The survival impact of preoperative FOLFOX for resectable locally advanced rectal cancer: the R-NAC-01 study.

PURPOSE: In this follow-up of the R-NAC-01 study, we assessed the long-term oncological benefit of four courses of modified leucovorin, 5-fluorouracil (FU), and oxaliplatin (mFOLFOX6) chemotherapy before rectal surgery. METHODS: In this prospective, multicenter study (UMIN 000012559) involving 11 hospitals in Japan, patients with lower rectal cancer underwent four cycles of mFOLFOX6 chemotherapy and subsequent surgery within four to six weeks. The 3-year recurrence-free survival and local recurrence rates were then reported. RESULTS: Of 41 patients (36 males, 5 females; mean age: 60.8 years old) who received 4 courses of chemotherapy, 40 underwent total mesorectal excision, and 1 underwent total pelvic exenteration. R0 resection was achieved in 40 patients, but none showed a pathological complete response. Twenty-nine patients received adjuvant chemotherapy for an average of 4 months. The 3 year recurrence-free survival and local recurrence rates in patients undergoing curable resection were 72.8% and 8.5%, respectively. cStage III patients with adjuvant chemotherapy had a significantly higher 3 year recurrence-free survival than those without adjuvant chemotherapy (76.6 vs. 40.0%, log-rank p = 0.03). CONCLUSION: Four courses of mFOLFOX6 chemotherapy before surgery may be a promising treatment strategy for locally advanced rectal cancer. Adjuvant chemotherapy might be needed for cStage III patients, even after four courses of neoadjuvant mFOLFOX6.

Correction to: Short-Term Symptomatic Relief in Gastroesophageal Reflux Disease: A Comparative Study of Esomeprazole and Vonoprazan.

The original version of the article unfortunately contained percentage errors in second and third paragraphs of GerdQ Score section. Below is the corrected version.

Short-Term Symptomatic Relief in Gastroesophageal Reflux Disease: A Comparative Study of Esomeprazole and Vonoprazan.

BACKGROUND AND AIM: Proton pump inhibitors and vonoprazan (a potassium-competitive acid blocker) are recommended as first-line treatments for gastroesophageal reflux disease (GERD). However, few reports have investigated the onset of action of these agents for GERD symptom relief. The present study compared the symptom relief of esomeprazole with that of vonoprazan via monitoring self-reported GERD symptoms after treatment initiation. METHODS: This was a prospective, multicenter, randomized, open-label, parallel group, comparative clinical study between esomeprazole (20 mg/day) and vonoprazan (20 mg/day) administered for 4 weeks to patients with GERD symptoms. Patients who had scores ≥ 8 on the Gastroesophageal Reflux Disease Questionnaire (GerdQ) were defined as having GERD and enrolled in this study. Sixty patients were randomly assigned to either the esomeprazole group (n = 30) or the vonoprazan group (n = 30). Treatment response rates in each drug group were evaluated according to the GerdQ. The Frequency Scale for the Symptoms of GERD (FSSG) scores from the 1st day after treatment initiation and the Global Overall Symptom (GOS) scale scores during treatment were also evaluated. RESULTS: At 4 weeks, the treatment response rates for symptom relief according to the GerdQ were 88.0% in the esomeprazole group and 81.8% in the vonoprazan group. The GOS scales, which reflect the impact of GERD symptoms, were similar for both groups. The FSSG scores decreased from the 1st to the 14th day in both groups. CONCLUSIONS: There were no substantial differences in the symptom relief between the two groups at any time point in this short-term study.

Preoperative FOLFOX in resectable locally advanced rectal cancer can be a safe and promising strategy: the R-NAC-01 study.

PURPOSE: The aim of this study was to assess the safety of rectal surgery after 5-fluorouracil-leucovorin-oxaliplatin chemotherapy (FOLFOX6). METHODS: This was a prospective, multicenter study in 11 Japanese hospitals. We included patients with rectal cancer who received 4 courses of modified FOLFOX6 (mFOLFOX6) before rectal surgery and examined the postoperative complication rate, the clinicopathological response, and the rate of chemotherapy-related adverse events (UMIN 000012559). RESULTS: The study population included 36 men and 5 women. The average age of the patients was 60.8 years and the average body mass index was 23.1 kg/m2. After 4 courses of chemotherapy, grade 2 peripheral nerve disorder and other grade 3 adverse events were seen in 3 patients each (7.3%). Twenty-eight (73.7%) and 8 (21.1%) patients underwent low anterior resection and abdominoperineal resection, respectively. The pelvic nerves were preserved in 35 patients. Surgical morbidity (grade ≥ 3) occurred in 4 patients (10.5%). Anastomotic leakage occurred after surgery in 2 patients (7.1%). No patients achieved pathologically complete remission. However, downstaging of the clinical stage and N stage was seen in 17 (41.5%) and 22 (53.7%) patients, respectively. CONCLUSIONS: Surgery after four courses of mFOLFOX6 chemotherapy can be a safe and promising strategy for patients with locally advanced rectal cancer.

A novel transmembrane protein defines the endoplasmic reticulum stress-induced cell death pathway.

Mitochondrial membrane potential (ΔΨm) maintenance is physiologically critical in cells; its loss causes apoptotic signalling and cell death. Accumulating DNA mutations and unfolded proteins in stressed cells activate signalling pathways for cell death induction. Cancer cells often fail to die even in the presence of some death signalling proteins. Here, we report a short hairpin RNA (shRNA) with an artificial sequence, denoted Psi1 shRNA, which leads to ΔΨm loss in HCT116 cells. The Psi1 shRNA target gene was shown to encode transmembrane protein 117 (TMEM117). TMEM117 knockdown led to ΔΨm loss, increased reactive oxygen species levels, up-regulation of an endoplasmic reticulum (ER) stress sensor C/EBP homologous protein and active caspase-3 expression, and cell growth impairment, altering homeostasis towards cell death. TMEM117 levels were down-regulated in response to the ER stressor thapsigargin and decreased when cells showed ΔΨm loss. These results suggested that TMEM117 RNAi allowed apoptotic cell death. Therefore, TMEM117 probably mediates the signalling of ΔΨm loss in ER stress-mediated mitochondria-mediated cell death.

SIMCOMP/SUBCOMP: chemical structure search servers for network analyses.

One of the greatest challenges in bioinformatics is to shed light on the relationship between genomic and chemical significances of metabolic pathways. Here, we demonstrate two types of chemical structure search servers: SIMCOMP (http://www.genome.jp/tools/simcomp/) for the chemical similarity search and SUBCOMP (http://www.genome.jp/tools/subcomp/) for the chemical substructure search, where both servers provide links to the KEGG PATHWAY and BRITE databases. The SIMCOMP is a graph-based method for searching the maximal common subgraph isomorphism by finding the maximal cliques in the association graph. In contrast, the SUBCOMP is an extended method for solving the subgraph isomorphism problem. The obtained links to PATHWAY or BRITE databases can be used to interpret as the biological meanings of chemical structures from the viewpoint of the various biological functions including metabolic networks.

PathPred: an enzyme-catalyzed metabolic pathway prediction server.

The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPred (http://www.genome.jp/tools/pathpred/), a web-based server to predict plausible pathways of muti-step reactions starting from a query compound, based on the local RDM pattern match and the global chemical structure alignment against the reactant pair library. In this server, we focus on predicting pathways for microbial biodegradation of environmental compounds and biosynthesis of plant secondary metabolites, which correspond to characteristic RDM patterns in 947 and 1397 reactant pairs, respectively. The server provides transformed compounds and reference transformation patterns in each predicted reaction, and displays all predicted multi-step reaction pathways in a tree-shaped graph.

Rapid Screening Using Pathomorphologic Interpretation to Detect BRAFV600E Mutation and Microsatellite Instability in Colorectal Cancer.

PURPOSE: Rapid decision-making is essential in precision medicine for initiating molecular targeted therapy for patients with cancer. This study aimed to extract pathomorphologic features that enable the accurate prediction of genetic abnormalities in cancer from hematoxylin and eosin images using deep learning (DL). EXPERIMENTAL DESIGN: A total of 1,657 images (one representative image per patient) of thin formalin-fixed, paraffin-embedded tissue sections from either primary or metastatic tumors with next-generation sequencing-confirmed genetic abnormalities-including BRAFV600E and KRAS mutations, and microsatellite instability high (MSI-H)-that are directly relevant to therapeutic strategies for advanced colorectal cancer were obtained from the nationwide SCRUM-Japan GI-SCREEN project. The images were divided into three groups of 986, 248, and 423 images to create one training and two validation cohorts, respectively. Pathomorphologic feature-prediction DL models were first developed on the basis of pathomorphologic features. Subsequently, gene-prediction DL models were constructed for all possible combinations of pathomorphologic features that enabled the prediction of gene abnormalities based on images filtered by the combination of pathomorphologic feature-prediction models. RESULTS: High accuracies were achieved, with AUCs > 0.90 and 0.80 for 12 and 27, respectively, of 33 analyzed pathomorphologic features, with high AUCs being yielded for both BRAFV600E (0.851 and 0.859) and MSI-H (0.923 and 0.862). CONCLUSIONS: These findings show that novel next-generation pathology methods can predict genetic abnormalities without the need for standard-of-care gene tests, and this novel next-generation pathology method can be applied for colorectal cancer treatment planning in the near future.

Proportion of flat- and depressed-type and laterally spreading tumor among advanced colorectal neoplasia.

BACKGROUND & AIMS: Flat- and depressed-type neoplasias along with laterally spreading tumors (LSTs) have been reported in colorectal neoplasias. We estimated the prevalence of flat and depressed types and LSTs along with their proportion among advanced neoplasias in a large average-risk population undergoing screening colonoscopy. METHODS: This was a cross-sectional study performed at a single, general community institution, with subjects who were 40 to 79 years old, asymptomatic, and who had undergone their first colonoscopy for screening between 2003 and 2009 (n = 4910). Among the neoplasias detected, advanced neoplasias were morphologically classified as the polypoid type, flat and depressed type, or LST. We determined the prevalence and proportion for each type among the advanced neoplasias, with morphologies defined according to the Japanese endoscopic classification. RESULTS: Advanced neoplasias were detected in 7.9% of men, 4.7% of women, and 6.1% of overall subjects. The polypoid type, the flat and depressed types, and the LSTs accounted for 75.3%, 7.5%, and 17.2% of advanced neoplasia, respectively. There was a high proportion of T1 cancers among the depressed types (40%). Approximately 80% of LSTs were located on the right side of the colon and more than 30% of LSTs showed high-grade dysplasia or T1 cancer. CONCLUSIONS: Most advanced neoplasias detected were of the polypoid type. LSTs accounted for a considerable proportion among advanced neoplasia and tended to be located on the right side of the colon. The influences of any LSTs need to be taken into consideration for preventing colorectal cancer.

Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism.

BACKGROUND: Understanding of secondary metabolic pathway in plant is essential for finding druggable candidate enzymes. However, there are many enzymes whose functions are not yet discovered in organism-specific metabolic pathways. Towards identifying the functions of those enzymes, assignment of EC numbers to the enzymatic reactions they catalyze plays a key role, since EC numbers represent the categorization of enzymes on one hand, and the categorization of enzymatic reactions on the other hand. RESULTS: We propose reaction graph kernels for automatically assigning EC numbers to unknown enzymatic reactions in a metabolic network. Reaction graph kernels compute similarity between two chemical reactions considering the similarity of chemical compounds in reaction and their relationships. In computational experiments based on the KEGG/REACTION database, our method successfully predicted the first three digits of the EC number with 83% accuracy. We also exhaustively predicted missing EC numbers in plant's secondary metabolism pathway. The prediction results of reaction graph kernels on 36 unknown enzymatic reactions are compared with an expert's knowledge. Using the same data for evaluation, we compared our method with E-zyme, and showed its ability to assign more number of accurate EC numbers. CONCLUSION: Reaction graph kernels are a new metric for comparing enzymatic reactions.

E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.

MOTIVATION: The IUBMB's Enzyme Nomenclature system, commonly known as the Enzyme Commission (EC) numbers, plays key roles in classifying enzymatic reactions and in linking the enzyme genes or proteins to reactions in metabolic pathways. There are numerous reactions known to be present in various pathways but without any official EC numbers, most of which have no hope to be given ones because of the lack of the published articles on enzyme assays. RESULTS: In this article we propose a new method to predict the potential EC numbers to given reactant pairs (substrates and products) or uncharacterized reactions, and a web-server named E-zyme as an application. This technology is based on our original biochemical transformation pattern which we call an 'RDM pattern', and consists of three steps: (i) graph alignment of a query reactant pair (substrates and products) for computing the query RDM pattern, (ii) multi-layered partial template matching by comparing the query RDM pattern with template patterns related with known EC numbers and (iii) weighted major voting scheme for selecting appropriate EC numbers. As the result, cross-validation experiments show that the proposed method achieves both high coverage and high prediction accuracy at a practical level, and consistently outperforms the previous method. AVAILABILITY: The E-zyme system is available at http://www.genome.jp/tools/e-zyme/.

Characterizing common substructures of ligands for GPCR protein subfamilies.

The G-protein coupled receptor (GPCR) superfamily is the largest class of proteins with therapeutic value. More than 40% of present prescription drugs are GPCR ligands. The high therapeutic value of GPCR proteins and recent advancements in virtual screening methods gave rise to many virtual screening studies for GPCR ligands. However, in spite of vast amounts of research studying their functions and characteristics, 3D structures of most GPCRs are still unknown. This makes target-based virtual screenings of GPCR ligands extremely difficult, and successful virtual screening techniques rely heavily on ligand information. These virtual screening methods focus on specific features of ligands on GPCR protein level, and common features of ligands on higher levels of GPCR classification are yet to be studied. Here we extracted common substructures of GPCR ligands of GPCR protein subfamilies. We used the SIMCOMP, a graph-based chemical structure comparison program, and hierarchical clustering to reveal common substructures. We applied our method to 850 GPCR ligands and we found 53 common substructures covering 439 ligands. These substructures contribute to deeper understanding of structural features of GPCR ligands which can be used in new drug discovery methods.

Comprehensive genomic analysis of sulfur-relay pathway genes.

Many cofactors and nucleotides containing sulfur atoms are known to have important functions in a variety of organisms. Recently, the biosynthetic pathways of these sulfur containing compounds have been revealed, where many enzymes relay sulfur atoms. Increasing evidence also suggests that the prokaryotic sulfur-relay enzymes might be the evolutionary origin of ubiquitination and the related systems that control a wide range of physiological processes in eukaryotic cells. However, these sulfur-relay enzymes have been studied in only a small number of organisms. Here we carried out comparative genomic analysis and examined the presence and absence of sulfurtransferases utilized in the biosynthetic pathways of molybdenum cofactor (Moco), 2-thiouridine (S(2)U), and 4-thiouridine (S(4)U), and IscS, a cysteine desulfurase. We found that all eukaryotes and many other organisms lack the intermediate enzymes in S(2)U biosynthesis. It is also found that most genes lack rhodanese homology domain (RHD), a catalytic domain of sulfurtransferase. Some organisms have a conserved sequence composed of about 100 residues in the C terminus of TusA, different from RHD. Host-associated organisms have a tendency to lose Moco biosynthetic enzymes, and some organisms have MoaD-MoaE fusion protein. Our findings suggest that sulfur-relay pathways have been so diversified that some putative sulfurtransferases possibly function in other unknown pathways.

KEGG for linking genomes to life and the environment.

KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target relationships, through the process of BRITE mapping. KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them. KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps. In addition, smaller pathway modules are defined and stored in KEGG MODULE that also contains other functional units and complexes. The KEGG resource is being expanded to suit the needs for practical applications. KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.

Utility of double arterial cannulation for surgical repair of acute type A dissection.

OBJECTIVES: Outcomes of planned and unplanned (rescue) double arterial cannulation (DAC) in surgery for acute type A aortic dissection were investigated retrospectively. METHODS: The study involved 805 patients who were divided into 4 groups according to the cannulation strategy: single cannulation of the femoral artery (n = 338), axillary artery (n = 256), left ventricular apex (n = 52) or ascending aorta (n = 5) (total, n = 57), and DAC (n = 154). Patients who underwent DAC were divided between planned (n = 132) and rescue (n = 22) usage. Characteristics and outcomes were compared between groups. Both unmatched and propensity score-matched analyses were performed. RESULTS: Shock (39%, 19%, 33% and 14%, in the femoral artery, axillary artery, left ventricular apex/ascending aorta and DAC, respectively) and leg malperfusion (5%, 16%, 16% and 26%, respectively) differed significantly (P < 0.001), but in-hospital mortality did not (9%, 8%, 18% and 7%, respectively; P = 0.096). The 5-year survival rates were 79.4%, 79.7%, 78.6% and 82.2%, respectively. Propensity score-matched analysis showed no statistically significant differences in in-hospital mortality rates (10%, 12%, 14% and 9%, respectively; P = 0.78) and 5-year survival rates (78.4%, 72.3%, 82.3% and 78.0%, respectively). The leading vessel combination and indications for planned and rescue DAC were the femoral and axillary arteries (98%) and true lumen narrowing and/or leg malperfusion (34%), and the axillary followed by femoral (77%) artery and low cardiopulmonary bypass flow (36%). In-hospital mortality in the planned and rescue DAC groups was 7% and 9%, respectively. CONCLUSIONS: DAC seems effective for both prevention and management of intraoperative malperfusion.

Generalized reaction patterns for prediction of unknown enzymatic reactions.

Prediction of unknown enzymatic reactions is useful for understanding biological processes such as reactions to external substances like endocrine disrupters. To create an accurate prediction, we need to define a similarity measure in the reaction. We have developed the KEGG RPAIR database which is a collection of chemical structure transformation patterns, called RDM patterns, for substrate-product pairs of enzymatic reactions. In this study, we compared RDM patterns with EC numbers which are the well-known hierarchical classification scheme for enzymes. Additionally, we performed hierarchical clustering of RDM patterns using the information stating whether each sub-subclass of EC has a particular RDM patterns or not. To represent the variation of RDM patterns in a cluster, we generalized RDM patterns in the same cluster using the hierarchy of KEGG Atomtypes, which are the components of RDM patterns. Using this generalized pattern, we can predict which cluster includes a given RDM pattern even if the reaction of the pattern has not been assigned any EC numbers. Thus we will be able to define the similarity between enzymatic reactions by using this cluster information.

From genomics to chemical genomics: new developments in KEGG.

The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. In accordance with the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules. Specifically, RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions, such as the prediction of new reactions and new enzyme genes that would degrade new environmental compounds. Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps.

Analysis of common substructures of metabolic compounds within the different organism groups.

With the increase in available post-genomic data and metabolic pathway information, we have been focusing on revealing the biological meaning of higher phenomena such as relationships of metabolic systems in different organisms. Metabolism plays an essential role in all cellular organisms, e.g. energy transportation, signal transduction and structural formation of cell components. The metabolic pathway of each organism has a different landscape from all others because of the different sets of enzymes encoded in the genome. The organisms that are incapable of producing their own essential chemical compounds should acquire them in some way from other organisms that can produce them. For example, several vitamins are required by animals to survive. In this manner we can assume that the different availabilities of metabolites may influence the relationship between organisms in nature. In this study, we focus on the differences in available metabolites among organisms. First, we divided 239 species with complete genomes into 9 organism groups in accordance with phylogeny and averaged out the annotation quality and the phylogenetic sparsity. Then, we calculated the commonly used chemical compounds between organism groups and the uniquely used chemical compounds in an organism group. The total number of metabolites we consider in this study is 1,074, which is about one-third of all metabolites that appear in the KEGG metabolic pathways. Finally we show the differences and the similarities between organism groups on every metabolic pathway map, illustrating the commonly observed substructures within the uniquely used metabolites. These results will help us to better comprehend the architecture of metabolic pathways and the relationships between organisms.

Comparative study: Vonoprazan and proton pump inhibitors in Helicobacter pylori eradication therapy.

AIM: To compare the effectiveness and safety of vonoprazan-based therapy with proton pump inhibitor (PPI)-based therapies to treat Helicobacter pylori (H. pylori). METHODS: We retrospectively analysed data from first-line (vonoprazan or PPI with 200 mg clarithromycin and 750 mg amoxicillin twice daily for 7 d) (n = 1353) and second-line (vonoprazan or PPI with 250 mg metronidazole and 750 mg amoxicillin twice daily for 7 d) (n = 261) eradication treatments for H. pylori -positive patients with associated gastrointestinal diseases from April 2014 to December 2015 at Hattori Clinic, Japan. The primary endpoint was the eradication rate, which was assessed with a full analysis set. The secondary endpoints were adverse events and related factors. RESULTS: After the first-line treatments, the eradication rates for vonoprazan, esomeprazol, rabeprazole, and lansoprazole were 87.9% (95%CI: 84.9%-90.5%), 71.6% (95%CI: 67.5%-75.5%), 62.9% (95%CI: 52.0%-72.9%), and 57.3% (95%CI: 50.4%-64.1%), respectively. The vonoprazan eradication rate was significantly higher than that of the PPIs (P < 0.01). Interestingly, smoking did not affect the H. pylori eradication rate in the vonoprazan group (P = 0.34), whereas it decreased the rates in the PPI groups (P = 0.013). The incidence of adverse events in the vonoprazan group was not different from the PPI group (P = 0.054), although the vonoprazan group exhibited a wider range of adverse events. Vonoprazan-based triple therapy was highly effective as a second-line treatment, with an eradication rate similar to that of PPI-based therapy. CONCLUSION: Vonoprazan might be superior to PPIs in first-line H. pylori therapy, particularly for smokers. However, caution is required due to possible adverse events.

Detection and analysis of Lactobacillus paracasei penicillin-binding proteins revealed the presence of cholate-sensitive penicillin-binding protein 3 and an elongated cell shape in a cholate-sensitive strain.

Penicillin-binding proteins (PBPs) are responsible for peptidoglycan synthesis. By using biotinylated ampicillin, we detected PBPs of Lactobacillus paracasei strains. Ten PBPs were identified, 7 of which had apparent molecular sizes similar to those of Escherichia coli. In the presence of cholate, strain NRIC 0625 showed an elongated shape, and its putative PBP3 showed cholate-sensitive penicillin-binding activity. Furthermore, this strain was highly sensitive to cefalexin, which is known to inhibit cell division by inactivating PBP3. These results suggest that the septum synthetase PBP3 of lactic acid bacteria can be one of the targets of intestinal bile acid.