Individual gene expression and molecular pathway activation profiles were shown to be effective biomarkers in many cancers. Here, we used the human interactome model to algorithmically build 7470 molecular pathways centered around individual gene products. We assessed their associations with tumor type and survival in comparison with the previous generation of molecular pathway biomarkers (3022 “classical” pathways) and with the RNA transcripts or proteomic profiles of individual genes, for 8141 and 1117 samples, respectively. For all analytes in RNA and proteomic data, respectively, we found a total of 7441 and 7343 potential biomarker associations for gene-centric pathways, 3020 and 2950 for classical pathways, and 24,349 and 6742 for individual genes. Overall, the percentage of RNA biomarkers was statistically significantly higher for both types of pathways than for individual genes (p < 0.05). In turn, both types of pathways showed comparable performance. The percentage of cancer-type-specific biomarkers was comparable between proteomic and transcriptomic levels, but the proportion of survival biomarkers was dramatically lower for proteomic data. Thus, we conclude that pathway activation level is the advanced type of biomarker for RNA and proteomic data, and momentary algorithmic computer building of pathways is a new credible alternative to time-consuming hypothesis-driven manual pathway curation and reconstruction.

The evolution of protein-coding genes has both structural and regulatory components. The first can be assessed by measuring the ratio of non-synonymous to synonymous nucleotide substitutions. The second component can be measured as the normalized proportion of transposable elements that are used as regulatory elements. For the first time, we characterized in parallel the regulatory and structural evolutionary profiles for 10,890 human genes and 2972 molecular pathways. We observed a ~0.1 correlation between the structural and regulatory metrics at the gene level, which appeared much higher (~0.4) at the pathway level. We deposited the data in the publicly available database RetroSpect. We also analyzed the evolutionary dynamics of six cancer pathways of two major axes: Notch/WNT/Hedgehog and AKT/mTOR/EGFR. The Hedgehog pathway had both components slower, whereas the Akt pathway had clearly accelerated structural evolution. In particular, the major hub nodes Akt and beta-catenin showed both components strongly decreased, whereas two major regulators of Akt TCL1 and CTMP had outstandingly high evolutionary rates. We also noticed structural conservation of serine/threonine kinases and the genes related to guanosine metabolism in cancer signaling: GPCRs, G proteins, and small regulatory GTPases (Src, Rac, Ras); however, this was compensated by the accelerated regulatory evolution.

Laser-driven accelerated particle beams have significantly advanced cancer treatment by facilitating the delivery of exceptionally high dose rates of radiation to solid tumors within femto- to picosecond timescales. This investigation compared the radiobiological effectiveness of ultrashort pulsed electron beams, generated by the Advanced Research Electron Accelerator Laboratory (AREAL) accelerator, with conventional X-rays on two non-small cell lung cancer (NSCLC) cell lines: A549 (wild-type p53) and H1299 (p53-deficient). NSCLC cells were irradiated using either the AREAL accelerator (with a peak dose rate of 1.6 × 10¹⁰ Gy/s, a pulse duration of 4.5 × 10⁻¹³ s, and a repetition rate of 20 Hz) or an X-ray unit at an absorbed dose rate of 0.85 Gy/min. Clonogenic survival analysis, γH2AX foci enumeration, and genome-wide transcriptome analysis were conducted. Clonogenic survival curves showed increased radiosensitivity of A549 cells following AREAL exposure compared to X-rays (RBE = 1.2), whereas H1299 radiosensitivity remained unchanged. In both cell lines, AREAL exposure resulted in a greater dose-dependent accumulation of residual γH2AX foci 24 h after irradiation than conventional X-rays, suggesting more persistent DNA damage signaling. Transcriptomic analyses revealed broader gene expression changes after AREAL irradiation and suggested distinct p53-related responses. Pathway-level analysis demonstrated that A549 cells exhibited reduced DNA repair activity, accompanied by dysregulation of cell cycle progression and apoptosis, whereas H1299 cells displayed transcriptomic signatures consistent with enhanced homologous recombination activity. Overall, these findings indicate that ultrashort pulsed electron beams induce p53-related responses distinct from those of conventional X-rays and warrant further investigation of this technology as a potential radiotherapy modality.

Laser-driven accelerated particle beams have revolutionized the field of cancer treatment by enabling the delivery of extremely high dose-rates of radiation to solid tumors in a matter of femto- to picoseconds. In this study, radiobiological effectiveness of ultrashort pulsed electron beams generated by Advanced Research Electron Accelerator Laboratory (AREAL) accelerator and conventional X-rays were compared on two non-small cell lung cancer (NSCLC) cell lines, A549 (wild-type p53) and H1299 (p53-deficient). NSCLC cells were irradiated at using a AREAL accelerator (a peak dose rate of 1.6 × 1010 Gy/s, pulse duration of 4.5 × 10–13 s, repetition rate of 20 Hz) or X-ray unit at an absorbed dose rate of 0.85 Gy/min. Clonogenic survival analysis, γH2AX foci enumeration and genome-wide transcriptome analysis were performed. Clonogenic survival curves showed increased ra-diosensitivity of A549 cells after AREAL exposure compared to X-rays (RBEs=1.2), while H1299 radiosensitivity has not changed. AREAL exposure caused higher linear dose–dependent increase in the number of residual γH2AX foci in both A549 and H1299 cells compared to X-rays. The DNA double-strand breaks in H1299 cells were mainly repaired through homologous recombination following AREAL exposure. However, the gene ex-pression analysis of pathway activation levels revealed a down-regulation of the same pathways in A549 cells. This resulted in activation of Integrin-linked kinase-dependent apoptosis, G2 and proliferation arrest of A549 cells.