Measuring nonhomologous end-joining, homologous recombination and alternative end-joining simultaneously at an endogenous locus in any transfectable human cell.

Double strand break (DSB) repair primarily occurs through 3 pathways: non-homologous end-joining (NHEJ), alternative end-joining (Alt-EJ), and homologous recombination (HR). Typical methods to measure pathway usage include integrated cassette reporter assays or visualization of DNA damage induced nuclear foci. It is now well understood that repair of Cas9-induced breaks also involves NHEJ, Alt-EJ, and HR pathways, providing a new format to measure pathway usage. Here, we have developed a simple Cas9-based system with validated repair outcomes that accurately represent each pathway and then converted it to a droplet digital PCR (ddPCR) readout, thus obviating the need for Next Generation Sequencing and bioinformatic analysis with the goal to make Cas9-based system accessible to more laboratories. The assay system has reproduced several important insights. First, absence of the key Alt-EJ factor Pol θ only abrogates ∼50% of total Alt-EJ. Second, single-strand templated repair (SSTR) requires BRCA1 and MRE11 activity, but not BRCA2, establishing that SSTR commonly used in genome editing is not conventional HR. Third, BRCA1 promotes Alt-EJ usage at two-ended DSBs in contrast to BRCA2. This assay can be used in any system, which permits Cas9 delivery and, importantly, allows rapid genotype-to-phenotype correlation in isogenic cell line pairs.

Human papillomavirus 16 promotes microhomology-mediated end-joining.

Squamous cell carcinomas (SCCs) arising from aerodigestive or anogenital epithelium that are associated with the human papillomavirus (HPV) are far more readily cured with radiation therapy than HPV-negative SCCs. The mechanism behind this increased radiosensitivity has been proposed to be secondary to defects in DNA repair, although the specific repair pathways that are disrupted have not been elucidated. To gain insight into this important biomarker of radiosensitivity, we first examined genomic patterns reflective of defects in DNA double-strand break repair, comparing HPV-associated and HPV-negative head and neck cancers (HNSCC). Compared to HPV-negative HNSCC genomes, HPV+ cases demonstrated a marked increase in the proportion of deletions with flanking microhomology, a signature associated with a backup, error-prone double-strand break repair pathway known as microhomology-mediated end-joining (MMEJ). Then, using 3 different methodologies to comprehensively profile double-strand break repair pathways in isogenic paired cell lines, we demonstrate that the HPV16 E7 oncoprotein suppresses canonical nonhomologous end-joining (NHEJ) and promotes error-prone MMEJ, providing a mechanistic rationale for the clinical radiosensitivity of these cancers.

Ionizing radiation induced signaling of DNA damage response molecules in RAW 264.7 and CD4⁺ T cells.

Ionizing radiation (IR) treatment results in activation of several DNA damage response molecules, such as ataxia telangiectasia, mutated (ATM), and DNA-dependent protein kinase (DNAPK) in mammals that are increasingly recognized for their potential roles in the sensing of DNA damage and initiating the subsequent protein kinase cascade. In vitro evidence indicates that both ATM and DNA-PK are responsible for efficient repair of DNA double strand breaks in response to IR exposure. To unravel the role of ATM and DNA-PK, we studied the mRNA and protein levels of ATM, DNA-PK and their downstream substrates in two different cell types after irradiation viz. macrophage like RAW264.7 cells and CD4(+) T cells isolated from mice spleen. Our results show that despite significant increase in phosphorylation of ATM, its mRNA levels continue to remain low after IR exposure in both the cell types. Conversely, the mRNA expression of DNAPK shows a considerable increase immediately after IR exposure. Moreover, no increase in ATM mRNA levels is seen in DNAPK deficit RAW264.7 cells treated with DNAPK siRNA, indicating that ATM does not undergo any change at its transcriptional levels in response to IR treatment. However, in a similar study in CD4(+) T cells, inhibition of DNAPK by siRNA, shows a considerable increase in ATM after IR exposure. Collectively, these results suggest a discrepancy in the role of the ATM and DNA-PK pathways in the cellular response to IR at the mRNA and protein levels in two different cell types.

Differential response of three cell types to dual stress of nitric oxide and radiation.

The perception of toxicity to nitric oxide (NO) and irradiation (IR) by three different cell types has been studied. The three cell types are the macrophage like RAW264.7 cells, EL4 lymphoma cells, and splenocytes, which represent the different components of a tumor. These three cell types respond differently to NO donors (SNP and SNAP) and radiation treatment. The macrophages were found to be most radio-resistant and insensitive to NO donors. The innate resistance of the macrophages was not due to its antioxidant defense system since there was no significant activation of the enzymes (superoxide dismutases, catalase, and glutathione peroxidase) in RAW264.7 cells after NO donor and irradiation. But the cell cycle arrest of the three cell types was different from each other. The EL4 cells were found to arrest in the G2/M phase while the macrophages were found arrested in the G1 phase of the cell cycle. Such specific killing of the tumor cell in response to NO donor while sparing the macrophages can be of immense importance to radiotherapy.

DNA damage response signaling in lung adenocarcinoma A549 cells following gamma and carbon beam irradiation.

Carbon beams (5.16MeV/u, LET=290keV/µm) are high linear energy transfer (LET) radiation characterized by higher relative biological effectiveness than low LET radiation. The aim of the current study was to determine the signaling differences between γ-rays and carbon ion-irradiation. A549 cells were irradiated with 1Gy carbon or γ-rays. Carbon beam was found to be three times more cytotoxic than γ-rays despite the fact that the numbers of γ-H2AX foci were same. Percentage of cells showing ATM/ATR foci were more with γ-rays however number of foci per cell were more in case of carbon irradiation. Large BRCA1 foci were found in all carbon irradiated cells unlike γ-rays irradiated cells and prosurvival ERK pathway was activated after γ-rays irradiation but not carbon. The noteworthy finding of this study is the early phase apoptosis induction by carbon ions. In the present study in A549 lung adenocarcinoma, authors conclude that despite activation of same repair molecules such as ATM and BRCA1, differences in low and high LET damage responses might be due to their distinct macromolecular complexes rather than their individual activation and the activation of cytoplasmic pathways such as ERK, whether it applies to all the cell lines need to be further explored.

Activation of DNA damage response signaling in lung adenocarcinoma A549 cells following oxygen beam irradiation.

Oxygen beams are high linear energy transfer (LET) radiation characterized by higher relative biological effectiveness than low LET radiation. The aim of the current study was to determine the signaling differences between γ- and oxygen ion-irradiation. Activation of various signaling molecules was looked in A549 lung adenocarcinoma cells irradiated with 2Gy oxygen, 2Gy or 6Gy γ-radiation. Oxygen beam was found to be three times more cytotoxic than γ-radiation. By 4h there was efficient repair of DNA in A549 cells exposed to 2Gy or 6Gy gamma radiation but not in cells exposed to 2Gy oxygen beam as determined by γ-H2AX counting. Number of ATM foci was found to be significantly higher in cells exposed to 2Gy oxygen beam. Percentage of cells showing ATR foci were more with gamma however number of foci per cell were more in case of oxygen beam. Oxygen beam irradiated cells showed phosphorylation of Chk1, Chk2 and p53. Many apoptotic nuclei were seen by DAPI staining in cells exposed to oxygen beam. The noteworthy finding of this study is the activation of the sensor proteins, ATM and ATR by oxygen irradiation and the significant activation of Chk1, Chk2 and p53 only in the oxygen beam irradiated cells.

Impact of COVID-19 Pandemic on Post-Graduate Medical Education and Training in India: Lessons Learned and Opportunities Offered.

Hands-on or practice-based learning is the foundational objective of postgraduate teaching and training. A skilled and competent postgraduate resident is critical to the country's health needs and is more relevant in the ongoing COVID-19 pandemic. The postgraduate medical training in India is speciality-specific and based on a structured curriculum and syllabus to achieve precise educational goals and objectives. The impact of this pandemic on postgraduate medical education and training is controversial, challenging, unknown, and far-reaching. The exceptional contagious nature of the virus and country-wide lockdowns have tremendously decreased hospital visiting patients. Abolition of outpatient and inpatient services, disruptions in clinical postings, curtailment of elective operations and procedures have adversely affected the training of residents and fellowship students in India and abroad. Apart from this, research work, mentoring, academic conferences, and workshops that offer learning experiences to these residents have been cancelled or suspended, thus denying them a chance to achieve domain knowledge and enhance their skills. Although this pandemic has offered new learning modes like teleconsultation, videoconferencing, virtual simulations, digital podcasts, etc., how much actual knowledge transfer and skill gain will be achieved is unanswered. Despite this disruption, this pandemic has offered a golden opportunity to relook at the current PG resident education and training programme. The lessons learned from this adversity offer medical universities, medical educators, and regulatory authorities many opportunities to develop a novel and innovative curriculum that enables the current and future residents to achieve the necessary proficiency and competency.

Differential activation of mitogen-activated protein kinases following high and low LET radiation in murine macrophage cell line.

Mitogen-activated protein kinases have been shown to respond to various stimuli including cytokines, mitogens and gamma irradiation, leading to cell proliferation, differentiation, or death. The duration of their activation determines the specificity of response to each stimulus in various cells. In this study, the crucial intracellular kinases, ERK, JNK, and p38 kinase involved in cell survival, death, or damage and repair were examined for their activity in RAW 264.7 cells at various time points after irradiation with 2 Gy doses of proton ions or X-rays. This is the first report that shows that the MAPK signaling induced after heavy ion or X-ray exposure is not the same. Unlike gamma irradiation, there was prolonged but marginal activation of prosurvival ERK pathway and significant activation of proapoptotic p38 pathway in response to high LET radiation.

Effect of nitric oxide donor and gamma irradiation on MAPK signaling in murine peritoneal macrophages.

Irradiation (IR) of cells is known to activate enzymes of mitogen activated protein kinase (MAPK) family. These are known to be involved in cellular response to stress and are determinants of cell death or survival. When radiotherapy is delivered to malignant cells, macrophages, being radioresistant, survive, get activated, and produce large amounts of nitric oxide. As a result of activation they recognize and phagocytose tumor and normal cell apoptotic bodies leading to tumor regression. In this study, the MAPK signaling in peritoneal macrophages was investigated which plays an important role in its various functions, in an environment which is predominantly nitric oxide, as is after IR. The behavior of macrophages in such an environment was also looked at. The three MAPK (ERK1/2, p38, and JNK) respond differently to Sodium nitroprusside (SNP) alone or IR alone. All the three were activated following IR but only JNK was activated following SNP treatment. Surprisingly, when both the stresses were given simultaneously or one after the other, this differential response was lost and there was a complete inhibition of phosphorylation of all the three MAPKs, irrespective of the order of the two insults (IR and SNP). The noteworthy observation was that despite the complete inhibition of MAPK signaling there was no effect on either the viability or the phagocytic efficiency of peritoneal macrophages.

Effect of proton and gamma irradiation on human lung carcinoma cells: Gene expression, cell cycle, cell death, epithelial-mesenchymal transition and cancer-stem cell trait as biological end points.

Proton beam therapy is a cutting edge modality over conventional gamma radiotherapy because of its physical dose deposition advantage. However, not much is known about its biological effects vis-a-vis gamma irradiation. Here we investigated the effect of proton- and gamma- irradiation on cell cycle, death, epithelial-mesenchymal transition (EMT) and "stemness" in human non-small cell lung carcinoma cells (A549). Proton beam (3MeV) was two times more cytotoxic than gamma radiation and induced higher and longer cell cycle arrest. At equivalent doses, numbers of genes responsive to proton irradiation were ten times higher than those responsive to gamma irradiation. At equitoxic doses, the proton-irradiated cells had reduced cell adhesion and migration ability as compared to the gamma-irradiated cells. It was also more effective in reducing population of Cancer Stem Cell (CSC) like cells as revealed by aldehyde dehydrogenase activity and surface phenotyping by CD44(+), a CSC marker. These results can have significant implications for proton therapy in the context of suppression of molecular and cellular processes that are fundamental to tumor expansion.

Poly (ADP-ribose) polymerase and DNA-dependent protein kinase: differential activation in vivo.

DNA damage-activated homodimer of PARP-1 binds to single-strand breaks and catalyzes the synthesis and transfer of negatively charged ADP-ribose polymers to nuclear protein acceptors, including itself. It also undergoes site-specific proteolysis during apoptosis. On the other hand, DNA-PK is a heterotrimeric enzyme that specifically binds to double-strand breaks and phosphorylates its target proteins. Because both DNA breaks and apoptosis are known to occur following irradiation, whole-body irradiation was administered to find out the temporal pattern and dose-response of PARP expression and the activity pattern of DNA-PK. To assess the temporal response, male Wistar rats were subjected to a radiation dose of 3Gy and killed at various time intervals (1-24 hours). Both the PARP activity and expression were enhanced 4 hours after irradiation. Fragmented PARP was not observed until 24 hours after irradiation. The differential expression at DNA-PK various doses (0.1-5.0 Gy) was examined. The maximum expression of PARP was noted at 1 Gy, whereas the activation of DNA-PK was maximally observed at 3 Gy. We did not observe any increase in the expression of PARP until the dose of 3Gy was reached, which contradicted the findings in previous in vitro reports of PARP activation at high radiation doses. DNA-PK, however, showed a dose-dependent increase. Our results indicate that although both the PARP and the DNA-PK are nuclear enzymes with similar roles, the activation of these enzymes is dependent on the dose, and any extrapolation of data from in vitro observations can lead to misinterpretation.

Effect of nitric oxide donor and gamma irradiation on modifications of ERK and JNK in murine peritoneal macrophages.

Mitogen activated protein kinases (MAPKs) play an important role in activation, differentiation and proliferation of macrophages. Macrophages, upon activation, produce large amounts of nitric oxide that inhibit the growth of variety of microorganisms and tumor cells. This nitric oxide which is known to interfere with tyrosine phosphorylation may result in changes in the pattern of activation of MAPKs. In a previous study we have found that tyrosine phosphorylation of MAPKs was completely abolished in the presence of nitric oxide donor and radiation but this did not affect the function of macrophages. In this study the other post translational modifications namely nitration and ubiquitination of JNK and ERK have been looked at. Both ERK and JNK were found to be nitrated. However, there was no increase in ubiquitination of ERK and JNK, indicating that ubiquitination, in this case was not a natural consequence of nitration and may serve in signaling. Additionally, when the nitration was extensive, phosphorylation was also inhibited. The activation of substrates of ERK and JNK were looked at to determine the consequences of such modifications. Inhibition of phosphorylation and extensive nitration of JNK did not prevent activation of its substrate, c-jun. This study indicates that ERK and JNK may be under regulation by different type of modifications in macrophages.

Inhibition of radiation induced nitration by curcumin and nicotinamide in mouse macrophages.

Nitric oxide plays an important role in inflammation and carcinogenesis and has now been implicated as an important signaling molecule under normal physiological conditions also. Increased nitric oxide (NO) results in increased nitration of proteins at tyrosine, which can cause protein dysfunction or alterations in signal transduction pathways. Irradiation of Lipopolysaccharide (LPS) activated mouse peritoneal macrophages was found to increase NO production, inducible nitric oxide synthase (iNOS) expression and nitration of proteins. The increase in iNOS expression was very less when compared to increase in NO production, indicating the possibility of post-translational activation of iNOS by LPS and ionising radiation. The addition of curcumin, nicotinamide and Jun N-terminal kinase (JNK) inhibitor, SP 600125, reduced the levels of NO, iNOS expression and nitration of proteins in macrophages. Closer scrutiny of the inhibition pattern of these modulators revealed that although the JNK inhibitor did not result in significant decrease in iNOS expression it led to a significant decrease in NO production, implying the possible involvement of JNK in the regulation of iNOS activity. Curcumin and JNK inhibitor directly inhibited the nitration of proteins and JNK inhibitor and curcumin, when added together, did not show synergistic effect.