Single-cell temporal transcriptomics from tiny cytoplasmic biopsies

The crosstalk role of CDKN2A between tumor progression and cuproptosis resistance in colorectal cancer

BACKGROUND

Cuproptosis is a type of cell death characterized by excessive copper-lipid reactions in the tricarboxylic acid cycle, resulting in protein toxicity stress and cell death. Although known as a cuproptosis inhibitor through CRISPR-Cas9 screening, the role of cyclin-dependent kinase inhibitor 2A (CDKN2A) in cuproptosis resistance and its connection to tumor development remains unclear.

METHODS

In this study, we combined single-cell sequencing, spatial transcriptomics, pathological image analysis, TCGA multi-omics analysis and in vitro experimental validation to comprehensively investigate CDKN2A distribution, expression, epigenetic modification, regulation and genomic features in colorectal cancer cells. We further explored the associations between CDKN2A and cellular pathway, immune infiltration and spatial signal communication.

RESULTS

Our findings showed an increasing trend in cuproptosis in the trajectory of tumor progression, accompanied by an upward trend of CDKN2A. CDKN2A underwent transcriptional activation by MEF2D and via the SNHG7/miR-133b axis, upregulating glycolysis, copper metabolism and copper ion efflux. CDKN2A likely drives epithelial-mesenchymal transition (EMT) and progression by activating Wnt signaling. CDKN2A is associated with high genomic instability and sensitivity to radiation and chemotherapy. Tumor regions expressing CDKN2A exhibit distinctive SPP1+ tumor-associated macrophage (TAM) infiltration and MMP7 enrichment, along with unique signaling crosstalk with adjacent areas.

CONCLUSIONS

CDKN2A mediates cuproptosis resistance through regulating glycolysis and copper homeostasis, accompanied by a malignant phenotype and pro-tumor niche. Radiation and chemotherapy are expected to potentially serve as therapeutic approaches for cuproptosis-resistant colorectal cancer with high CDKN2A expression.

Hydrodynamic function and spring constant calibration of FluidFM micropipette cantilevers

Fluidic force microscopy (FluidFM) fuses the force sensitivity of atomic force microscopy with the manipulation capabilities of microfluidics by using microfabricated cantilevers with embedded fluidic channels. This innovation initiated new research and development directions in biology, biophysics, and material science. To acquire reliable and reproducible data, the calibration of the force sensor is crucial. Importantly, the hollow FluidFM cantilevers contain a row of parallel pillars inside a rectangular beam. The precise spring constant calibration of the internally structured cantilever is far from trivial, and existing methods generally assume simplifications that are not applicable to these special types of cantilevers. In addition, the Sader method, which is currently implemented by the FluidFM community, relies on the precise measurement of the quality factor, which renders the calibration of the spring constant sensitive to noise. In this study, the hydrodynamic function of these special types of hollow cantilevers was experimentally determined with different instruments. Based on the hydrodynamic function, a novel spring constant calibration method was adapted, which relied only on the two resonance frequencies of the cantilever, measured in air and in a liquid. Based on these results, our proposed method can be successfully used for the reliable, noise-free calibration of hollow FluidFM cantilevers.