Background: Therapy resistance is a great challenge in cancer treatment. Among numerous factors, cell adhesion to extracellular matrix is a well-known determinant of radiochemo-resistance. It has been shown that targeting focal adhesion proteins (FAPs), e.g. β1 integrin, enhances tumor cell radio(chemo)sensitivity in various entities such as head and neck squamous cell carcinoma (HNSCC), lung carcinoma, glioblastoma, breast carcinoma and leukemia. Previous studies demonstrated a functional crosstalk between specific FAPs and DNA repair processes; however, the molecular circuitry underlying this crosstalk remains largely unsolved. Hence, this study in HNSCC aimed to identify alternative FAPs associated with DNA damage repair mechanisms and radioresistance. Materials and Methods: A novel 3D High Throughput RNAi Screen (3DHT-RNAi-S) using laminin-rich extracellular matrix (lrECM) was established to determine radiation-induced re-sidual DNA double strand breaks (DSBs; foci assay) and clonogenic radiation survival. In the screen, we used UTSCC15 HNSSC cells stably expressing the DSB marker protein 53BP1 tagged to pEGFP. Validations were performed in 10 additional HNSCC cell lines (Cal33, FaDu, SAS, UTSCC5, UTSCC8, UTSCC14, UTSCC15, UTSCC45 and XF354fl2) grown in 3D lrECM. Immunofluorescence staining, immunoblotting, chromatin fractionation were utilized to evaluate protein expression, dynamics and kinetics post irradiation. Investigations of molecular mechanisms of DNA repair and radio(chemo)resistance employed DSB repair reporter assays for non-homologous end joining (NHEJ) and homologous recombination (HR), cell cycle analysis, chromatin fractionation levels evaluation and kinase activity profiling (PamGene) upon protein knockdown in combination with/-out X-ray exposure. Foci assay and clonogenic survival assay were performed after single or multiple knockdowns of synemin and associated proteins such as DNA-PKcs and c-Abl. Protein-protein interactions between synemin and associated proteins were determined using immunoprecipitation and proximity ligation assay. Mutant/depletion constructs of synemin (ΔLink-Tail, ΔHead-Link, Synemin_301-961, Synemin_962-1565, S1114A and S1159A) were generated in order to identify essential synemin’s sites controlling DNA repair functions. Results: Among the targets found in the 3DHT-RNAi-S, synemin was one of the most promising FAP candidates to determine HNSCC cell survival and DNA damage repair. Synemin silencing radiosensitized HNSCC cells, while its exogenous overexpression induced radio-protection. Radiation induced an increased synemin/chromatin interaction and a marked ac-cumulation of synemin in the perinuclear area. Intriguingly, synemin depletion elicited a 40% reduction in NHEJ activity without affecting HR or Alt-EJ. In line, ATM, DNA-PKcs and c-Abl phosphorylation as well as Ku70 expression strongly declined in synemin depleted and irra-diated cells relative to controls, whereas an opposite effect was observed under synemin overexpression. Single, double and triple depletion of synemin, DNA-PKcs and c-Abl resulted in a similar radiosensitizing effect and DSB levels as detected upon single knockdown of synemin, describing its upstream role. In kinome analysis, tyrosine kinases showed signifi-cantly reduced activity after synemin silencing relative to controls. Furthermore, immunoprecipitation assays revealed a protein complex formed between synemin, DNA-PKcs and c-Abl under pre- and post-irradiation conditions. This protein complex dispersed when ATM was pharmacologically inhibited, implying synemin function to be dependent on ATM kinase activity. By means of the different mutation/deletion constructs of synemin, the phosphorylation site at serine 1114 located on the distal portion of synemin’s tail was identified as essential protein-protein interaction site for synemin’s function in DNA repair. Conclusions: The established 3DHT-RNAi-S provides a robust screening platform for identifying novel targets involved in therapy resistance. Based on this screen and detailed mechanistic analyses, the intermediate filament synemin was discovered as a novel important determinant of DNA repair, tyrosine kinase activity and radiochemoresistance of HNSCC cells. These results further support the notion that DNA repair is controlled by cooperative interactions between nuclear and cytoplasmic proteins.

The muscle fibre cytoskeleton of skeletal and heart muscle cells is composed mainly of intermediate filaments (IFs), that surround the myofibrils and connect the peripheral myofibrils with the sarcolemma and the nuclear membrane. Desmin is the first muscle specific IF protein to be produced in developing muscles and is the main IF protein in mature muscles. In skeletal muscle, desmin is particularly abundant at myotendinous and neuromuscular junctions. In the heart an increased amount of desmin is found at intercalated discs and in Purkinje fibres of the conduction system. Interactions between the IFs themselves, and between IFs and other structures such as Z-discs and the sarcolemma, are mediated by intermediate filament associated proteins (IFAPs). A transgenic mice model, which lacks the desmin gene have been developed to study the function of desmin. In these mice, morphological abnormalities are observed in both heart and skeletal muscles. Similar defects have been observed in human myopathies, caused by different mutations in the desmin gene. In the present thesis, skeletal and heart muscles of both wild type and desmin knock-out (K/O) mice have been investigated. Furthermore the cytoskeletal organisation in skeletal muscles from human controls and from a patient with desmin myopathy was examined. In the desmin K/O mice, no morphological alterations were observed during embryogenesis. These mice postnatally developed a cardiomyopathy and a muscle dystrophy in highly used skeletal muscles. Ruptures of the sarcolemma appear to be the primary event leading to muscle degeneration and fibrosis both in cardiac and affected skeletal muscles. In the heart the muscle degeneration gave rise to calcifications, whereas in skeletal muscles regeneration of affected muscle was seen. In mature wild type mice, the IF proteins synemin and paranemin, and the IFAP plectin were present together with desmin at the myofibrillar Z-discs, the sarcolemma, the neuromuscular junctions and the myotendinous junctions. Nestin was only found in these junctional regions. In desmin K/O mice, all four proteins were detected at neuromuscular and myotendinous junctions. The normal network of synemin and paranemin were not observed, whereas the distribution of plectin was preserved. In normal human muscles, synemin, paranemin, plectin and αB-crystallin were colocalised with desmin in between the myofibrils, at the sarcolemma and at myotendinous and neuromuscular junctions. In the human desmin myopathy, the distribution of desmin varied considerably. A normal pattern was seen in some fibres areas, whereas other regions either contained large subsarcolemmal and intermyofibrillar accumulations of desmin or totally lacked desmin. Nestin, synemin, paranemin, plectin and αB-crystallin also exhibited an abnormal distribution. They were often aggregated in the areas that contained accumulations of desmin. In cultured satellite cells from the patient, a normal network of desmin was present in early passages, whereas aggragates of desmin occurred upon further culturing. In the latter, also the nestin network was disrupted, whereas vimentin showed a normal pattern. αB-crystallin was only present in cells with a disrupted desmin network. Plectin was present in a subset of cells, irrespective of whether desmin was aggregated or showed a normal network. From the present study it can be concluded that an intact desmin network is needed to maintain the integrity of muscle fibres. Desmin may be an important component in the assembly of proteins, which connect the extrasarcomeric cytoskeleton with the extracellular matrix.