The diverse repertoire of ISG15: more intricate than initially thought

ISG15, the product of interferon (IFN)-stimulated gene 15, is the first identified ubiquitin-like protein (UBL), which plays multifaceted roles not only as a free intracellular or extracellular molecule but also as a post-translational modifier in the process of ISG15 conjugation (ISGylation). ISG15 has only been identified in vertebrates, indicating that the functions of ISG15 and its conjugation are restricted to higher eukaryotes and have evolved with IFN signaling. Despite the highlighted complexity of ISG15 and ISGylation, it has been suggested that ISG15 and ISGylation profoundly impact a variety of cellular processes, including protein translation, autophagy, exosome secretion, cytokine secretion, cytoskeleton dynamics, DNA damage response, telomere shortening, and immune modulation, which emphasizes the necessity of reassessing ISG15 and ISGylation. However, the underlying mechanisms and molecular consequences of ISG15 and ISGylation remain poorly defined, largely due to a lack of knowledge on the ISG15 target repertoire. In this review, we provide a comprehensive overview of the mechanistic understanding and molecular consequences of ISG15 and ISGylation. We also highlight new insights into the roles of ISG15 and ISGylation not only in physiology but also in the pathogenesis of various human diseases, especially in cancer, which could contribute to therapeutic intervention in human diseases.

Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes

Interferon (IFN)-related DNA damage resistant signature (IRDS) genes are a subgroup of interferon-stimulated genes (ISGs) found upregulated in different cancer types, which promotes resistance to DNA damaging chemotherapy and radiotherapy. Along with briefly discussing IFNs and signalling in this review, we highlighted how different IRDS genes are affected by viruses. On the contrary, different strategies adopted to suppress a set of IRDS genes (STAT1, IRF7, OAS family, and BST2) to induce (chemo- and radiotherapy) sensitivity were deliberated. Significant biological pathways that comprise these genes were classified, along with their frequently associated genes (IFIT1/3, IFITM1, IRF7, ISG15, MX1/2 and OAS1/3/L). Major upstream regulators from the IRDS genes were identified, and different IFN types regulating these genes were outlined. Functional interfaces of IRDS proteins with DNA/RNA/ATP/GTP/NADP biomolecules featured a well-defined pharmacophore model for STAT1/IRF7-dsDNA and OAS1/OAS3/IFIH1-dsRNA complexes, as well as for the genes binding to GDP or NADP+. The Lys amino acid was found commonly interacting with the ATP phosphate group from OAS1/EIF2AK2/IFIH1 genes. Considering the premise that targeting IRDS genes mediated resistance offers an efficient strategy to resensitize tumour cells and enhances the outcome of anti-cancer treatment, this review can add some novel insights to the field.

Combining Radiation Therapy With Interferons: Back to the Future

Radiation therapy has been linked to the induction of an intratumoral type I interferon (IFN) response, which positively affects the response to treatment. This has spiked the interest to combine radiation therapy with IFN-based treatment. Interestingly, this combination treatment has been considered previously, since preclinical studies demonstrated a radiosensitizing effect of interferons. As a result, multiple clinical trials have been performed combining radiation therapy with interferons in different tumor types. Although potential benefit has been suggested, the outcomes of the trials are diverse and challenging to interpret. In addition, increased grade ≥3 toxicity frequently resulted in a negative recommendation regarding the combination therapy. The latter appears premature because many studies were small and several aspects of the combination treatment have not yet been sufficiently explored to justify such a definite conclusion. This review summarizes the available literature on this combination therapy, with a focus on IFN-α and IFN-β. Based on preclinical studies and clinical trials, we evaluated the potential opportunities and describe the current challenges. In addition, we identify several issues that should be addressed to fully exploit the potential benefit of this combinatorial treatment approach.

TRAF3/CYLD mutations identify a distinct subset of human papillomavirus-associated head and neck squamous cell carcinoma

BACKGROUND

The incidence of human papillomavirus (HPV)‐associated (HPV‐positive) head and neck squamous cell carcinoma (HNSCC) of the oropharynx has dramatically increased over the last decade and continues to rise. Newly diagnosed HPV‐positive HNSCCs in the United States currently outnumber any other HPV‐associated cancers, including cervical cancer. Despite introduction of the HPV vaccine, the epidemic of HPV‐positive HNSCC is expected to continue for approximately 60 years. Compared with patients who have tobacco‐associated HNSCC, those who have HPV‐positive HNSCC have better overall survival and response to treatment. Current treatment, including chemotherapy and radiation therapy, is associated with lifelong morbidity, and there are limited treatments and no curative options for patients who develop recurrent metastatic disease. Therapeutic de‐escalation (decreased radiation dose) is being tested through clinical trials; however, those studies select patients based solely on tumor and patient smoking characteristics. Mechanisms of HPV‐driven carcinogenesis in HNSCC are not well understood, which limits new therapeutic strategies and hinders the appropriate selection of patients for de‐escalation therapy.

METHODS

The authors analyzed HNSCC data from The Cancer Genome Atlas to identify molecular characteristics that correlate with outcomes and integration status of the HPV genome.

RESULTS

The current investigations identified a subset of HPV‐positive HNSCCs with mutations in the genes TRAF3 (tumor necrosis factor receptor‐associated factor 3) and CYLD (cylindromatosis lysine 63 deubiquitinase). Defects in TRAF3 and CYLD correlated with the activation of transcriptional factor nuclear factor κB, episomal HPV status of tumors, and improved patient survival.

CONCLUSIONS

Defects in TRAF3/CYLD were accompanied with the activation of nuclear factor κB signaling and maintenance of episomal HPV in tumors, suggesting that these mutations may support an alternative mechanism of HPV tumorigenesis in head and neck tumors. Cancer 2017;123:1778–1790. © 2017 The Authors. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Human papillomavirus‐associated head and neck cancer tends to respond better to treatment compared with tobacco‐associated tumors; however, patients suffer severe and long‐lasting side effects. Somatic mutations in the genes TRAF3 and CYLD identified in The Cancer Genome Atlas data set are correlated with the activation of nuclear factor‐κB, define a distinct etiologic subset of head and neck cancers, and will be useful as biomarkers for predicting improved prognosis and selecting patients with human papillomavirus‐positive head and neck cancer who may be successfully treated with de‐escalating therapy.

See also pages 1695‐98.

Dietary nucleotides protect thymocyte DNA from damage induced by cyclophosphamide in mice

The effects of dietary nucleotides on thymocyte DNA damages induced by cyclophosphamide (CP) in mice were examined. First, phase I experiment was conducted to determine the optimal timing of detecting thymocyte DNA damages induced by CP (150 mg/kg body weight) in mice. Thymocyte DNA damages was determined at 6, 12, 18, 24 h by single-cell gel electrophosphoresis assay (comet assay) after intraperitoneal injection of CP. The levels of DNA damage at 6, 12, 18, 24 h were all significantly higher than that of the control group (p < 0.01). The highest level of DNA damage appeared at 18 h and then decreased at 24 h. Therefore, 18 h was selected to determine DNA damages induced by CP in subsequent experiments. In phase II experiment, 30 male KunMing mice were divided into three treatments: negative control (NC), positive control (PC) and nucleotides group (NG). Mice in NC and PC were fed nucleotide-free diet, and mice in NG were fed nucleotide-supplemented diet (supplemented with 0.25% nucleotides, a mixture containing equal amounts of AMP, CMP, GMP and UMP). Mice in PC and NG groups were injected with CP (150 mg/kg body weight) at 21 days. DNA damage in thymocytes was evaluated at 18 h after CP treatment. The results indicate that dietary nucleotides do not affect the weights of the thymus and the spleen, or their organ indices (p > 0.05), but significantly decrease the percentage of comet cells and comet tail sizes (p < 0.01). This study demonstrates that dietary nucleotides could reduce the level of thymocyte DNA damage induced by CP in mice.

STAT1 signaling is associated with acquired crossresistance to doxorubicin and radiation in myeloma cell lines

The myeloma cell line RPMI 8226/S and its doxorubicin resistant subline 8226/Dox40 were used as models to explore the potential importance of the STAT1 signaling pathway in drug and radiation resistance. The 40-fold doxorubicin resistant subline 8226/Dox40 was found to be crossresistant to single doses of 4 and 8 Gy of radiation. A genome-wide mRNA expression study comparing the 8226/Dox40 cell line to its parental line was performed to identify the underlying molecular mechanisms. Seventeen of the top 50 overexpressed genes have previously been implicated in the STAT1 signaling pathway. STAT1 was over expressed both at the mRNA and protein level. Moreover, analyses of nuclear extracts showed higher abundance of phosphorylated STAT1 (Tyr 701) in the resistant subline. Preexposure of the crossresistant cells to the STAT1 inhibiting drug fludarabine reduced expression of overexpressed genes and enhanced the effects of both doxorubicin and radiation. These results show that resistance to doxorubicin and radiation is associated with increased STAT1 signaling and can be modulated by fludarabine. The data support further development of therapies combining fludarabine and radiation.

Normal human keratinocytes pretreated with damaged mRNA are resistant to UVB damage and exhibit increased DNA repair

Treatment of normal human keratinocytes with UVC-irradiated rabbit globin mRNA 24 h before and after UVB exposure increased the survival of the human keratinocytes. We also observed that UVC-damaged mRNA reduced the formation of sunburn cells in skin models. We next tested the effects of UVC-damaged mRNA on cellular repair of DNA. DNA repair was evaluated using 2 assay methods. The first method used a damaged plasmid that is transfected back into the cell where it is repaired by the host cell repair mechanism. In these experiments, we observed that externally added UVC-damaged rabbit globin mRNA enhanced the repair of a plasmid transfected into the host keratinocyte cells. The second method used to determine the effects on DNA repair was direct immunostaining for thymidine-thymidine dimers (TT dimers) in histological sections of the skin models. Skin models were irradiated with UVB and then fixed immediately or after 24 h and stained for TT dimers. UVB irradiation immediately caused an increase in the number of stained keratinocytes in the skin. The number of stained cells decreased in skin fixed 24 h after UVB. This is due to repair of the TT dimers and their removal. Sections of skin models pretreated with UV-damaged mRNA exhibit greater removal of these TT dimers after 24 h. The above evidence suggests that damaged mRNA can trigger a host cell DNA repair pathway.

Effect of recombinant interferon-alpha on streptozotocin-induced chromosome aberrations and sister-chromatid exchanges in hamster cells

We assessed the effect of recombinant IFN-alpha-2a (rIFN-alpha-2a) on the induction of CAs and sister-chromatid exchanges (SCEs) by the methylating compound streptozotocin (STZ), in Chinese Hamster Ovary (CHO) cells. The cytokine was added to cell cultures 30 min before STZ and left in the culture medium until the end of the treatment. A statistically significant increase in the frequency of CAs and SCEs was observed following treatment with STZ alone (p < 0.05) compared to control, whereas treatments with rIFN-alpha-2a alone did not produce any significant increase of CAs or SCEs over the control values (p < 0.05). Moreover, rIFN-alpha-2a had a marked inhibitory effect on the frequency of STZ-induced CAs--both chromosome- and chromatid-type--(p < 0.05) but was unable to prevent SCEs induced by the antibiotic (p > 0.05). A decrease in the replication index (RI) was observed in the combined treatments compared with STZ alone-treated cultures, indicating inhibition of DNA synthesis. It is suggested that rIFN-alpha-2a exerts its protective action against the induction of CAs by STZ by stimulating DNA repair.

DNA damage in frog erythrocytes after in vitro exposure to a high peak-power pulsed electromagnetic field

Till the present time, the genotoxic effects of high peak-power pulsed electromagnetic fields (HPPP EMF) on cultured cells have not been studied. We investigated possible genotoxic effects of HPPP EMF (8.8 GHz, 180 ns pulse width, peak power 65 kW, repetition rate 50 Hz) on erythrocytes of the frog Xenopus laevis. We used the alkaline comet assay, which is a highly sensitive method to assess DNA single-strand breaks and alkali-labile lesions. Blood samples were exposed to HPPP EMF for 40 min in rectangular wave guide. The specific absorption rate (SAR) calculated from temperature kinetics was about 1.6 kW/kg (peak SAR was about 300 MW/kg). The temperature rise in the blood samples at steady state was 3.5 +/- 0.1 degrees C. The data show that the increase in DNA damage after exposure of erythrocytes to HPPP EMF was induced by the rise in temperature in the exposed cell suspension. This was confirmed in experiments in which cells were incubated for 40 min under the corresponding temperature conditions. The results allow us to conclude that HPPP EMF-exposure at the given modality did not cause any a-thermal genotoxic effect on frog erythrocytes in vitro.

STAT1 is overexpressed in tumors selected for radioresistance and confers protection from radiation in transduced sensitive cells

Nu61, a radiation-resistant human tumor xenograft, was selected from a parental radiosensitive tumor SCC-61 by eight serial cycles of passage in athymic nude mice and in vivo irradiation. Replicate DNA array experiments identified 52 genes differentially expressed in nu61 tumors compared with SCC-61 tumors. Of these, 19 genes were in the IFN-signaling pathway and moreover, 25 of the 52 genes were inducible by IFN in the nu61 cell line. Among the genes involved in IFN signaling, STAT1alpha and STAT1beta were the most highly overexpressed in nu61 compared to SCC-61. STAT1alpha and STAT1beta cDNAs were cloned and stably transfected into SCC-61 tumor cells. Clones of SCC-61 tumor cells transfected with vectors expressing STAT1alpha and STAT1beta demonstrated radioprotection after exposure to 3 Gy (P < 0.038). The results indicate that radioresistance acquired during radiotherapy treatment may account for some treatment failures and demonstrate an association of acquired tumor radioresistance with up-regulation of components of the IFN-related signaling pathway.

Transcriptional response of lymphoblastoid cells to ionizing radiation

The effects of ionizing radiation (IR) on the temporal transcriptional response of lymphoblastoid cells were investigated in this study. We used oligonucleotide microarrays to assess mRNA levels of genes in lymphoblastoid cells at various time points within 24 h following gamma-irradiation. We identified 319 and 816 IR-responsive genes following 3 Gy and 10 Gy of IR exposure, respectively, with 126 genes in common between the two doses. A high percentage of IR-responsive genes are involved in the control of cell cycle, cell death, DNA repair, DNA metabolism, and RNA processing. We determined the temporal expression profiles of the IR-responsive genes and assessed effects of IR dose on this temporal pattern of expression. By combining dose-response data with temporal profiles of expression, we have identified sets of coordinately responding genes. Through a genomic approach, we characterized a set of genes that are implicated in cellular adaptation to IR stress. These findings will allow a better understanding of complex processes such as radiation-induced carcinogenesis and the development of biomarkers for radiation exposure.

Involvement of LEU13 in interferon-induced refractoriness of human RSa cells to cell killing by X rays

Culture of human cells with human interferon alpha and beta (IFNA and IFNB) results in increased resistance of the cells to cell killing by X rays. To identify candidate genes responsible for the IFN-induced X-ray resistance, we searched for genes whose expression levels are increased in human RSa cells treated with IFNA, using an mRNA differential display method and Northern blotting analysis. RSa cells, which showed increased survival (assayed by colony formation) after X irradiation when they were treated with IFNA prior to irradiation, showed increased expression levels of LEU13 (IFITM1) mRNA after IFNA treatment alone. In contrast, IF(r) and F-IF(r) cells, both of which are derived from RSa cells, showed increased X-ray resistance and high constitutive LEU13 mRNA expression levels compared to the parental RSa cells. Furthermore, the IFNA-induced resistance of RSa cells to killing by X rays was suppressed by antisense oligonucleotides for LEU13 mRNA. LEU13, a leukocyte surface protein, was previously reported to mediate the actions of IFN such as inhibition of cell proliferation. The present results suggest a novel role of LEU13 different from that in the inhibition of cell proliferation, involved in IFNA-induced refractoriness of RSa cells to X rays.

Effect of recombinant interferon-alpha on streptonigrin-induced chromosome aberrations and sister-chromatid exchanges in hamster cells

The effect of recombinant interferon-alpha-2a (rIFN-alpha-2a) on the induction of chromosomal aberrations (CAs) and sister-chromatid exchanges (SCEs) by the radiomimetic antibiotic streptonigrin (SN, 250 ng/ml, 20 min, 37 degrees C) in Chinese hamster ovary (CHO) cells was investigated. Recombinant IFN-alpha-2a (4500-45,000 IU/ml) was added to the cell cultures 30 min before SN and left in the culture medium until the end of SN treatment or until cell harvesting. A statistically significant increase in the frequency of CAs and SCEs was observed following treatment with SN (P < 0.05), whereas treatments with rIFN-alpha-2a alone did not produce any significant increase of CAs and SCEs over control values. Low rIFN-alpha-2a doses produced a reduction in the frequency of CAs and an increase in the yield of SCEs induced by SN, while high doses of the cytokine caused an increase in the yield of CAs and a reduction in the frequency of SCEs induced by the antibiotic. In addition, rIFN-alpha-2a caused a marked inhibition (around 50%) on the yield of SN-induced chromatid-type aberrations in the G(2) phase of the cell cycle. It is suggested that the inhibitory effect of rIFN-alpha-2a on the SN-induced chromosome damage is due to the stimulation of DNA synthesis and repair by the cytokine. On the other hand, our results give further support to our previous hypothesis that the induction of CAs and SCEs by SN is based on different mechanisms.

Effect of recombinant interferon-alpha on bleomycin-induced chromosome damage in hamster cells

The effect of recombinant interferon-alpha-2a (rIFN-alpha-2a) on the induction of chromosomal aberrations (CAs) by the radiomimetic antibiotic bleomycin (BLM, 5 microg/ml, 30 min, 37 degrees C) in Chinese hamster ovary (CHO) cells was investigated. Recombinant IFN-alpha-2a (4500-180,000IU/ml) was added to the cell cultures 0.5 or 24h before BLM (and left in the culture medium until the end of treatments) or immediately after BLM treatment (and left in the culture medium until harvesting). Cells were sampled at 18 or 2.5h after the end of treatments, in order to determine, respectively, the effect of rIFN-alpha-2a on the total chromosome damage induced by BLM and on the chromosome damage induced by this antibiotic in the G(2) phase of the cell cycle. A statistically significant increase in the frequency of CAs was observed following treatment with BLM (P<0.05), whereas treatments with rIFN-alpha-2a alone did not produce any significant increase of CAs over control values (P>0.05). The yield of CAs by BLM was significantly inhibited by rIFN-alpha-2a (P<0.05, 65.3% maximum inhibition). A strong inhibitory effect (around 80%) of rIFN-alpha-2a on the yield of BLM-induced CAs in the G(2) phase of the cell cycle was also observed. It is suggested that the inhibitory effect of rIFN-alpha-2a on the induction of CAs by BLM is mainly due to the stimulation of DNA synthesis and repair by the cytokine.

Evaluation of a tissue homogenization technique that isolates nuclei for the in vivo single cell gel electrophoresis (comet) assay: a collaborative study by five laboratories

We evaluated a tissue homogenization technique that isolates nuclei for use in the in vivo comet assay. Five laboratories independently tested the technique using the liver, kidney, lung, spleen, and bone marrow of untreated and mutagen-treated male CD-1 mice. The direct mutagen methylmethanesulfonate (MMS) or the promutagen diethylnitrosamine (DEN) were injected intraperitoneally at maximum tolerated doses. Three and twenty-four hours later, the organs were removed and, except for bone marrow, were minced and homogenized and a nuclear suspension was prepared. The nuclear suspensions and bone marrow cells were used in the comet assay. None of the nuclear suspensions from the non-treated mice induced a positive response. All nuclear suspensions derived from the MMS-treated mice and those of the liver, kidney, and lung from DEN-treated mice induced positive responses in all the laboratories similarly. Reproducibility was demonstrated by five replicate studies in one laboratory. Furthermore, the organ-specific responses to MMS and DEN reflected the characteristic genotoxicity of the chemicals. We concluded from these results that the homogenization technique is a valid one to be used for mouse organs in the in vivo comet assay.

Protective effects of extracted human-liver RNA, a known interferon inducer, against radiation-induced cytogenetic damage in male mice

Cells in vitro or in vivo pre-exposed to low-dose radiation (LDR) or low concentrations of chemical mutagens became more resistant to large-dose radiation-induced DNA or chromosome damage. This was known as radio-adaptive response, for which the exact mechanism was unclear. However, multiple cellular and molecular responses to LDR have been documented, for instance, the induction of some cytokines such as interferon (IFN). Administration of exogenous IFN to cultured cells or mice showed marked radio-protection. In the present study, we investigated the in vivo radio-protective effects of extracted human liver RNA (HL-RNA), a known IFN inducer, indirectly to determine the radio-protective action of endogenous IFN. First, mice were administered with 6.25 mg/kg HL-RNA at different times before exposure to radiation and the 24 h pretreatment offered the optimal protective action for HL-RNA on cytogenetic effects in bone marrow cells. When the mice were treated with different concentrations of HL-RNA for 24 h, a wide dose-range (25-100 mg/kg) of HL-RNA resulted in a marked protection from X-ray-induced chromosome aberrations in both bone marrow cells and germ cells. In subsequent experiments, a protective effect of pretreatment with 25 mg/kg HL-RNA for 24 h was also found for radiation-induced micronuclei in polychromatic erythrocytes (PCE), and inhibition of DNA repair ability (unscheduled DNA synthesis, UDS). These results demonstrated that HL-RNA, an IFN inducer, is able to offer significant cytogenetic protection from radiation, implying indirectly that the induction of IFN by LDR may also play a protective role as one of the mechanisms in the induction of the cytogenetic adaptive response.