Energetic, charged particles elicit an orchestrated DNA damage response (DDR) during their traversal through healthy tissues and tumors. Complex DNA damage formation, after exposure to high linear energy transfer (LET) charged particles, results in DNA repair foci formation, which begins within seconds. More protein modifications occur after high-LET, compared with low-LET, irradiation. Charged-particle exposure activates several transcription factors that are cytoprotective or cytodestructive, or that upregulate cytokine and chemokine expression, and are involved in bystander signaling. Molecular signaling for a survival or death decision in different tumor types and healthy tissues should be studied as prerequisite for shaping sensitizing and protective strategies. Long-term signaling and gene expression changes were found in various tissues of animals exposed to charged particles, and elucidation of their role in chronic and late effects of charged-particle therapy will help to develop effective preventive measures.A major difference between low-LET and high-LET radiation is the microscopic dose deposition. Charged particles deposit their energy along densely ionized tracks [5]. In chromosomes within those tracks, complex damage is produced, defined as 2 or more abasic sites, oxidized bases on opposing strands or the same strand, and strand breaks on opposite DNA strands within a few helical turns ( Figure 1) [5][6][7][8][9][10][11][12]. That damage is difficult to repair and affects rejoining faithfulness [13][14][15]. DNA repair systems have an intrinsic weakness in processing complex damages [16]. Molecular signaling in response to charged-particle exposure is predominantly a DNA damage response (DDR), turning the switch toward cellular survival or death ( Figure 2).Ionizing radiation activates phosphatidylinositol-3-kinase-related enzymes, including ataxia telangiectasia mutant (ATM), ataxia telangiectasia, Rad3-related protein (ATR), and DNA-dependent protein kinase (DNA-PK) [21]. The ATM and ATR are recruited to complex double-strand breaks (DSBs) (Figure 3) [22].Mutations in ATM cause radiation hypersensitivity in patients with the autosomal recessive disorder ataxia-telangiectasia [16]. Mice with ATM haploinsufficiency develop cataracts earlier compared with wild-type animals, and the enhanced sensitivity was greater for high-LET heavy ions compared with low-LET x-rays [23].There are 4 autophosphorylation sites in ATM: Ser-367, Ser-1893, Ser-1981, and Ser-2996. Ser-1981 phosphorylation is associated with ATM monomerization. In human fibroblasts, ATM phosphorylated at Ser-367 is recruited to DNA damage sites after exposure to xenon ions (LET 800 keV/lm) [24]. Very early events include phosphorylation of the histone variant H2AX on Ser-139 (cH2AX) by ATM [25]. That results in protein recruitment to the DNA lesions, forming foci in LET-dependent kinetics [26]. The fast-recruited proteins are responsible for damage recognition, and slower accumulating proteins are predominantly involved in subsequent repai...