Establishment of permutation for cancer risk estimation in the urothelium based on genome-wide DNA methylation analysis.

The aim of this study was to establish permutation for cancer risk estimation in the urothelium. Twenty-six samples of normal control urothelium obtained from patients without urothelial carcinomas (C), 47 samples of non-cancerous urothelium without noticeable morphological changes obtained from patients with urothelial carcinomas (N), and 46 samples of the corresponding cancerous tissue (T) in the learning cohort and 64 N samples in the validation cohort, i.e. 183 tissue samples in total, were analyzed. Genome-wide DNA methylation analysis was performed using the Infinium HumanMethylation 450K BeadChip, and DNA methylation levels were verified using pyrosequencing and MassARRAY. Amplicon sequencing was performed using the GeneRead DNAseq Targeted Panels V2. Although N samples rarely showed genetic mutations or copy number alterations, they showed DNA methylation alterations at 2502 CpG sites compared to C samples, and such alterations were inherited by or strengthened in T samples, indicating that DNA methylation alterations may participate in field cancerization in the urothelium. Receiver operating characteristic curve analysis confirmed the feasibility of cancer risk estimation to identify urothelium at the precancerous stage by DNA methylation quantification. Cancer risk estimation permutation was established using a combination of two marker CpG loci on the HOXC4, TENM3 and TLR1 genes (sensitivity and specificity 96-100%). Among them, the diagnostic impact of 10 patterns of permutation was successfully validated in the validation cohort (sensitivity and specificity 94-98%). These data suggest that cancer risk estimation using procedures such as urine tests during health checkups might become applicable for clinical use.

The Japanese Society of Pathology Guidelines on the handling of pathological tissue samples for genomic research: Standard operating procedures based on empirical analyses.

Genome research using appropriately collected pathological tissue samples is expected to yield breakthroughs in the development of biomarkers and identification of therapeutic targets for diseases such as cancers. In this connection, the Japanese Society of Pathology (JSP) has developed "The JSP Guidelines on the Handling of Pathological Tissue Samples for Genomic Research" based on an abundance of data from empirical analyses of tissue samples collected and stored under various conditions. Tissue samples should be collected from appropriate sites within surgically resected specimens, without disturbing the features on which pathological diagnosis is based, while avoiding bleeding or necrotic foci. They should be collected as soon as possible after resection: at the latest within about 3 h of storage at 4°C. Preferably, snap-frozen samples should be stored in liquid nitrogen (about -180°C) until use. When intending to use genomic DNA extracted from formalin-fixed paraffin-embedded tissue, 10% neutral buffered formalin should be used. Insufficient fixation and overfixation must both be avoided. We hope that pathologists, clinicians, clinical laboratory technicians and biobank operators will come to master the handling of pathological tissue samples based on the standard operating procedures in these Guidelines to yield results that will assist in the realization of genomic medicine.

Genome-wide DNA methylation analysis during non-alcoholic steatohepatitis-related multistage hepatocarcinogenesis: comparison with hepatitis virus-related carcinogenesis.

The aim of this study was to clarify the significance of DNA methylation alterations during non-alcoholic steatohepatitis (NASH)-related hepatocarcinogenesis. Single-CpG-resolution genome-wide DNA methylation analysis was performed on 264 liver tissue samples using the Illumina Infinium HumanMethylation450 BeadChip. After Bonferroni correction, 3331 probes showed significant DNA methylation alterations in 113 samples of non-cancerous liver tissue showing NASH (NASH-N) as compared with 55 samples of normal liver tissue (NLT). Principal component analysis using the 3331 probes revealed distinct DNA methylation profiles of NASH-N samples that were different from those of NLT samples and 37 samples of non-cancerous liver tissue showing chronic hepatitis or cirrhosis associated with hepatitis B virus (HBV) or hepatitis C virus (HCV) infection (viral-N). Receiver operating characteristic curve analysis identified 194 probes that were able to discriminate NASH-N samples from viral-N samples with area under the curve values of more than 0.95. Jonckheere-Terptsra trend test revealed that DNA methylation alterations in NASH-N samples from patients without hepatocellular carcinoma (HCC) were inherited by or strengthened in NASH-N samples from patients with HCC, and then inherited by or further strengthened in 22 samples of NASH-related HCC (NASH-T) themselves. NASH- and NASH-related HCC-specific DNA methylation alterations, which were not evident in viral-N samples and 37 samples of HCC associated with HBV or HCV infection, were observed in tumor-related genes, such as WHSC1, and were frequently associated with mRNA expression abnormalities. These data suggested that NASH-specific DNA methylation alterations may participate in NASH-related multistage hepatocarcinogenesis.

Genes involved in development and differentiation are commonly methylated in cancers derived from multiple organs: a single-institutional methylome analysis using 1007 tissue specimens.

The aim of this study was to clarify the significance of DNA methylation alterations shared by cancers derived from multiple organs. We analyzed single-institutional methylome data by single-CpG-resolution Infinium assay for 1007 samples of non-cancerous tissue (N) and corresponding cancerous tissue (T) obtained from lung, stomach, kidney, breast and liver. Principal component analysis revealed that N samples of each organ showed distinct DNA methylation profiles, DNA methylation profiles of N samples of each organ being inherited by the corresponding T samples and DNA methylation profiles of T samples being more similar to those of N samples in the same organ than those of T samples in other organs. In contrast to such organ and/or carcinogenetic factor-specificity of DNA methylation profiles, when compared with the corresponding N samples, 231 genes commonly showed DNA hypermethylation in T samples in four or more organs. Gene ontology enrichment analysis showed that such commonly methylated genes were enriched among "transcriptional factors" participating in development and/or differentiation, which reportedly show bivalent histone modification in embryonic stem cells. Pyrosequencing and quantitative reverse transcription-PCR revealed an inverse correlation between DNA methylation levels and mRNA expression levels of representative commonly methylated genes, such as ALX1, ATP8A2, CR1 and EFCAB1, in tissue samples. These data suggest that disruption of the differentiated state of precancerous cells via alterations of expression, independent of differences in organs and/or carcinogenetic factors, may be a common feature of DNA methylation alterations during carcinogenesis in multiple organs.

Development and validation of a high-quality simulator with exchangeable peritoneum for transabdominal preperitoneal laparoscopic inguinal hernia repair.

INTRODUCTION: Practical simulation training with proper haptic feedback and the fragility of the human body is required to overcome the long learning curve associated with laparoscopic inguinal hernia repair (LIHR). However, few hernia models accurately reflect the texture and fragility of the human body. Therefore, in this study, we developed a novel model for transabdominal preperitoneal (TAPP) LIHR training and evaluated its validity. METHODS: We developed a high-quality mock peritoneum with a hydrated polyvinyl alcohol layer and a unique two-way crossing cellulose fiber layer. To complete the simulation, the peritoneum was adhered to a urethane foam inguinal base with surgical landmarks. Participants could perform all the procedures required for the TAPP LIHR. Twenty-four surgeons performed TAPP LIHR simulation using a novel simulator. Their opinions were rated on a 5-point Likert scale. Additionally, 6 surgical residents and 10 surgical experts performed the procedure. Their performance was evaluated using the TAPP checklist score and procedure time. RESULTS: Most participants strongly agreed that the TAPP LIHR simulator with an exchangeable peritoneum model was useful. The participants agreed on the model fidelity for tactile sensation, forceps handling, and humanlike anatomy. In comparisons between surgical residents and experts, the experts had significantly higher scores (10.6 vs. 17.2, p < 0.05) and shorter procedure times (92.3 vs. 55.9 min; p < .05) than did surgical residents. CONCLUSIONS: We developed a high-quality exchangeable peritoneal model that mimics the human peritoneum's texture and fragility. This model enhances laparoscopic simulation training, potentially shortening TAPP LIHR learning curves.

Does the placement of a cystic duct tube after a hepatic resection help reduce the incidence of post-operative bile leak?

BACKGROUND: In this retrospective study, the effects of cystic duct (C) tube use on the incidence of post-hepatectomy bile leak were assessed. METHODS: The subjects were 550 patients who underwent a hepatectomy during 1990-2011, with (n = 83) and without (n = 467) C tube drainage. The use of a C tube was based on the surgeon's choice. RESULTS: Bile leakage was observed in 44 (8%) patients, and its incidence post-operatively correlated with intrahepatic cholangiocarcinoma, parenchymal transection with forceps fracture and tie, a major hepatectomy, prolonged surgery and excessive blood loss (P < 0.050) but not with the use of a C tube. The incidence of an intra-abdominal infection was higher and the hospital stay was longer in the leak (49 days) than non-leak group (21 days, P < 0.001). ISGLS grade B and C bile leak post-hemi-hepatectomy and extended-hepatectomy were more frequent in the non-C than C tube group (P = 0.016). The duration of hospitalization was not different between the two groups; however, 7 patients in the non-C tube group had prolonged hospitalization (> 60 days) compared with none in the C tube group (P = 0.454). CONCLUSION: The usefulness of the C tube in preventing post-hepatectomy bile leak could not be confirmed; however, both bile leak requiring clinical management and long hospitalization after a major hepatectomy could be reduced with C tube use.

Persistent Descending Mesocolon as An Intraoperative Risk Factor in Laparoscopic Surgery for Left-Sided Colon and Rectal Cancer.

INTRODUCTION: Persistent descending mesocolon (PDM) represents a failure of fusion of the descending mesentery, leading to anatomical abnormalities. This study aimed to examine the effects of anatomical features of PDM on laparoscopic surgical outcomes. METHODS: Patient backgrounds, surgical outcomes, anatomical characteristics, and operative findings were retrospectively compared between 186 patients classified into PDM and non-PDM groups who underwent primary resection for left-sided colon and rectal cancer at our hospital from January 2019 to December 2020. RESULTS: PDM was diagnosed in nine patients (4.8%). The operative time (337 ± 165 vs 239 ± 107 min, p = 0.010) was significantly different between PDM and non-PDM groups, but bleeding loss was not different (108 ± 97 ml vs 53 ± 142 ml, p = 0.259). In PDM patients, in addition to abnormal fixation of the sigmoid-descending colon junction, adhesion of the mesentery of the colon and small intestine in 100%, and adhesion between the mesocolon in 33% patients was confirmed intraoperatively. Ileus was more common in the PDM group (two cases, 22%) and in the non-PDM group (10 cases, 5.6%), but there was no significant difference in overall postoperative complications between the two groups (p = 0.215). The duration of postoperative hospital stay (28 ± 20 vs 16 ± 11 days, p = 0.002) was significant between the two groups. The left colonic artery (LCA) could not be preserved in six patients in the PDM group, one of whom had anastomotic leakage and two of whom required additional resections due to intraoperative intestinal blood flow failure. CONCLUSION: PDM prolonged operative times and duration of postoperative stay in laparoscopic surgery for left-sided colon and rectal cancer. Division of the LCA in PDM patients should be considered an intraoperative risk factor for injury to the marginal artery.

Short- and Long-term Outcome After Gastric Cancer Resection in Patients Aged 80 Years and Older.

Background/Aim: We aimed to assess the risk factors for postoperative complications and long-term outcome of patients aged ≥80 years after curative resection for gastric cancer (GC). Patients and Methods: Patients aged ≥80 years who underwent curative gastrectomy for stage I-III GC between 2013 and 2020 were included. Clinical factors were retrospectively analyzed. Results: Of all 109 patients, 29 (26.6%) had 33 postoperative complications (Clavien-Dindo grade ≥2). The rate of postoperative complications was higher in those with greater blood loss (≥170 ml, p<0.001). In multivariate analysis, greater blood loss was confirmed as an independent predictor of postoperative complications (p<0.001). The 30-day, 180-day, 1-year, and 3-year cumulative overall survival rates were 100%, 97.0%, 91.6%, and 74.7%, respectively. Multivariate analysis showed postoperative complications (p=0.014) and low prognostic nutritional index (PNI, p=0.044) were independent prognostic factors for poor overall survival. Conclusion: Performing operations with less bleeding is important to reduce postoperative complications. According to the analysis of long-term survival, patients who experience postoperative complications and patients with a low preoperative PNI require special attention in the follow-up period. Nutritional support should be considered in patients with malnutrition.

Short- and long-term survival after curative resection for colorectal cancer in nonagenarian patients.

BACKGROUND/OBJECTIVE: With increased life expectancy, the incidence of colorectal cancer in oldest-old patients has been rising. Advanced age is a risk factor for adverse outcomes after surgery. This study aimed to evaluate the short- and long-term outcomes of curative resection for colorectal cancer in nonagenarians. METHODS: Patients who had undergone curative resection for colorectal cancer (CRC) at Stage I to III from January 2010 to December 2019 were included. Cases of emergent surgery were excluded. The clinical characteristics were documented retrospectively, and factors affecting the long-term outcome were analyzed using multivariate analysis. RESULTS: Fifty patients met the selection criteria. Most of them were women (58.0%), and the median age was 92 years. Among these patients, 29 (58.0%) had a poor performance status (ASA-PS≥3). Laparoscopic surgery was performed in 42.0% of the patients, and 50% of the patients had postoperative complications classified as Clavien-Dindo grade 2 or severer, including 3 patients (6.0%) with grade 3 disease. No postoperative mortality occurred. The 30-day, 180-day, 1-year, 3-year and 5-year survival rates were 100%, 80.4%, 71.0%, 46.3%, and 33.8%, respectively. Multivariate analysis showed that a preoperative poor performance status (ASA-PS≥3) (HR: 3.067; 95% CI: 1.220-7.709; p = 0.017) was an independent prognostic factor for OS. CONCLUSION: Curative elective resections for CRC in nonagenarians were performed safely without postoperative mortality. The preoperative performance status was significantly associated with OS after curative elective resection of colorectal cancer in nonagenarians. Our results suggest that excellent long-term outcomes can be achieved in a selected group with a good performance status.

Long-Term Prognosis after Surgery for Locally Recurrent Rectal Cancer: A Retrospective Study.

OBJECTIVE: Resection is usually recommended for locally recurrent rectal cancer (LRRC) for which R0 resection is possible, but its suitability varies by individual patient risk. Here, we report outcomes of resected LRRC in our hospital. METHODS: We retrospectively evaluated short- and long-term results of 33 patients who underwent resections for LRRC from January 2003 to December 2019. RESULTS: At the initial surgeries for these 33 patients, their disease stages at that time were Stage I: n=2, Stage II: n=12, Stage III: n=11, Stage IV: n=6, and unknown: n=2. Patients with Stage IV disease at their initial surgeries underwent radical one-step or two-step procedures. Metastasis to other organs was observed in 5 patients at the their initial LRRC diagnoses. At the LRRC surgeries, 7 patients received palliative surgeries; 26 received intent-to-treat resections, of which 17 were R0 resections. All-grade postoperative complications were observed in 11 patients, including 1 surgery-related death. Five-year overall survival rates were all cases: 38.4%; R0 group: 52.3%, R1 or R2 group: 19.4%, and palliative surgery group: 0%. The R0 group thus had significantly better prognosis than other patients (P = 0.0012). Eleven patients in the R0 group (64.7%) suffered re-recurrences but some patients achieved long-term survival through chemotherapy, radiation therapy, and surgery for metastasis to other organs, even after re-recurrence. CONCLUSION: Long-term prognosis after surgery for LRRC was significantly better for patients with R0 margins. Multimodal treatments may greatly improve survival for patients who suffer re-recurrences after local recurrence resections.

Safe laparoscopic resection of a giant schwannoma in the retroperitoneum using a fluorescent ureteral stent: a case report.

Schwannomas that occur in the retroperitoneal cavity are rare. We herein report a patient who underwent safe laparoscopic resection by using a preoperative 3D computed tomography (CT) image and a fluorescent ureteral stent during the surgery. A 47-year-old man presented with left lower abdominal pain. CT showed a 10-cm continuous retroperitoneal tumor originating at the third lumbar nerve in the lower left abdomen. Schwannoma was suspected. We underwent laparoscopic resection of the tumor guided by 3D images obtained preoperatively. A fluorescent ureteral stent was implanted during the surgery to improve visibility and protect the left ureter. The resection was completed without injury of other organs and vessels. The patient was discharged on postoperative Day 5. By performing a preoperative simulation using 3D CT images, we could anticipate the anatomical findings and easily identify them intraoperatively. In addition, the fluorescent ureteral stent provided visual support, thereby contributing to safe surgery.

Postoperative Complications Predict Long-term Outcome After Curative Resection for Perforated Colorectal Cancer.

BACKGROUND/AIM: Perforation and postoperative complications have a negative effect on long-term outcomes in patients with colorectal cancer (CRC). The aim of this study was to evaluate the clinical factors with special reference to postoperative complications predicting the long-term outcome in those for whom curative resection for perforated CRC was performed. PATIENTS AND METHODS: Patients who underwent curative resection for perforated CRC at stage II or III from April 2003 to March 2020 were included. Clinical factors were retrospectively analyzed. RESULTS: Forty-four patients met the selection criteria. The 30-day mortality rate was 4.5% and the complication rate was 47.7%. Excluding 30-day mortality, five-year recurrence-free survival (RFS) and overall survival (OS) were 62.3% and 73.6%, respectively. Multivariate analysis showed that postoperative complications (p=0.005) and pT4 pathological factor (p=0.009) were independent prognostic factors for RFS. Only postoperative complications (p=0.023) were an independent prognostic factor for OS. CONCLUSION: Postoperative complications were significantly associated with RFS and OS, and pT4 was associated with RFS. The prevention and management of postoperative adverse events may be important for perforated CRC.

Occurrence of the European subgroup of subtype I BK polyomavirus in Japanese-Americans suggests transmission outside the family.

To examine the mode of transmission of BK polyomavirus (BKV), urine samples were collected from Japanese-Americans in Los Angeles and from other southern Californians. Subtype I was the main subtype found in samples from both groups. The subtype I subgroup Ib-2, which is predominant in Europe, was the primary subgroup detected in second-generation Japanese-Americans and in southern Californians; however, the Ic subgroup prevalent in native Japanese was rare in these populations. Since the European subgroup (Ib-2) predominated in the studied geographic area, the findings demonstrate that transmission outside the family is common in the spread of BKV, unlike previous findings for JC polyomavirus.

Impact of fatty acids on human UDP-glucuronosyltransferase 1A1 activity and its expression in neonatal hyperbilirubinemia.

While breast milk has been known as a cause of neonatal hyperbilirubinemia, the underlying mechanism of breast milk-induced jaundice has not been clarified. Here, the impact of fatty acids on human UDP-glucuronosyltransferase (UGT) 1A1--the sole enzyme that can metabolize bilirubin--were examined. Oleic acid, linoleic acid, and docosahexaenoic acid (DHA) strongly inhibited UGT1A1 activity. Forty-eight hours after a treatment with a lower concentration of DHA (10 mg/kg), total bilirubin significantly increased in neonatal hUGT1 mice, which are human neonatal jaundice models. In contrast, treatments with higher concentrations of fatty acids (0.1-10 g/kg) resulted in a decrease in serum bilirubin in hUGT1 mice. It was further demonstrated that the treatment with higher concentrations of fatty acids induced UGT1A1, possibly by activation of peroxisome proliferator-activated receptors. Our data indicates that activation of peroxisome proliferator-activated receptors would increase UGT1A1 expression, resulting in reduction of serum bilirubin levels in human infants.

Distribution patterns of BK polyomavirus (BKV) subtypes and subgroups in American, European and Asian populations suggest co-migration of BKV and the human race.

BK polyomavirus (BKV) is ubiquitous in the human population, infecting children asymptomatically and then persisting in the kidney. Based on serological and genotyping methods, BKV isolates worldwide are classified into four subtypes (I-IV), with subtype I prevalent throughout the world, subtype IV prevalent in Asia and part of Europe, and subtypes II and III rare throughout the world. Phylogenetic analyses of complete genome sequences have identified several geographically distinct subgroups of subtypes I and IV. To explain how the geographical distribution patterns of BKV subtypes and subgroups were formed, this study hypothesized that BKV co-migrated with human populations (the co-migration hypothesis), and examined this hypothesis by comparing the BKV subtype and subgroup profiles among two American populations in North-east USA and southern California, two European populations in Finland and Ireland/England, and two Asian populations in Japan and China (both American populations were composed mainly of European Americans). The frequency of subtype I was always the highest throughout the populations, but that of subtype IV was variable among populations. A subgroup of subtype I (I/b-2) was detected primarily in all of the European and American populations, whereas subgroup I/c was predominant in the Asian populations (the observed difference was statistically significant). Additionally, all of the five fully sequenced subtype IV isolates from the American and European populations belonged to subgroup IV/c-2, whereas all subtype IV isolates from the Asian populations belonged to the other subgroups. Collectively, the current findings provide support for the co-migration hypothesis.

Transcriptional control region rearrangements associated with the evolution of JC polyomavirus.

JC polyomavirus (JCV) isolates worldwide are classified into three super-lineages (A, B and C), with A and B further split into several lineages and sub-lineages. The transcriptional control region (TCR) of the JCV genome generally has the archetypal configuration, but rearranged TCRs have occasionally been detected in isolates from immunocompetent individuals. To investigate the phylogenetic significance of these rearrangements, we analyzed 298 TCR sequences all derived from complete JCV genomes directly cloned from the urine of non-immunocompromised individuals. While sporadic rearrangements were found in many lineages and sub-lineages, common rearrangements were identified in all, or essentially all, isolates belonging to particular lineages or sub-lineages. Interestingly, several common rearrangements were also detected as sporadic rearrangements in other lineages or sub-lineages. This observation suggests that during the course of JCV evolution, JCV strains with sporadic rearrangements became predominant over archetypal TCRs in some JCV lineages or sub-lineages.

Conserved archetypal configuration of the transcriptional control region during the course of BK polyomavirus evolution.

BK polyomavirus (BKV) is widespread among humans, asymptomatically infecting children and then persisting in renal tissue. The transcriptional control region (TCR) of the BKV genome is variable among clinical isolates. Thus, archetypal TCRs with a common basic configuration generally occur in BKV isolates from the urine of immunocompromised patients, but rearranged TCRs that possibly arise from the archetypal configuration have also been detected in clinical specimens. To examine the hypothesis that archetypal strains represent wild-type strains circulating in the human population (the archetype hypothesis), we analysed 145 complete viral genomes amplified directly from the urine of non-immunocompromised individuals worldwide. These genomes included 82, three, two and 58 sequences classified as belonging to subtypes I, II, III and IV, respectively. Rearranged TCRs with long duplications or deletions were detected from two subtype I and two subtype IV genomes, but not from the other 141 genomes (thus, the TCRs of these genomes were judged to be archetypal). The variations in the archetypal TCRs were nucleotide substitutions and single-nucleotide deletions, most of which were unique to particular subtypes or subgroups. We confirmed that the four complete BKV genomes with rearranged TCRs did not form a unique lineage on a phylogenetic tree. Collectively, the findings demonstrate that the archetypal TCR configuration has been conserved during the evolution of BKV, providing support for the archetype hypothesis. Additionally, we suggest that 'archetype' should be used as a conceptual term that denotes a prototypical structure that can generate various rearranged TCRs during viral growth in vivo and in vitro.