Colorectal cancer (CRC) remains a leading cause of cancer-related mortality, underscoring the urgent need for more effective and curative treatment strategies. While immunotherapy has revolutionized the treatment of solid tumours, including melanoma and lung cancer, its efficacy in CRC remains limited. This resistance is largely attributed to CRC’s immunosuppressive tumour microenvironment (TME), which insulates the tumour from the surrounding normal colon tissue. Within the TME, immune cell function is dysregulated to support tumourigenesis, with tumour-associated macrophages (TAMs) driving immune suppression in CRC. Long non-coding RNAs (lncRNAs) – functional transcripts over 200 nucleotides – are emerging regulators of TAM activity. They frequently exhibit tissue-specific expression and have been implicated in various diseases, including CRC. LncRNA knockdown has reduced cancer phenotypes in a range of model systems, where antisense oligonucleotides (ASOs) offer a promising modality for therapeutic targeting. Here, we look to utilise gapmer ASOs to target upregulated lncRNAs in CRC TAMs and will determine whether these knockdowns elicit an anti-cancer effect.
To identify candidate targets, we mined a publicly available single-cell RNAseq dataset of myeloid cells from CRC patient tissue. Bioinformatic analysis identified 12 lncRNAs significantly upregulated in TAMs relative to macrophages from matched normal colon tissue (Adj P < 0.05). The candidates were processed by a quantitative scoring matrix that assessed the tractability of each lncRNA as a therapeutic target. This incorporated survival analyses, normal expression, reported functional evidence, and target novelty. Three candidates – ‘CTAMI’, ‘CTAMII’, and MALAT1 – ranked highest, thus gapmer ASOs were designed and synthesized for each. MALAT1 was significantly knocked down (0.49-fold change) in HCT116 cells (Adjusted P < 0.05), with no effect on proliferation. Current experiments in ex vivo macrophages will elucidate the impact of targeted CTAMI and CTAMII knockdown on TAM activity. We then look to build a co-culture model of the two cell types, mimicking the CRC TME, to further test the lncRNA knockdowns. Collectively, these experiments will evaluate the potential of this approach to making CRC amenable to immunotherapeutics.