Bevacizumab increases the sensitivity of olaparib to homologous recombination-proficient ovarian cancer by suppressing CRY1 via PI3K/AKT pathway.

PARP inhibitors have changed the management of advanced high-grade epithelial ovarian cancer (EOC), especially homologous recombinant (HR)-deficient advanced high-grade EOC. However, the effect of PARP inhibitors on HR-proficient (HRP) EOC is limited. Thus, new therapeutic strategy for HRP EOC is desired. In recent clinical study, the combination of PARP inhibitors with anti-angiogenic agents improved therapeutic efficacy, even in HRP cases. These data suggested that anti-angiogenic agents might potentiate the response to PARP inhibitors in EOC cells. Here, we demonstrated that anti-angiogenic agents, bevacizumab and cediranib, increased the sensitivity of olaparib in HRP EOC cells by suppressing HR activity. Most of the γ-H2AX foci were co-localized with RAD51 foci in control cells. However, most of the RAD51 were decreased in the bevacizumab-treated cells. RNA sequencing showed that bevacizumab decreased the expression of CRY1 under DNA damage stress. CRY1 is one of the transcriptional coregulators associated with circadian rhythm and has recently been reported to regulate the expression of genes required for HR in cancer cells. We found that the anti-angiogenic agents suppressed the increase of CRY1 expression by inhibiting VEGF/VEGFR/PI3K pathway. The suppression of CRY1 expression resulted in decrease of HR activity. In addition, CRY1 inhibition also sensitized EOC cells to olaparib. These data suggested that anti-angiogenic agents and CRY1 inhibitors will be the promising candidate in the combination therapy with PARP inhibitors in HR-proficient EOC.

Molecular biological analysis revealed a case of synchronous endometrial and ovarian cancer with different histological grade as metastatic ovarian cancer from endometrial cancer: Case report and review of literature.

The diagnosis of synchronous endometrial and ovarian cancer or metastatic cancer of the same histological type is difficult. In this study, molecular biology analysis was performed to determine ovarian metastasis from endometrial cancer. A 38-year-old woman had pathological evidence of endometrial cancer (endometrioid carcinoma, grade 1) and ovarian cancer (endometrioid carcinoma, grade 3); a disseminated nodule in the serosa uteri was also diagnosed as endometrioid carcinoma (grade 3). Customized panel sequencing revealed a common mutation pattern in ovarian cancer and disseminated nodules. Furthermore, endometrial cancer showed the same mutation patterns for FGFR3 and PTEN as ovarian cancer and disseminated nodules. All tumors were microsatellite instability high. Clinicopathological and molecular biology analyses suggested that the patient had ovarian metastasis from endometrial cancer. The patient underwent adjuvant chemotherapy with paclitaxel and carboplatin, with no recurrence. Molecular biology techniques may enable appropriate treatment based on clinically accurate diagnosis.

Genetic characteristics of platinum-sensitive ovarian clear cell carcinoma.

OBJECTIVE: Most ovarian clear cell carcinomas are resistant to platinum-based chemotherapy, while a small subset shows a positive response. The aim of this study was to clarify the clinical, pathological and genetic characteristics of platinum-sensitive ovarian clear cell carcinomas. METHODS: The study included 53 patients with stage III-IV ovarian clear cell carcinoma who had residual tumours after primary surgery and received platinum-based therapy between 2009 and 2018. A retrospective examination of platinum sensitivity was performed using the criterion of ≥6 months from the last day of first-line platinum therapy until recurrence/progression. Cases determined to be platinum-sensitive were subjected to immunohistochemical staining, genomic analyses using target sequencing (i.e. NCC Oncopanel) and homologous recombination deficiency (myChoice® HRD Plus) assays. RESULTS: Of the 53 stage III-IV ovarian clear cell carcinoma cases, 11 (21%) were platinum-sensitive. These cases showed better progression-free and overall survival than platinum-resistant cases (hazard ratio = 0.16, P < 0.001). Among the seven sensitive cases whose tumour tissues were available for molecular profiling, five were pure ovarian clear cell carcinoma based on pathological and genetic features, whereas the remaining two cases were re-diagnosed as high-grade serous ovarian carcinoma. The pure ovarian clear cell carcinomas lacked BRCA1 and BRCA2 mutations, consistent with the absence of the homologous recombination deficiency phenotype, whereas two cases (40%) had ATM mutations. By contrast, the two high-grade serous ovarian carcinoma cases had BRCA1 or BRCA2 mutations associated with the homologous recombination deficiency phenotype. CONCLUSION: The subset of platinum-sensitive ovarian clear cell carcinomas includes a majority with pure ovarian clear cell carcinoma features that lack the homologous recombination deficiency phenotype.

Centennial scale sequences of environmental deterioration preceded the end-Permian mass extinction.

The exact drivers for the end-Permian mass extinction (EPME) remain controversial. Here we focus on a ~10,000 yr record from the marine type section at Meishan, China, preceding and covering the onset of the EPME. Analyses of polyaromatic hydrocarbons at sampling intervals representing 1.5-6.3 yr reveal recurrent pulses of wildfires in the terrestrial realm. Massive input pulses of soil-derived organic matter and clastic materials into the oceans are indicated by patterns of C2-dibenzofuran, C30 hopane and aluminum. Importantly, in the ~2,000 years preceding the main phase of the EPME, we observe a clearly defined sequence of wildfires, soil weathering, and euxinia provoked by the fertilization of the marine environment with soil-derived nutrients. Euxinia is indicated by sulfur and iron concentrations. Our study suggests that, in South China, centennial scale processes led to a collapse of the terrestrial ecosystem ~300 yr (120-480 yr; ± 2 s.d.) before the onset of the EPME and that this collapse induced euxinic conditions in the ocean, ultimately resulting in the demise of marine ecosystems.

Maleimide index: a paleo-redox index based on fragmented fossil-chlorophylls obtained by chromic acid oxidation.

The composition of past photosynthetic organisms provides information about the paleo-environment based on the habitat characteristics of photosynthetic organisms. Therefore, analysis of chlorophyll-derived materials from photosynthetic organisms in sedimentary rocks is important for understanding paleo-environmental changes. Fossilized chlorophylls present in sedimentary rocks can be detected by their conversion into maleimides and phthalimides. This can be achieved through the chromic acid oxidation of sedimentary rocks. Since the maleimides and phthalimides are derived from the pyrrole skeleton of fossil chlorophylls, their composition reflects the composition of paleo-photosynthetic organisms. We herein propose an indicator for detecting anoxic-sulfidic conditions in the paleo oceanic photic zone, which is based on the composition ratio of the maleimides produced during the oxidation process. The maleimide index in this study would be a useful analytical method to indicate that anoxic-sulfidic conditions in the paleo oceanic photic zone, which is associated with mass extinction events, have occurred.

Fluid drag reduction by penguin-mimetic laser-ablated riblets with yaw angles.

The bodies of penguins, which swim underwater to forage, are densely covered with feathers, in which the barbs are oriented in the longitudinal direction. We hypothesize that these barbs act as riblets and reduce friction drag during swimming. Considering various real-world swim conditions, the drag reduction effect is expected to be robust against changes in the flow speed and yaw angle relative to the flow. To test this hypothesis, we created trapezoidal riblets based on the morphology of these barbs and measured the drag of flat plates with these fabricated riblets in a water tunnel. The spacing, width, and height of the barbs were found to be approximately 100, 60, and 30 µm, respectively. This spacing resulted in a nondimensional spacings+of 5.5 for a typical penguin swimming speed of 1.4 m s-1. We fabricated four types of riblets on polyimide films by ultraviolet laser ablation. The first was a small-scale riblet for which the spacing was decreased to 41 µm to simulate the surface flow condition of the usual and slower swim behaviors in our water tunnel. The other three were manufactured to the actual scale of real barbs (spacing of 100 µm) with three different rib ridge widths: 10, 25, and 50 µm. Yaw angles of 0°, 15°, 30°, and 45° were also tested with the actual-scale riblets. The drag reduction rate of the small-scale riblet was maximized to 1.97% by the smallests+of 1.59. For all three actual-scale riblets, increasing the yaw angle from zero to 15° enhanced the drag reduction rate for the full range ofs+up to 13.5. The narrow-ridge riblet reduced drag at an even higher yaw angle of 45°, but the drag increased with zero yaw angle. Overall, the medium-ridge riblet, which was representative of the barbs, was well-balanced.

Water molecule-mediated selective inhibition of bacterial zinc metalloproteinases by non-hydroxamate compounds: Ab initio molecular simulations.

UDP-3-O-acyl-N acetylglucosamine deacetylase (LpxC), Zn metalloenzyme for Gram-negative bacteria is an attractive target for developing novel therapeutic agents. Since LpxC has the similar binding pocket as the human matrix metalloproteinases (MMPs), LpxC inhibitors might also inhibit MMP functions producing side effects in human bodies. Here, we investigated specific interactions between LpxC/MMP and their inhibitors using ab initio molecular simulations to elucidate the reason of selective inhibition for LpxC by non-hydroxamate compounds. The evaluated binding properties between LpxC and the compounds are comparable to the trend of their observed inhibitory affinities. It was also elucidated that compound 22 binds most strongly to LpxC due to its specific interactions with Zn ion and Asp241 side chain of LpxC. In contrast, the interactions between the compounds and MMP are significantly weakened due to the water molecules, which are tightly coordinated with the Zn ion in MMP and interrupt the binding of the compounds to the Zn ion. Accordingly, the present molecular simulations revealed that these water molecules around the Zn ion in MMP are causally related to the selective inhibition of these compounds for LpxC rather than MMP.

Proposal of selective inhibitor for bacterial zinc metalloprotease: Molecular mechanics and ab initio molecular orbital calculations.

The zinc metalloprotease pseudolysin (PLN) secreted from Pseudomonas aeruginosa degrades extracellular proteins to produce bacterial nutrition, and various types of PLN inhibitors have been developed to suppress the bacterial growth. However, as the structure of the ligand-binding pocket of PLN has large similarities to those of human matrix metalloproteinases (MMPs) and other human zinc metalloprotease, there is a risk that PLN inhibitors also inhibit human zinc proteases. In this study, we propose a novel agent that may bind stronger to PLN than to MMPs. The compound is proposed based on the specific molecular interactions between existing agents and PLN/MMP metalloproteases evaluated by the present molecular simulations. First, we confirmed that the binding energies of PLN agents evaluated using the ab initio fragment molecular orbital method were comparable to the IC50 values obtained through previous experiments. In addition, the specific molecular interactions between these agents and MMP-9 were investigated to elucidate the fact that some of the agents bind weaker to MMP than PLN. Based on the results, we proposed a novel agent having a succinimide group introduce by a hydroxamic acid group and investigated its binding properties with PLN and MMP. The results may provide useful information for the development of potent inhibitors for PLN with few potential side effects in human bodies.

Specific interactions between the alkaline protease of P. aeruginosa and its natural peptide inhibitor: ab initio molecular simulations.

Alkaline protease aeruginolysin (APR) is an important virulence factor in the evasion of the immune system by Pseudomonas aeruginosa (P. aeruginosa). The P. aeruginosa genome also encodes the highly potent and specific APR peptide inhibitor (APRin). However, the structural reason for the significant inhibition has not been revealed. Using ab initio molecular simulations, we here investigated the specific interactions between APR and APRin to elucidate which amino acid residues of APRin and APR contribute strongest to the inhibition. Since APR has a Zn2+ ion at the ligand-binding site and histidine and glutamic acid residues are coordinated with Zn2+, it is essential to precisely describe these coordination bonds to elucidate the specific interactions between APR and APRin. Therefore, we employed the ab initio fragment molecular orbital method to investigate the specific interactions at an electronic level. The results revealed that Ser1 and Ser2 at the N-terminus of APRin significantly contribute to the binding between APRin and APR. In particular, Ser1 binds strongly to Zn2+ as well as to the sidechains of His176(Hid), His180(Hid), and His186(Hid) in APR. This is the main reason for the strong interaction between APR and APRin. The results also elucidated significant contributions of the positively charged Arg83 and Arg90 residues of APRin to the binding with APR. These findings may provide information useful for the design of novel small agents as potent APR inhibitors.

Evaluation of ultrasonic fibrosis diagnostic system using convolutional network for ordinal regression.

PURPOSE: Diagnosis of liver fibrosis is important for establishing treatment and assessing the risk of carcinogenesis. Ultrasound imaging is an excellent diagnostic method as a screening test in terms of non-invasiveness and simplicity. The purpose of this study was to automatically diagnose liver fibrosis using ultrasound images to reduce the burden on physicians. METHODS: We proposed and implemented a system for extracting regions of liver parenchyma utilizing U-Net. Using regions of interest, the stage of fibrosis was classified as F0, F1, F2, F3, or F4 utilizing CORALNet, an ordinal regression model based on ResNet18. The effectiveness of the proposed system was verified. RESULTS: The system implemented using U-Net had a maximum mean Dice coefficient of 0.929. The results of classification of liver fibrosis utilizing CORALNet had a mean absolute error (MAE) of 1.22 and root mean square error (RMSE) of 1.60. The per-case results had a MAE of 1.55 and RMSE of 1.34. CONCLUSION: U-Net extracted regions of liver parenchyma from the images with high accuracy, and CORALNet showed effectiveness using ordinal information to classify fibrosis in the images. As a future task, we will study a model that is less dependent on teaching data.

Prognostic significance of Ki67 during neoadjuvant chemotherapy in primary unresectable ovarian cancer.

AIM: The purpose of this study was to investigate whether the Ki67 values were associated with survival for predicting prognosis in patients with advanced ovarian cancer receiving neoadjuvant chemotherapy (NACT). METHODS: Among 17 patients treated with NACT, 13 patients were available for tissue samples from matched pre- and post-therapy tissues. Ki67 scores were transformed to a logarithmic scale for the statistical analyses. The optimal cutoff values of the log-phase Ki67 were assessed by receiver operating characteristic (ROC) analysis. Kaplan-Meier analysis, the log-rank test, and Cox regression analysis were carried out to analyze survival. RESULTS: The Ki67-decrease and post-NACT Ki67 were the independent factors associated with relapse-free survival (RFS) (p < 0.001 and p = 0.003). No association was observed on overall survival. The optimal cutoff values for the Ki67-decrease and the post-NACT Ki67 were 6.67% and 5.46 based on ROC where the area under ROC curves (AUC) were 1.00 (p < 0.001) with the 100% sensitivity and specificity. The median RFS was 537 days in patients showing Ki67-decrease >6.66% or post-NACT Ki67 level <5.46, while it was 224 days in those with Ki67 decrease ≤6.66% or post-NACT Ki67 level ≥5.46 (p = 0.001). CONCLUSIONS: The Ki67-decrease and the lower post-NACT Ki67 are independent factors associated with favorable RFS, indicating that they could be precise biomarker candidates for prognosis in NACT-administered patients with advanced ovarian cancer.

Proposal of novel natural inhibitors of severe acute respiratory syndrome coronavirus 2 main protease: Molecular docking and ab initio fragment molecular orbital calculations.

This paper proposes natural drug candidate compounds for the treatment of coronavirus disease 2019 (COVID-19). We investigated the binding properties between the compounds in the Moringa oleifera plant and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 using molecular docking and ab initio fragment molecular orbital calculations. Among the 12 compounds, niaziminin was found to bind the strongest to Mpro. We furthermore proposed novel compounds based on niaziminin and investigated their binding properties to Mpro. The results reveal that the introduction of a hydroxyl group into niaziminin enhances its binding affinity to Mpro. These niaziminin derivatives can be promising candidate drugs for the treatment of COVID-19.

Proposal of novel potent inhibitors against androgen receptor based on ab initio molecular orbital calculations.

The androgen receptor (AR), a family of nuclear receptor proteins, stimulates the transcription of androgen-responsive genes. As its abnormal activation can cause the progression of prostate cancer, numerous types of ligands for AR have been developed as promising antagonists for the treatment of prostate cancer. We previously investigated the specific interactions between AR and nine types of existing non-steroidal ligands, using molecular simulations based on molecular mechanics and ab initio fragment molecular orbital methods. The results were confirmed to be comparable to the binding affinities of these ligands observed in experiments. We here propose novel ligands as potent inhibitors against AR and investigate their binding properties to AR, using the same molecular simulations. The results indicate that the most promising ligand binds stronger to AR than the existing non-steroidal ligands, and that our proposed ligand binds strongly to a mutant-type AR, which has drug resistance to the existing non-steroidal ligands.

Proposal of novel inhibitors for vitamin-D receptor: Molecular docking, molecular mechanics and ab initio molecular orbital simulations.

The specific binding of active vitamin-D to the vitamin-D receptor (VDR) is closely related to the onset of immunological diseases. To inhibit the binding, various compounds have been developed as potent inhibitors against VDR. Among them, a compound NS-54c, which was developed based on the first VDR antagonist TEI-9647 (25-dehydro-1α-hydroxyvitamin D3-26,23-lactone), was revealed to posse almost 1000-fold improved antagonistic activity over the original TEI-9647. However, the reason for this significant improvement has not been elucidated. In the present study, we investigated the specific interactions between VDR and these inhibitors, using molecular simulations based on molecular docking, molecular mechanics and ab initio fragment molecular orbital calculations. Based on the results simulated, we furthermore proposed novel inhibitors and investigated their binding properties to VDR. The results elucidate that the replacement of propyl group at the 24th site of NS-54c by a phenethyl group can enhance the binding affinity of the inhibitor to VDR. This finding provides useful information for developing novel potent inhibitors against VDR.

Analysis of risk factors for patients with early-stage cervical cancer: A study of 374 patients.

AIM: This study aimed to identify the postoperative histological features affecting the prognosis of patients with early-stage cervical cancer who underwent open radical hysterectomy. METHODS: This retrospective study enrolled 374 patients with pT1a, 1b1 and 2a1 early-stage cervical cancer who underwent open radical hysterectomy between 2001 and 2018. Survival outcomes were analyzed by Kaplan-Meier method and compared with log-rank test. Using the Cox proportional hazards regression test, we conducted a multivariate analysis for disease-free survival and overall survival. RESULTS: Others histology, including other epithelial tumors and neuroendocrine tumors, had a significantly worse prognosis in both disease-free survival and overall survival than those of squamous cell carcinoma and adenocarcinoma (hazard ratio, 4.37 and 11.76; P = 0.006 and P = 0.002, respectively), along with lymph node metastasis (hazard ratio, 2.99 and 7.03; P = 0.009 and P = 0.001, respectively). CONCLUSION: Others histology including adenosquamous carcinoma had a poor prognosis in early-stage cervical cancer as with high-risk factors.

Proposal of Potent Inhibitors for a Bacterial Cell Division Protein FtsZ: Molecular Simulations Based on Molecular Docking and ab Initio Molecular Orbital Calculations.

The inhibition of a bacterial cell division protein, filamentous temperature-sensitive Z (FtsZ), prevents the reproduction of Mycobacteria. To propose potent inhibitors of FtsZ, the binding properties of FtsZ with various derivatives of Zantrin ZZ3 were investigated at an electronic level, using molecular simulations. We here employed protein-ligand docking, classical molecular mechanics (MM) optimizations, and ab initio fragment molecular orbital (FMO) calculations. Based on the specific interactions between FtsZ and the derivatives, as determined by FMO calculations, we proposed novel ligands, which can strongly bind to FtsZ and inhibit its aggregations. The introduction of a hydroxyl group into ZZ3 was found to enhance its binding affinity to FtsZ.

Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations.

To elucidate structural changes in the retinoic acid receptor-related orphan receptor gamma (RORγt) induced by the binding of an agonist or an inverse agonist, we conducted molecular dynamics (MD) simulations in explicit water. In addition, ab initio fragment molecular orbital calculations were carried out for certain characteristic structures obtained from the MD simulations to reveal important interactions between the amino acid residues of RORγt, and to distinguish the different effects in the binding of an agonist and an inverse agonist on the structure of RORγt. The results elucidate that the hydrogen bond between His479 of helix11 (H11) and Tyr502 of helix12 (H12) is important to keep the H12 conformation in the agonist-bound RORγt. In contrast, in the inverse-agonist-bound RORγt, the side chain of His479 rotates, significantly weakening the interaction between His479 and Tyr502, leading to a conformational change in H12. Therefore, the present molecular simulations clearly indicate that the conformational change in the side chain of His479 in the inverse-agonist-bound RORγt is the main reason for the H12 destabilization induced by the binding of the inverse agonist. Such a conformational change does not occur on the binding of the agonist in RORγt, owing to the strong hydrogen bond between His479 and Tyr502.

Protonation states of central amino acids in a zinc metalloprotease complexed with inhibitor: Molecular mechanics optimizations and ab initio molecular orbital calculations.

The zinc-metalloprotease pseudolysin (PLN) secreted from bacteria degrades extracellular proteins to produce bacterial nutrition. Since PLN has a Zn ion at the inhibitor-binding site, the interactions between Zn and PLN residues as well as inhibitor can be significantly changed depending on the protonation states of PLN residues at the inhibitor-binding site. To determine stable protonation states of these residues, we here considered different protonation states for Glu and His residues located around Zn and investigated the electronic states of the PLN + inhibitor complex, using ab initio molecular simulations. The protonation state of His223 was found to significantly affect the specific interactions between PLN and the inhibitor.

Application of Artificial Intelligence for Preoperative Diagnostic and Prognostic Prediction in Epithelial Ovarian Cancer Based on Blood Biomarkers.

PURPOSE: We aimed to develop an ovarian cancer-specific predictive framework for clinical stage, histotype, residual tumor burden, and prognosis using machine learning methods based on multiple biomarkers. EXPERIMENTAL DESIGN: Overall, 334 patients with epithelial ovarian cancer (EOC) and 101 patients with benign ovarian tumors were randomly assigned to "training" and "test" cohorts. Seven supervised machine learning classifiers, including Gradient Boosting Machine (GBM), Support Vector Machine, Random Forest (RF), Conditional RF (CRF), Naïve Bayes, Neural Network, and Elastic Net, were used to derive diagnostic and prognostic information from 32 parameters commonly available from pretreatment peripheral blood tests and age. RESULTS: Machine learning techniques were superior to conventional regression-based analyses in predicting multiple clinical parameters pertaining to EOC. Ensemble methods combining weak decision trees, such as GBM, RF, and CRF, showed the best performance in EOC prediction. The values for the highest accuracy and area under the ROC curve (AUC) for segregating EOC from benign ovarian tumors with RF were 92.4% and 0.968, respectively. The highest accuracy and AUC for predicting clinical stages with RF were 69.0% and 0.760, respectively. High-grade serous and mucinous histotypes of EOC could be preoperatively predicted with RF. An ordinal RF classifier could distinguish complete resection from others. Unsupervised clustering analysis identified subgroups among early-stage EOC patients with significantly worse survival. CONCLUSIONS: Machine learning systems can provide critical diagnostic and prognostic prediction for patients with EOC before initial intervention, and the use of predictive algorithms may facilitate personalized treatment options through pretreatment stratification of patients.

Stepwise increase of MIB-1 index in frequently relapsed malignant peritoneal mesothelioma.

We identified the stepwise increase of MIB-1 index in a long-surviving malignant peritoneal mesothelioma (MPM) patient with a history of frequent relapse. A 29-year-old Japanese woman showed upper abdominal induration with adnexal tumor. Imaging study with biochemical analyses strongly suggested peritoneal tumor. On primary surgery, all tumors were resected completely without any residual tumor. Histologically, the tumor was diagnosed as MPM, for which she received adjuvant chemotherapy containing platinum agent. Two years later, the tumor relapsed in her pelvic cavity, but was resected completely with hysterectomy and salpingo-oophorectomy. Histologically, the tumor was diagnosed as MPM relapse. She underwent intraperitoneal chemotherapy with cisplatin that achieved progression-free survival of 5 years. However, relapse was detected again in pelvic cavity without any dissemination in upper abdominal cavity. The tumors were completely removed and were revealed to be compatible with MPM. She received gemcitabine and carboplatin chemotherapy. However, 2 years later, the tumor relapsed again in left upper abdominal cavity, for which she wouldn't receive 4th treatment. To investigate the longevity of this patient in association with the histologic findings, the MIB-1 index was examined in the primary and relapse tumors. The rate of MIB-1 index positive cells was calculated by counting 500 cells. MIB-1 indices were 4.2 ± 1.1 (mean ± SE), 11.8 ± 2.3, and 37.3 ± 2.5 in primary, 1st- and 2nd-relapsed tumor, respectively, demonstrating stepwise increase of MIB-1 expression over the surviving time of more than 9 years. Increase in MIB-1 index was not associated with mitotic index but may be indicating drug sensitivity, resulting in >2-year progression-free interval in each relapse.