Biochemical reconstitution of a major age-related cancer mutational signature by heat-induced spontaneous deamination of 5-methylcytosine residues, repair of uracil residues, and DNA replication.

Non-enzymatic spontaneous deamination of 5-methylcytosine, producing thymine, is the proposed etiology of cancer mutational signature 1, which is the most predominant signature in all cancers. Here, the proposed mutational process was reconstituted using synthetic DNA and purified proteins. First, single-stranded DNA containing 5-methylcytosine at CpG context was incubated at an elevated temperature to accelerate spontaneous DNA damage. Then, the DNA was treated with uracil DNA glycosylase to remove uracil residues that were formed by deamination of cytosine. The resulting DNA was then used as a template for DNA synthesis by yeast DNA polymerase δ. The DNA products were analyzed by next-generation DNA sequencing, and mutation frequencies were quantified. The observed mutations after this process were exclusively C>T mutations at CpG context, which was very similar to signature 1. When 5-methylcytosine modification and uracil DNA glycosylase were both omitted, C>T mutations were produced on C residues in all sequence contexts, but these mutations were diminished by uracil DNA glycosylase-treatment. These results indicate that the CpG>TpG mutations were produced by the deamination of 5-methylcytosine. Additional mutations, mainly C>G, were introduced by yeast DNA polymerase ζ on the heat-damaged DNA, indicating that G residues of the templates were also damaged. However, the damage on G residues was not converted to mutations with DNA polymerase δ or ε. These results provide biochemical evidence to support that the majority of mutations in cancers are produced by ordinary DNA replication on spontaneously damaged DNA.

Biochemical analysis of H2O2-induced mutation spectra revealed that multiple damages were involved in the mutational process.

Reactive oxygen species (ROS) are a major threat to genomic integrity and believed to be one of the etiologies of cancers. Here we developed a cell-free system to analyze ROS-induced mutagenesis, in which DNA was exposed to H2O2 and then subjected to translesion DNA synthesis by various DNA polymerases. Then, frequencies of mutations on the DNA products were determined by using next-generation sequencing technology. The majority of observed mutations were either C>A or G>A, caused by dAMP insertion at G and C residues, respectively. These mutations showed similar spectra to COSMIC cancer mutational signature 18 and 36, which are proposed to be caused by ROS. The in vitro mutations can be produced by replicative DNA polymerases (yeast DNA polymerase δ and ε), suggesting that ordinary DNA replication is sufficient to produce them. Very little G>A mutation was observed immediately after exposure to H2O2, but the frequency was increased during the 24 h after the ROS was removed, indicating that the initial oxidation product of cytosine needs to be maturated into a mutagenic lesion. Glycosylase-sensitivities of these mutations suggest that the C>A were made on 8-oxoguanine or Fapy-guanine, and that G>A were most likely made on 5-hydroxycytosine modification.

Biochemical and photochemical mechanisms that produce different UV-induced mutation spectra.

Although UV-induced mutagenesis has been studied extensively, the precise mechanisms that convert UV-induced DNA damage into mutations remain elusive. One well-studied mechanism involves DNA polymerase (Pol) η and ζ, which produces C > T transitions during translesion synthesis (TLS) across pyrimidine dimers. We previously proposed another biochemical mechanism that involves multiple UV-irradiations with incubation in the dark in between. The incubation facilitates spontaneous deamination of cytosine in a pyrimidine dimer, and the subsequent UV irradiation induces photolyase-independent (direct) photoreversal that converts cytosine into monomeric uracil residue. In this paper, we first demonstrate that natural sunlight can induce both mutational processes in vitro. The direct photoreversal was also reproduced by monochromatic UVB at 300 nm. We also demonstrate that post-irradiation incubation in the dark is required for both mutational processes, suggesting that cytosine deamination is required for both the Pol η/ζ-dependent and the photoreversal-dependent mechanisms. Another Y-family polymerase Pol ι also mediated a mutagenic TLS on UV-damaged templates when combined with Pol ζ. The Pol ι-dependent mutations were largely independent of post-irradiation incubation, indicating that cytosine deamination was not essential for this mutational process. Sunlight-exposure also induced C > A transversions which were likely caused by oxidation of guanine residues. Finally, we constructed in vitro mutation spectra in a comparable format to cancer mutation signatures. While both Pol η-dependent and photoreversal-dependent spectra showed high similarities to a cancer signature (SBS7a), Pol ι-dependent mutation spectrum has distinct T > A/C substitutions, which are found in another cancer signature (SBS7d). The Pol ι-dependent T > A/C substitutions were resistant to T4 pyrimidine dimer glycosylase-treatment, suggesting that this mutational process is independent of cis-syn pyrimidine dimers. An updated model about multiple mechanisms of UV-induced mutagenesis is discussed.

Acute cytomegalovirus infection in an immunocompetent patient with ulcerative colitis: A case report.

Cytomegalovirus (CMV) is a ubiquitous member of the Herpesviridae family that can present with a variety of clinical manifestations, including encephalitis, retinitis, interstitial pneumonia and colitis. These serious symptoms are generally observed as opportunistic infections in immunocompromised hosts, including patients with acquired immunodeficiency syndrome and those receiving steroids and/or immunosuppressants. Symptomatic CMV infections in patients with ulcerative colitis are found in patients treated with steroids and/or immunosuppressants but rarely affect those who are not taking these agents. The present study reported the case of a young patient without concurrent use of immunosuppressive agents for the treatment of ulcerative colitis. The patient presented with acute mononucleosis and colitis caused by primary CMV infection. This was characterized by the presence of atypical lymphocytes and hepatosplenomegaly, elevation of transaminase levels, serology-positive anti-CMV IgM, and CMV antigenemia. Additionally, CMV-positive cells were histologically detected in colonic biopsy specimens. The patient's symptoms and clinical parameters improved following initiation of intravenous ganciclovir. It was concluded that even if patients with ulcerative colitis are not treated with steroids and/or immunosuppressants, significant attention should be paid to acute CMV infections in the context of severe or persistent colonic inflammation.

Idiopathic Ileocolonic Varices Coexisting with a Colon Polyp Treated Successfully by Endoscopy: A Case Report and Literature Review.

Colonic varices are usually associated with portal hypertension. Idiopathic colonic varices are extremely rare. A 68-year-old man with a positive fecal occult blood test result underwent colonoscopy. We detected idiopathic ileocolonic varices and a coexisting ascending colon polyp. While reviewing the literature, we found cases of biopsies and polypectomies resulting in significant bleeding. We herein report a case of idiopathic ileocolonic varices coexisting with a colon polyp treated successfully by endoscopy. The coexistence of colonic varices and a colorectal lesion that requires endoscopic treatment may lead to significant bleeding. During management, the development of a treatment strategy and obtaining informed consent are necessary.

Biochemical reconstitution of UV-induced mutational processes.

We reconstituted two biochemical processes that may contribute to UV-induced mutagenesis in vitro and analysed the mutational profiles in the products. One process is translesion synthesis (TLS) by DNA polymerases (Pol) δ, η and ζ, which creates C>T transitions at pyrimidine dimers by incorporating two dAMPs opposite of the dimers. The other process involves spontaneous deamination of cytosine, producing uracil in pyrimidine dimers, followed by monomerization of the dimers by secondary UV irradiation, and DNA synthesis by Pol δ. The mutational spectrum resulting from deamination without translesion synthesis is similar to a mutational signature found in melanomas, suggesting that cytosine deamination encountered by the replicative polymerase has a prominent role in melanoma development. However, CC>TT dinucleotide substitution, which is also commonly observed in melanomas, was produced almost exclusively by TLS. We propose that both TLS-dependent and deamination-dependent mutational processes are likely involved in UV-induced melanoma development.

Safety of Carbon Dioxide Insufflation during Endoscopic Submucosal Dissection for Esophageal Squamous Cell Carcinoma.

BACKGROUND: Pulmonary dysfunction often accompanies esophageal squamous cell carcinoma (SCC). AIMS: This study examined the use of carbon dioxide (CO2) insufflation and its safety during esophageal endoscopic submucosal dissection (ESD) while under conscious sedation. METHODS: ESD using CO2 insufflation (1.4 L/min) was performed in 102 consecutive esophageal SCC patients. Patients with a forced expiratory volume of 1.0 s/forced vital capacity (FEV1.0%) < 70% or a vital capacity < 80% were defined as having pulmonary dysfunction. Transcutaneous partial pressure of CO2 (PtcCO2) was recorded before, during, and after ESD. RESULTS: A history of smoking was found in 90 patients (88%), while 43 patients (42%) had pulmonary dysfunction. No significant differences were found between the pulmonary dysfunction and normal groups for the baseline PtcCO2 before ESD, peak PtcCO2 during ESD, and median PtcCO2 after ESD. There was a significant correlation between the PtcCO2 elevation from baseline and the ESD procedure time (r = 0.32, p < 0.01), with the correlation for the pulmonary dysfunction group much stronger (r = 0.39, p < 0.05) than that for the normal group (r = 0.30, p < 0.01). Neither of the groups exhibited any differences for either the complication incidence or the hospital stay. CONCLUSIONS: Although the use of CO2 insufflation during esophageal ESD under conscious sedation is safe with regard to the risk of complications, longer procedure times can potentially induce CO2 retention in patients with obstructive lung disease. Thus, it is necessary to both shorten the procedure times and perform CO2 monitoring.

Carbon dioxide insufflation reduces residual gas in the gastrointestinal tract following colorectal endoscopic submucosal dissection.

Quantitative examinations evaluating the effects of CO2 insufflation on residual gas in the gastrointestinal tract following colorectal endoscopic submucosal dissection (ESD) are lacking. The present study aimed to assess whether CO2 insufflation could decrease the amount of residual gas in the gastrointestinal tract following ESD in patients with colorectal neoplasms. Computed tomography (CT) was used to objectively examine whether CO2 insufflation during colorectal ESD reduced residual gas levels in the gastrointestinal tract following ESD. A total of 83 patients who underwent colorectal ESD between January and December 2009 at Gifu University Hospital (Gifu, Japan) were enrolled. Following exclusion of 17 patients with chronic pulmonary dysfunction, 66 patients were randomized into a CO2 insufflation group (n=34) and an air insufflation group (n=32). The level of residual gas and the presence of transmural and free-air leaks following ESD were evaluated in both groups using CT. Transcutaneous CO2 tension (PtcCO2) and ESD-related complications were also compared between the groups. CT measurements of the major and minor axes of the cecal lumen, and of the terminal ileum diameter, indicated the level of residual gas following ESD to be significantly reduced in the CO2 insufflation group compared with the air insufflation group (P<0.001). Neither the incidences of ESD-related complications, including post-procedure hemorrhage and air leak, nor the abnormalities in vital signs differed between the groups. No significant between-group differences were identified in the baseline and peak PtcCO2 levels during ESD or in the median PtcCO2 following ESD. In conclusion, CO2 insufflation during colorectal ESD was effective in reducing residual gas in the gastrointestinal tract following ESD.

[A case of an elderly patient with inverted Meckel's diverticulum with small intestinal bleeding detected using capsule and double-balloon endoscopies].

An 80-year-old man was examined with esophagogastroduodenoscopy and colonoscopy because of digestive tract hemorrhage;however, no specific cause was found. Small intestinal capsule endoscopy revealed a reddish elevated lesion in the ileum. This lesion was also detected using double-balloon endoscopy as a 5-cm reddish elevated lesion covered with normal villous architecture in the 95-cm part of the Bauhin valve on the oral side. The lesion was laparoscopically resected and diagnosed as inverted Meckel's diverticulum based on pathological examination. This was a rare case where Meckel's diverticulum was inverted, and the lesion was observed using capsule and double-balloon endoscopies before surgery. Although complications of Meckel's diverticulum are rare in the elderly, it is necessary to identify this disease as a cause of small intestinal bleeding, even in elderly patients.

NGS-based analysis of base-substitution signatures created by yeast DNA polymerase eta and zeta on undamaged and abasic DNA templates in vitro.

Translesion synthesis (TLS) is the mechanism in which DNA polymerases (TLS polymerases) bypass unrepaired template damage with high error rates. DNA polymerase η and ζ (Polη and Polζ) are major TLS polymerases that are conserved from yeast to humans. In this study, we quantified frequencies of base-substitutions by yeast Polη and Polζ on undamaged and abasic templates in vitro. For accurate quantification, we used a next generation sequencing (NGS)-based method where DNA products were directly analyzed by parallel sequencing. On undamaged templates, Polη and Polζ showed distinct base-substitution profiles, and the substitution frequencies were differently influenced by the template sequence. The base-substitution frequencies were influenced mainly by the adjacent bases both upstream and downstream of the substitution sites. Thus we present the base-substitution signatures of these polymerases in a three-base format. On templates containing abasic sites, Polη created deletions at the lesion in more than 50% of the TLS products, but the formation of the deletions was suppressed by the presence of Polζ. Polζ and Polη cooperatively facilitated the TLS reaction over an abasic site in vitro, suggesting that these two polymerases can cooperate in efficient and high fidelity TLS.

Acetylation of PCNA Sliding Surface by Eco1 Promotes Genome Stability through Homologous Recombination.

During DNA replication, proliferating cell nuclear antigen (PCNA) adopts a ring-shaped structure to promote processive DNA synthesis, acting as a sliding clamp for polymerases. Known posttranslational modifications function at the outer surface of the PCNA ring to favor DNA damage bypass. Here, we demonstrate that acetylation of lysine residues at the inner surface of PCNA is induced by DNA lesions. We show that cohesin acetyltransferase Eco1 targets lysine 20 at the sliding surface of the PCNA ring in vitro and in vivo in response to DNA damage. Mimicking constitutive acetylation stimulates homologous recombination and robustly suppresses the DNA damage sensitivity of mutations in damage tolerance pathways. In comparison to the unmodified trimer, structural differences are observed at the interface between protomers in the crystal structure of the PCNA-K20ac ring. Thus, acetylation regulates PCNA sliding on DNA in the presence of DNA damage, favoring homologous recombination linked to sister-chromatid cohesion.

Roles of C-Terminal Region of Yeast and Human Rad52 in Rad51-Nucleoprotein Filament Formation and ssDNA Annealing.

Yeast Rad52 (yRad52) has two important functions at homologous DNA recombination (HR); annealing complementary single-strand DNA (ssDNA) molecules and recruiting Rad51 recombinase onto ssDNA (recombination mediator activity). Its human homolog (hRAD52) has a lesser role in HR, and apparently lacks mediator activity. Here we show that yRad52 can load human Rad51 (hRAD51) onto ssDNA complexed with yeast RPA in vitro. This is biochemically equivalent to mediator activity because it depends on the C-terminal Rad51-binding region of yRad52 and on functional Rad52-RPA interaction. It has been reported that the N-terminal two thirds of both yRad52 and hRAD52 is essential for binding to and annealing ssDNA. Although a second DNA binding region has been found in the C-terminal region of yRad52, its role in ssDNA annealing is not clear. In this paper, we also show that the C-terminal region of yRad52, but not of hRAD52, is involved in ssDNA annealing. This suggests that the second DNA binding site is required for the efficient ssDNA annealing by yRad52. We propose an updated model of Rad52-mediated ssDNA annealing.

A case of a teenage boy with eosinophilic gastroenteritis with esophageal involvement developing a hemorrhagic duodenal ulcer.

A boy in his early teens visited our hospital with chief complaints of hematemesis and tarry stools. Upper gastrointestinal endoscopy identified a hemorrhagic duodenal ulcer, for which hemostasis was performed using a clip. Proton pump inhibitor (PPI) administration diminished the ulcer but relapse occurred after PPI discontinuation. The esophagus showed concentric rings and longitudinal linear furrows considered to be characteristic of eosinophilic esophagitis. Biopsies of the duodenal ulcer and the esophagus revealed marked infiltration of eosinophils, leading to a diagnosis of eosinophilic gastroenteritis with esophageal involvement. Steroid treatment was initiated, and the duodenal ulcer and esophagitis resolved. Endoscopic findings characteristic of eosinophilic esophagitis were key to the diagnosis of eosinophilic gastroenteritis.

PCNA is efficiently loaded on the DNA recombination intermediate to modulate polymerase δ, η, and ζ activities.

Proliferating cell nuclear antigen (PCNA) is required for DNA homologous recombination (HR), but its exact role is unclear. Here, we investigated the loading of PCNA onto a synthetic D-loop (DL) intermediate of HR and the functional interactions of PCNA with Rad51 recombinase and DNA polymerase (Pol) δ, Pol η, and Pol ζ. PCNA was loaded onto the synthetic DL as efficiently as it was loaded onto a primed DNA substrate. Efficient PCNA loading requires Replication Protein A, which is associated with the displaced ssDNA loop and provides a binding site for the clamp-loader Replication Factor C. Loaded PCNA greatly stimulates DNA synthesis by Pol δ within the DL but does not affect primer recognition by Pol δ. This suggests that the essential role of PCNA in HR is not recruitment of Pol δ to the DL but stimulation of Pol δ to displace a DNA strand during DL extension. Both Pol η and Pol ζ extended the DL more efficiently than Pol δ in the absence of PCNA, but little or no stimulation was observed in the presence of PCNA. Finally, Rad51 inhibited both the loading of PCNA onto the DL and the extension of the DL by Pol δ and Pol η. However, preloaded PCNA on the DL counteracts the Rad51-mediated inhibition of the DL extension. This suggests that the inhibition of postinvasion DNA synthesis by Rad51 occurs mostly at the step of PCNA loading.

Diagnosis of the jejunoileal lymphoma by double-balloon endoscopy.

AIM: To investigate the feasibility of double-balloon endoscopy (DBE) to detect jejunoileal lymphoma, compared with fluorodeoxyglucose positron emission tomography (FDG-PET). METHODS: Between March 2004 and January 2011, we histologically confirmed involvement of malignant lymphoma of the jejunoileum in 31 patients by DBE and biopsy. In 20 patients of them, we performed with FDG-PET. We retrospectively reviewed the records of these 20 patients. Their median age was 64 years (range 50-81). In the 20 patients, the pathological diagnosis of underlying non-Hodgkin's lymphoma (NHL) comprised follicular lymphoma (FL, n = 12), diffuse large B cell lymphoma (DLBCL, n = 4), mantle cell lymphoma (MCL, n = 2), enteropathy associated T cell lymphoma (ETL, n = 1) and anaplastic large cell lymphoma (ALCL, n = 1). RESULTS: Ten cases showed accumulation by FDG-PET (50%). FDG-PET was positive in 3 of 12 FL cases (25%) while in 7 of 8 non-FL cases (88%, P < 0.05). Intestinal FL showed a significantly lower rate of positive FDG-PET, in comparison with other types of lymphoma. Cases with endoscopically elevated lesions (n = 10) showed positive FDG-PET in 2 (20%), but those with other type NHL did in 8 of 10 (80%, P < 0.05). When the cases having elevated type was compared with those not having elevated type lesion, the number of cases that showed accumulation of FDG was significantly smaller in the former than in the latter. CONCLUSION: In a significant proportion, small intestinal involvement cannot be pointed out by FDG-PET. Especially, FL is difficult to evaluate by FDG-PET but essentially requires DBE.

Combination of proton pump inhibitor and rebamipide, a free radical scavenger, promotes artificial ulcer healing after endoscopic submucosal dissection with dissection size >40 mm.

In our previous study, the healing effect of proton pump inhibitor plus rebamipide for endoscopic submucosal dissection-related artificial ulcer smaller than 40 mm showed statistical significance. However, such effect of the combination was not yet clear for ulcers with dissected diameter more than 40 mm. The aim of this present study was to resolve this problem under sufficient statistical power, with adequate sample size. We conducted a randomized controlled study. Either the proton pump inhibitor mono-therapy or the combination therapy was prescribed for 28 days after endoscopic submucosal dissection. Eighty-seven patients were eligible for outcome evaluation. Combination therapy was significantly superior to mono-therapy, 27.8% vs 0% reached healing stage (scar stage) in cases with ulcers of dissection diameter more than 40 mm. In conclusion, the combination therapy with rebamipide was favorable regimen in patients with larger artificial ulcer after endoscopic submucosal dissection.

Characterization of an insertion sequence-like element, ISBlo15, identified in a size-increased cryptic plasmid pBK283 in Bifidobacterium longum BK28.

The characteristics of mobile genetic elements in bifidobacteria are not well understood. We characterized an insertion sequence-like element of the IS200/IS605 family found in a size-increased cryptic plasmid in Bifidobacterium longum. During a plasmid profile analysis of B. longum BK strains, we encountered a 6.5-kbp cryptic plasmid pBK283 in B. longum BK28, the size of which has not been identified in bifidobacteria. Nucleotide sequence analysis indicated that an insertion sequence-like element was inserted into the 5.0-kbp pKJ50-like plasmid and resulted in a size increase of pBK283. The element, named ISBlo15, was 1593 bp in length and contained a single ORF encoding a putative transposase, which is similar to the transposase OrfB encoded by IS200/IS605 family elements. Several sequence characteristics, including conserved transposase motifs in OrfB and terminal palindromic sequences that differ from the typical terminal inverted repeats, strongly suggested that ISBlo15 is a member of the IS200/IS605 family. Sequences similar to ISBlo15 were widely distributed among the nine Bifidobacterium species tested, and those of highly homologous sequences were detected only in Bifidobacterium gallicum JCM8224(T).

Dynamic regulatory interactions of rad51, rad52, and replication protein-a in recombination intermediates.

Rad51, Rad52, and replication protein-A (RPA) play crucial roles in the repair of DNA double-strand breaks in Saccharomyces cerevisiae. Rad51 mediates DNA strand exchange, a key reaction in DNA recombination. Rad52 recruits Rad51 into single-stranded DNAs (ssDNAs) that are saturated with RPA. Rad52 also promotes annealing of ssDNA strands that are complexed with RPA. Specific protein-protein interactions are involved in these reactions. Here we report new biochemical characteristics of these protein interactions. First, Rad52-RPA interaction requires multiple molecules of RPA to be associated with ssDNA, suggesting that multiple contacts between the Rad52 ring and RPA-ssDNA filament are needed for stable binding. Second, RPA-t11, which is a recombination-deficient mutant of RPA, displays a defect in interacting with Rad52 in the presence of salt above 50 mM, explaining the defect in Rad52-mediated ssDNA annealing in the presence of this mutation. Third, ssDNA annealing promoted by Rad52 is preceded by aggregation of multiple RPA-ssDNA complexes with Rad52, and Rad51 inhibits this aggregation. These results suggest a regulatory role for Rad51 that suppresses ssDNA annealing and facilitates DNA strand invasion. Finally, the Rad51-double-stranded DNA complex disrupts Rad52-RPA interaction in ssDNA and titrates Rad52 from RPA. This suggests an additional regulatory role for Rad51 following DNA strand invasion, where Rad51-double-stranded DNA may inhibit illegitimate second-end capture to ensure the error-free repair of a DNA double-strand break.

Rad51 protein controls Rad52-mediated DNA annealing.

In Saccharomyces cerevisiae, Rad52 protein plays an essential role in the repair of DNA double-stranded breaks (DSBs). Rad52 and its orthologs possess the unique capacity to anneal single-stranded DNA (ssDNA) complexed with its cognate ssDNA-binding protein, RPA. This annealing activity is used in multiple mechanisms of DSB repair: single-stranded annealing, synthesis-dependent strand annealing, and cross-over formation. Here we report that the S. cerevisiae DNA strand exchange protein, Rad51, prevents Rad52-mediated annealing of complementary ssDNA. Efficient inhibition is ATP-dependent and involves a specific interaction between Rad51 and Rad52. Free Rad51 can limit DNA annealing by Rad52, but the Rad51 nucleoprotein filament is even more effective. We also discovered that the budding yeast Rad52 paralog, Rad59 protein, partially restores Rad52-dependent DNA annealing in the presence of Rad51, suggesting that Rad52 and Rad59 function coordinately to enhance recombinational DNA repair either by directing the processed DSBs to repair by DNA strand annealing or by promoting second end capture to form a double Holliday junction. This regulation of Rad52-mediated annealing suggests a control function for Rad51 in deciding the recombination path taken for a processed DNA break; the ssDNA can be directed to either Rad51-mediated DNA strand invasion or to Rad52-mediated DNA annealing. This channeling determines the nature of the subsequent repair process and is consistent with the observed competition between these pathways in vivo.