Gastroenteropancreatic neuroendocrine carcinoma tumor spheroid drug screen reveals vulnerability to tyrosyl-DNA phosphodiesterase 1 inhibitors.

BACKGROUND: Gastroenteropancreatic neuroendocrine carcinomas are rare neoplasms with no effective treatments and poor prognosis. Few reliable preclinical models exist for the study of gastroenteropancreatic neuroendocrine carcinomas, limiting investigation of novel treatments. We used tumor spheroids from our recently established gastroenteropancreatic neuroendocrine carcinoma patient-derived xenograft models to systematically screen for compounds with diverse structures to identify potential new categories of therapeutic agents that can target gastroenteropancreatic neuroendocrine carcinomas. METHODS: Tumor spheroids were derived from our NEC913 and NEC1452 gastroenteropancreatic neuroendocrine carcinoma patient-derived xenograft models. Gastroenteropancreatic neuroendocrine carcinoma spheroids were screened against a library of 885 compounds from the National Cancer Institute Diversity Set VII collection. Cell viability was measured via AlamarBlue assay. After identification of potential therapeutic compounds, synergy screening of a selected group with temozolomide and doxorubicin was performed, and these combinations were further analyzed for γH2AX and phosphorylated-ERK proteins. RESULTS: We identified 16 compounds that inhibit over 75% of gastroenteropancreatic neuroendocrine carcinoma spheroid survival. Seven are inhibitors of tyrosyl-DNA phosphodiesterase 1, a DNA repair enzyme working closely with the topoisomerase I complex. When combined with temozolomide or doxorubicin, the tyrosyl-DNA phosphodiesterase 1 inhibitor cytarabine increased the cytotoxic effects of these drugs on NEC1452 cells which was further evidenced by increasing γH2AX and decreasing phosphorylated-ERK in combination treatment compared to temozolomide alone. CONCLUSION: Both NEC913 and NEC1452 gastroenteropancreatic neuroendocrine carcinoma spheroid lines are useful preclinical models for drug testing. Our library screen revealed these gastroenteropancreatic neuroendocrine carcinoma spheroids are highly sensitive to a novel class of anti-cancer drugs that target nuclear genome stability.

Recent Advances in Biological Applications of Aptamer-Based Fluorescent Biosensors.

Aptamers have been spotlighted as promising bio-recognition elements because they can be tailored to specific target molecules, bind to targets with a high affinity and specificity, and are easy to chemically synthesize and introduce functional groups to. In particular, fluorescent aptasensors are widely used in biological applications to diagnose diseases as well as prevent diseases by detecting cancer cells, viruses, and various biomarkers including nucleic acids and proteins as well as biotoxins and bacteria from food because they have the advantages of a high sensitivity, selectivity, rapidity, a simple detection process, and a low price. We introduce screening methods for isolating aptamers with q high specificity and summarize the sequences and affinities of the aptamers in a table. This review focuses on aptamer-based fluorescence detection sensors for biological applications, from fluorescent probes to mechanisms of action and signal amplification strategies.

Advances and Trends in miRNA Analysis Using DNAzyme-Based Biosensors.

miRNAs are endogenous small, non-coding RNA molecules that function in post-transcriptional regulation of gene expression. Because miRNA plays a pivotal role in maintaining the intracellular environment, and abnormal expression has been found in many cancer diseases, detection of miRNA as a biomarker is important for early diagnosis of disease and study of miRNA function. However, because miRNA is present in extremely low concentrations in cells and many types of miRNAs with similar sequences are mixed, traditional gene detection methods are not suitable for miRNA detection. Therefore, in order to overcome this limitation, a signal amplification process is essential for high sensitivity. In particular, enzyme-free signal amplification systems such as DNAzyme systems have been developed for miRNA analysis with high specificity. DNAzymes have the advantage of being more stable in the physiological environment than enzymes, easy to chemically synthesize, and biocompatible. In this review, we summarize and introduce the methods using DNAzyme-based biosensors, especially with regard to various signal amplification methods for high sensitivity and strategies for improving detection specificity. We also discuss the current challenges and trends of these DNAzyme-based biosensors.

MP-LASSO chart: a multi-level polar chart for visualizing group LASSO analysis of genomic data.

Penalized regression has been widely used in genome-wide association studies for jointanalyses to find genetic associations. Among penalized regression models, the least absolute shrinkage and selection operator (Lasso) method effectively removes some coefficientsfrom the model by shrinking them to zero. To handle group structures, such as genes andpathways, several modified Lasso penalties have been proposed, including group Lasso andsparse group Lasso. Group Lasso ensures sparsity at the level of pre-defined groups, eliminating unimportant groups. Sparse group Lasso performs group selection as in group Lasso,but also performs individual selection as in Lasso. While these sparse methods are useful inhigh-dimensional genetic studies, interpreting the results with many groups and coefficients is not straightforward. Lasso's results are often expressed as trace plots of regressioncoefficients. However, few studies have explored the systematic visualization of group information. In this study, we propose a multi-level polar Lasso (MP-Lasso) chart, which caneffectively represent the results from group Lasso and sparse group Lasso analyses. An Rpackage to draw MP-Lasso charts was developed. Through a real-world genetic data application, we demonstrated that our MP-Lasso chart package effectively visualizes the resultsof Lasso, group Lasso, and sparse group Lasso.

The Impact of the COVID-19 Pandemic on the Unpredictable Dynamics of the Cryptocurrency Market.

The global economy is under great shock again in 2020 due to the COVID-19 pandemic; it has not been long since the global financial crisis in 2008. Therefore, we investigate the evolution of the complexity of the cryptocurrency market and analyze the characteristics from the past bull market in 2017 to the present the COVID-19 pandemic. To confirm the evolutionary complexity of the cryptocurrency market, three general complexity analyses based on nonlinear measures were used: approximate entropy (ApEn), sample entropy (SampEn), and Lempel-Ziv complexity (LZ). We analyzed the market complexity/unpredictability for 43 cryptocurrency prices that have been trading until recently. In addition, three non-parametric tests suitable for non-normal distribution comparison were used to cross-check quantitatively. Finally, using the sliding time window analysis, we observed the change in the complexity of the cryptocurrency market according to events such as the COVID-19 pandemic and vaccination. This study is the first to confirm the complexity/unpredictability of the cryptocurrency market from the bull market to the COVID-19 pandemic outbreak. We find that ApEn, SampEn, and LZ complexity metrics of all markets could not generalize the COVID-19 effect of the complexity due to different patterns. However, market unpredictability is increasing by the ongoing health crisis.

Effectiveness of Plasma-Treated Hydrogen Peroxide Mist Disinfection in Various Hospital Environments.

Hospital environments are associated with a high risk of infection. As plasma-treated hydrogen peroxide mist disinfection has a higher disinfection efficacy, we tested the efficacy of plasma-treated hydrogen peroxide mist disinfection on several surfaces in various hospital environments. Disinfection was performed in 23 rooms across different hospital environments, including hospital wards, outpatient departments (OPDs), and emergency rooms. A total of 459 surfaces were swabbed before/after disinfection. Surfaces were also divided into plastic, metal, wood, leather, ceramic, silicone, and glass for further analyses. Only gram-positive bacteria were statistically analyzed because the number of gram-negative bacteria and mold was insufficient. Most colony-forming units (CFUs) of gram-positive bacteria were observed in OPDs and on leather materials before disinfection. The proportion of surfaces that showed a percentage decrease in CFU values of more than 90% after disinfection were as follows: OPDs (85%), hospital wards (99%), and emergency rooms (100%); plastic (97%), metal (83%), wood (84%), leather (81%), and others (87%). Plasma-treated hydrogen peroxide mist disinfection resulted in a significant decrease in the CFU values of gram-positive bacteria in various environments. Plasma-treated hydrogen peroxide mist disinfection is an effective and efficient method of disinfecting various hospital environments.

Review of machine learning methods in soft robotics.

Soft robots have been extensively researched due to their flexible, deformable, and adaptive characteristics. However, compared to rigid robots, soft robots have issues in modeling, calibration, and control in that the innate characteristics of the soft materials can cause complex behaviors due to non-linearity and hysteresis. To overcome these limitations, recent studies have applied various approaches based on machine learning. This paper presents existing machine learning techniques in the soft robotic fields and categorizes the implementation of machine learning approaches in different soft robotic applications, which include soft sensors, soft actuators, and applications such as soft wearable robots. An analysis of the trends of different machine learning approaches with respect to different types of soft robot applications is presented; in addition to the current limitations in the research field, followed by a summary of the existing machine learning methods for soft robots.

Isoflavone intake on the risk of overall breast cancer and molecular subtypes in women at high risk for hereditary breast cancer.

PURPOSE: We investigated the association between isoflavone (ISF) intake and hereditary breast cancer (BC) risk, particularly by molecular subtype, in East-Asian BRCA1/2 mutation carriers and non-carriers at a high risk of hereditary breast cancer (i.e., family history of BC (FHBC) and early-onset BC [EOBC, age < 40 years]). METHODS: The association between ISF intake and BC risk by molecular subtypes was assessed in 1709 participants (407 BRCA1/2 carriers, 585 FHBC non-carriers, 586 EOBC non-carriers, and 131 unaffected non-carriers) from the Korean Hereditary Breast Cancer Study using hazard ratios (HRs) and 95% confidence intervals (CIs) in weighted Cox regression models. Daily ISF intake was assessed using a validated food frequency questionnaire. We evaluated gene-environment interactions between BRCA1/2 mutation and ISF intake in 1604 BC cases by calculating the case-only odds ratios (CORs) and 95% CIs in logistic regression models. RESULTS: ISF intake was inversely associated with luminal A BC risk in BRCA2 mutation carriers and FHBC non-carriers (HR = 0.14, 95% CI = 0.04-0.50 for high intake [ISF intake ≥ 15.50 mg/day]; HR = 0.27, 95% CI = 0.11-0.69 for high intake, respectively). We observed a reduced risk of triple negative BC (TNBC) in BRCA1 carriers and FHBC non-carriers (HR = 0.09, 95% CI = 0.02-0.40 for high intake; HR = 0.19, 95% CI = 0.05-0.69 for high intake, respectively). In the case-only design, an interaction between BRCA1 mutation carrier status and ISF intake emerged in TNBC patients (COR = 0.39, 95% CI = 0.16-0.95). CONCLUSIONS: This study suggests that ISF intake is inversely associated with BC risk in women at high risk of hereditary BC and that the effect could differ by molecular subtypes.

Evaluation of Finger Force Control Ability in terms of Multi-finger Synergy.

In this study, finger force control abilities are quantified by the concept of multi-finger synergy in conjunction with uncontrolled manifold (UCM) analysis. Two indices, named repeatability and flexibility, representing features of multi-finger synergy were proposed to overcome the limitation of previously introduced indices, such as floor effects and distortion problems. The proposed indices were applied to stroke patients and healthy adults through specifically designed experiments. The experimental results showed a clear difference between stroke patients and healthy adults. Also, interestingly, there was a difference in outcome between two stroke patient subgroups: stroke patients in whom the dominant hand was affected and non-dominant hand was affected groups.

Evaluation of Finger Force Control Ability in Terms of Multi-Finger Synergy.

In this study, finger force control abilities are quantified by the concept of multi-finger synergy in conjunction with uncontrolled manifold (UCM) analysis. Two indices, namely, repeatability and flexibility, representing features of multi-finger synergy were proposed to overcome the limitation of previously introduced indices, such as floor effects and distortion problems. The proposed indices were applied to stroke patients and healthy adults through specifically designed experiments. The experimental results showed a clear difference between stroke patients and healthy adults. Also, interestingly, there was a difference in an outcome between two-stroke patient subgroups: stroke patients in whom the dominant hand was affected and non-dominant hand was affected groups.

Reclassification of BRCA1 and BRCA2 variants of uncertain significance: a multifactorial analysis of multicentre prospective cohort.

BACKGROUND: BRCA1 and BRCA2 (BRCA1/2) variants classified ambiguously as variants of uncertain significance (VUS) are a major challenge for clinical genetic testing in breast cancer; their relevance to the cancer risk is unclear and the association with the response to specific BRCA1/2-targeted agents is uncertain. To minimise the proportion of VUS in BRCA1/2, we performed the multifactorial likelihood analysis and validated this method using an independent cohort of patients with breast cancer. METHODS: We used a data set of 2115 patients with breast cancer from the nationwide multicentre prospective Korean Hereditary Breast Cancer study. In total, 83 BRCA1/2 VUSs (BRCA1, n=26; BRCA2, n=57) were analysed. The multifactorial probability was estimated by combining the prior probability with the overall likelihood ratio derived from co-occurrence of each VUS with pathogenic variants, personal and family history, and tumour characteristics. The classification was compared with the interpretation according to the American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG/AMP) guidelines. An external validation was conducted using independent data set of 810 patients. RESULTS: We were able to redefine 38 VUSs (BRCA1, n=10; BRCA2, n=28). The revised classification was highly correlated with the ACMG/AMP guideline-based interpretation (BRCA1, p for trend=0.015; BRCA2, p=0.001). Our approach reduced the proportion of VUS from 19% (154/810) to 8.9% (72/810) in the retrospective validation data set. CONCLUSION: The classification in this study would minimise the 'uncertainty' in clinical interpretation, and this validated multifactorial model can be used for the reliable annotation of BRCA1/2 VUSs.

A RNA producing DNA hydrogel as a platform for a high performance RNA interference system.

RNA interference (RNAi) is a mechanism in which small interfering RNA (siRNA) silences a target gene. Herein, we describe a DNA hydrogel capable of producing siRNA and interfering with protein expression. This RNAi-exhibiting gel (termed I-gel for interfering gel) consists of a plasmid carrying the gene transcribing siRNA against the target mRNA as part of the gel scaffold. The RNAi efficiency of the I-gel has been confirmed by green fluorescent protein (GFP) expression assay and RNA production quantification. The plasmid stability in the I-gel results in an 8-times higher transcription efficiency than that of the free plasmid. We further applied the I-gel to live cells and confirmed its effect in interfering with the GFP expression. The I-gel shows higher RNAi effect than plasmids in free form or complexed with Lipofectamine. This nanoscale hydrogel, which is able to produce RNA in a cell, provides a platform technology for efficient RNAi system.

DNA hydrogel microspheres and their potential applications for protein delivery and live cell monitoring.

Microfluidic devices have been extensively developed as methods for microscale materials fabrication. It has also been adopted for polymeric microsphere fabrication and in situ drug encapsulation. Here, we employed multi-inlet microfluidic channels for DNA hydrogel microsphere formation and in situ protein encapsulation. The release of encapsulated proteins from DNA hydrogels showed different profiles accordingly with the size of microspheres.

Concurrent celecoxib with 5-fluorouracil/epirubicin/cyclophosphamide followed by docetaxel for stages II - III invasive breast cancer: the OOTR-N001 study.

OBJECTIVES: This prospective study aimed at investigating the efficacy and safety of the concurrent use of celecoxib (CXB) with 5-fluorouracil, epirubicin and cyclophosphamide (FEC), followed by docetaxel (T) in the neoadjuvant setting. PATIENTS AND METHODS: A total of 64 invasive breast cancer patients were recruited in the N001 Phase II, multicenter, open-label, single-arm study to receive four cycles of FEC (500, 100, 500 mg/m(2)) followed by four cycles of T (100 mg/m(2)) with concurrent CXB (200 mg b.i.d.) as neoadjuvant therapy (NAT). The combined chemotherapies were administered on day 1 of each cycle every 3 weeks. Primary endpoints were pathologic complete response (pCR) rate and objective response rate (ORR). Quasi-pCR (QpCR), pCR and near pCR (npCR) were discussed considering their similar survival outcomes. ORR included clinical complete response (cCR) and clinical partial response (cPR). Secondary endpoints included safety, breast conservation rate and disease-free survival. RESULTS: Between February 2006 and January 2010, 57 of 64 evaluable patients with luminal A (n = 35, 61.4%), luminal B (n = 12, 21.1%), HER-2 positive (n = 8, 14%) and triple-negative (n = 2, 3.5%) breast cancer completed NAT and surgery. QpCR rate was observed in 18 (31.6%) patients. Exclusive of triple-negative subtype, pCR (p = 0.761) did not differ compared to other subtypes, while npCR (p = 0.043) exhibited a difference. Patients with HER-2 overexpression had a significantly higher QpCR than those of the disease attribute (10/20 vs 8/37, p = 0.029). After NAT, 43 (75.4%) and 13 (22.8%) patients achieved cCR and cPR, respectively. Patients responding to FEC were more likely to achieve a better ORR after subsequent T (p = 0.004). Over 80% of all patients received breast-conserving therapy (BCT) after receiving NAT, and 11 of 14 (78.6%) patients with T3 tumor at diagnosis became eligible for BCT after NAT. A total of 60 patients completed ≥ 6 cycles of NAT, followed by surgery; at a median follow-up of 50 months, 80% of the patients are disease-free. Neither drug-induced life-threatening toxicity nor cardiotoxicity was observed. CONCLUSIONS: Neoadjuvant use of FEC-T with concurrent CXB is active and safe for treatment of operable invasive breast cancer. The ORR was higher, but QpCR was comparable to other studies. Most patients are still disease-free, and BCT became an option for the females. Further clinical and translational studies on the use of cyclooxygenase-2 inhibitors with neoadjuvant chemotherapy are warranted.