery of specific RNA–protein interactomes.	Versatile method for probing in vivo protein interactomes of target RNAs	Multiplexing capacity beyond three targets and applicability to other RNA species (e.g., rRNA and tRNA) remain untested.	Prostate: HyPR-MS maps MALAT1, NEAT1, and NORAD interactomes in PC3 cells	[66]
TOBAP-MS	Integrates tobramycin affinity purification with quantitative mass spectrometry.	It enables the isolation of native RNP complexes and the identification of RNA-associated proteins and supports both biochemical and structural studies of these complexes.		Liver: In liver cancer, HULC—a lncRNA prominently overexpressed in the disease—engages with 140 interacting proteins.	[34]
BioID-MS	Fuses a promiscuous biotin ligase to a target protein to tag nearby proteins for MS analysis.	Captures transient, weak, and insoluble protein interactions in living cells via biotin tagging for high-affinity purification.	Lower sensitivity, slower labeling kinetics, and higher non-specific biotinylation.	RNA-BioID in HEK293T and MCF-7 cells reveals HOTAIR’s association with mitoribosomes, suggesting functions beyond (post)transcriptional regulation.	[55]
SILAC-MS	Uses non-radioactive isotopic labeling to quantify protein abundance differences across samples.	Accurate, multiplexed quantitative proteomics via metabolic labeling with broad proteome coverage and reproducibility.	Restricted to cell culture systems (not applicable to primary tissues/biofluids directly) and limited multiplexing capacity (typically 2–3 samples).	LincNMR promotes tumor proliferation via a YBX1-RRM2-TYMS-TK1 axis in nucleotide metabolism in liver, lung, and breast cancer cell lines. GLCC1 drives colorectal cancer through oncogenic mechanisms, functions, and clinical relevance.	[55] [66,67]