Supporting data for "Spatial and Temporal Adaptation in Cancer: From the Metastatic Niche to the Drug-Tolerant Persister State"

More coherent differences emerged at the transcriptomic and proteomic levels, where pLN+ tumours were associated with cell-cycle, extracellular-matrix (ECM), TGF-β-related and immune-associated programmes. Proteomic network analysis identified periostin (POSTN) as a highly connected component of an ECM-related module, and higher POSTN abundance was associated with shorter overall survival. In the four tumours examined by snRNAseq, <i>POSTN</i> transcripts were concentrated predominantly in cancer-associated fibroblasts (CAFs), which were also important transcript-level sources of <i>TGFB1</i> and <i>TGFB2</i>.

TGFBI-high malignant-cell states showed greater pooled representation in the two tumours with pathological LNM and were regionally associated with CAF-related programmes.</p><p dir="ltr">Across the targeted-therapy models, <i>telomerase reverse transcriptase</i> (<i>TERT)</i> expression and telomerase activity decreased during the adaptive and drug-tolerant persister (DTP) phases but recovered as stable resistance developed.

Representative DTP models also showed increased telomere dysfunction-induced foci (TIF). Genetic disruption of <i>TERT</i>and treatment with the telomerase-mediated telomere-dysfunction agent, 6-thio-2′-deoxyguanosine (6-thio-dG), restricted clonogenic recovery and enhanced the effects of targeted inhibitors. Combination treatment produced more sustained tumour control in melanoma and lung cancer xenografts.

Transcriptomic and functional analyses further prioritised <i>SUCLG2</i> as a candidate dependency associated with the response to 6-thio-dG. Exploratory chromatin accessibility analysis indicated lower accessibility at the <i>SUCLG2</i> locus in A375 cells, while tumour transcriptomics showed changes in mitochondrial-associated programmes.</p><p><br></p><p dir="ltr"><b>Conclusion</b></p><p dir="ltr">The two studies examined different forms of cancer adaptation.

In OSCC, LNM was associated with the spatial organisation of stromal and malignant cell programmes. During targeted therapy, resistance development involved temporal changes in telomerase activity, telomere integrity and associated chromatin and mitochondrial transcriptional programmes. Both studies indicate that tumour behaviour depends on the current cellular state and the conditions under which that state is relied on.</p>