bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeting MERTK and AXL in EGFR Mutant Non-Small Cell Lung Cancer
Authors: Yan Dan , Earp H. Shelton , DeRyckere Deborah , Graham Douglas K.
Published: November 2021

MERTK and AXL are members of the TAM family of receptor tyrosine kinases and are abnormally expressed in 69% and 93% of non-small cell lung cancers (NSCLCs), respectively. Expression of MERTK and/or AXL provides a survival advantage for NSCLC cells and correlates with lymph node metastasis, drug resistance, and disease progression in patients with NSCLC. The TAM receptors on host tumor infiltrating cells also play important roles in the immunosuppressive tumor microenvironment. Thus, MERTK and AXL are attractive biologic targets for NSCLC treatment. Here, we will review physiologic and oncologic roles for MERTK and AXL with an emphasis on the potential to target these kinases in NSCLCs with activating EGFR mutations.
Molecular Profiling of Endometrial Cancer: An Exploratory Study in Aotearoa, New Zealand
Authors: Henry Claire E. , Phan Khoi , Orsman Elena J. , Kenwright Diane , Thunders Michelle C. , Filoche Sara K.
Published: November 2021

Background: Aotearoa, New Zealand, has one of the fastest-rising rates of endometrial cancer (EC) worldwide, increasing particularly in younger Māori and Pasifika women. There is a move towards using molecular profiling to direct treatment for each EC subtype. Aim: This study aimed to explore the molecular profiling of primary EC tissue in Aotearoa. Methods: We used the PORTEC guidelines for the molecular subtyping of 90 patients’ samples into four categories: POLE-mutated, p53 abnormal, mismatch repair deficient (MMRd) and no specific molecular profile (NSMP). The CTNNB1 mutation and L1CAM expression were also included in the analysis. POLE and CTNNB1 mutations were analysed using targeted next-generation sequencing (NGS). Novel mutations were assessed using VarSome. MMRd, L1CAM and p53 abnormalities were analysed using immunohistochemistry. Results: In total, 15 samples were MMRd, 9 were p53 abnormal, 8 were POLE-mutated and the rest (56) were NSMP. Eleven samples had exon 3 CTNNB1 mutations and eleven novel POLE mutations were described. Conclusion: Surrogate markers for POLE mutations should be investigated. The validation of POLE variants and CTNNB1 mutations as part of an Aotearoa-based molecular panel is warranted.
(Pro)renin Receptor Is a Novel Independent Prognostic Marker in Invasive Urothelial Carcinoma of the Bladder
Authors: Larrinaga Gorka , Calvete-Candenas Julio , Solano-Iturri Jon Danel , Martín Ana M. , Pueyo Angel , Nunes-Xavier Caroline E. , Pulido Rafael , Dorado Juan F. , López José I. , Angulo Javier C.
Published: November 2021

(Pro)renin receptor (PRR) is being investigated in several malignancies as it activates pathogenic pathways that contribute to cell proliferation, immunosuppressive microenvironments, and acquisition of aggressive neoplastic phenotypes. Its implication in urothelial cancer (UC) has not been evaluated so far. We retrospectively evaluate the prognostic role of PRR expression in a series of patients with invasive UC treated with radical cystectomy and other clinical and histopathological parameters including p53, markers of immune-checkpoint inhibition, and basal and luminal phenotypes evaluated by tissue microarray. Cox regression analyses using stepwise selection evaluated candidate prognostic factors and disease-specific survival. PRR was expressed in 77.3% of the primary tumors and in 70% of positive lymph nodes. PRR expression correlated with age (p = 0.006) and was associated with lower preoperatively hemoglobin levels. No other statistical association was evidenced with clinical and pathological variables (gender, ASA score, Charlson comorbidity index, grade, pT, pN) or immunohistochemical expressions evaluated (CK20, GA-TA3, CK5/6, CD44, PD-L1, PD-1, B7-H3, VISTA, and p53). PRR expression in primary tumors was associated with worse survival (log-rank, p = 0.008). Cox regression revealed that PRR expression (HR 1.85, 95% CI 1.22–2.8), pT (HR 7.02, 95% CI 2.68–18.39), pN (HR 2.3, 95% CI 1.27–4.19), and p53 expression (HR 1.95, 95% CI 1.1–3.45) were independent prognostic factors in this series. In conclusion, we describe PRR protein and its prognostic role in invasive UC for the first time. Likely mechanisms involved are MAPK/ERK activation, Wnt/β-catenin signaling, and v-ATPAse function.
Phenotypic Consequences of SLC25A40-ABCB1 Fusions beyond Drug Resistance in High-Grade Serous Ovarian Cancer
Authors: Pishas Kathleen I. , Cowley Karla J. , Pandey Ahwan , Hoang Therese , Beach Jessica A. , Luu Jennii , Vary Robert , Smith Lorey K. , Shembrey Carolyn E. , Rashoo Nineveh , White Madelynne O. , Simpson Kaylene J. , Bild Andrea , Griffiths Jason I. , Cheasley Dane , Campbell Ian , Bowtell David D. L. , Christie Elizabeth L.
Published: November 2021

Despite high response rates to initial chemotherapy, the majority of women diagnosed with High-Grade Serous Ovarian Cancer (HGSOC) ultimately develop drug resistance within 1–2 years of treatment. We previously identified the most common mechanism of acquired resistance in HGSOC to date, transcriptional fusions involving the ATP-binding cassette (ABC) transporter ABCB1, which has well established roles in multidrug resistance. However, the underlying biology of fusion-positive cells, as well as how clonal interactions between fusion-negative and positive populations influences proliferative fitness and therapeutic response remains unknown. Using a panel of fusion-negative and positive HGSOC single-cell clones, we demonstrate that in addition to mediating drug resistance, ABCB1 fusion-positive cells display impaired proliferative capacity, elevated oxidative metabolism, altered actin cellular morphology and an extracellular matrix/inflammatory enriched transcriptional profile. The co-culture of fusion-negative and positive populations had no effect on cellular proliferation but markedly altered drug sensitivity to doxorubicin, paclitaxel and cisplatin. Finally, high-throughput screening of 2907 FDA-approved compounds revealed 36 agents that induce equal cytotoxicity in both pure and mixed ABCB1 fusion populations. Collectively, our findings have unraveled the underlying biology of ABCB1 fusion-positive cells beyond drug resistance and identified novel therapeutic agents that may significantly improve the prognosis of relapsed HGSOC patients.
Biomarker Expression in Multifocal Vulvar High-Grade Squamous Intraepithelial Lesions
Authors: Thuijs Nikki B. , Schonck Willemijn A. M. , Klaver Linde L. J. , Fons Guus , van Beurden Marc , Steenbergen Renske D. M. , Bleeker Maaike C. G.
Published: November 2021

In patients with high-grade squamous intraepithelial lesion (HSIL) of the vulva, the presence of multiple lesions, called multifocal HSIL, is common. The aim of this exploratory study was to investigate biomarker expression profiles in multifocal HSIL. In total, 27 lesions from 12 patients with high-risk human papillomavirus (HPV)-positive multifocal HSIL were tested for HPV genotype, expression of p16INK4a and Ki-67, and DNA methylation of six genes. HPV16 was found most commonly in 21 (77.8%) HSILs. In two (16.4%) patients, HPV genotype differed between the lesions. All lesions demonstrated diffuse p16INK4a staining, of which three (11.1%) were combined with patchy staining. One patient (8.3%) demonstrated markedly different DNA methylation levels between lesions. Generally, heterogeneity in methylation profiles was observed between different patients, even when other biomarkers showed similar expression. In conclusion, this study is the first to demonstrate heterogeneity of individual lesions in patients with multifocal HSIL. The studied biomarkers have the potential to refine prognostic and predictive diagnostics. Future prospective, longitudinal studies are needed to further explore the potential of a biomarker profile for management of patients with multifocal HSIL.
Dysregulation of Translation Factors EIF2S1, EIF5A and EIF6 in Intestinal-Type Adenocarcinoma (ITAC)
Authors: Schatz Christoph , Sprung Susanne , Schartinger Volker , Codina-Martínez Helena , Lechner Matt , Hermsen Mario , Haybaeck Johannes
Published: November 2021

Intestinal-type adenocarcinoma (ITAC) is a rare cancer of the nasal cavity and paranasal sinuses that occurs sporadically or secondary to exposure to occupational hazards, such as wood dust and leather. Eukaryotic translation initiation factors have been described as promising targets for novel cancer treatments in many cancers, but hardly anything is known about these factors in ITAC. Here we performed in silico analyses, evaluated the protein levels of EIF2S1, EIF5A and EIF6 in tumour samples and non-neoplastic tissue controls obtained from 145 patients, and correlated these results with clinical outcome data, including tumour site, stage, adjuvant radiotherapy and survival. In silico analyses revealed significant upregulation of the translation factors EIF6 (ITGB4BP), EIF5, EIF2S1 and EIF2S2 (p < 0.05) with a higher arithmetic mean expression in ITAC compared to non-neoplastic tissue (NNT). Immunohistochemical analyses using antibodies against EIF2S1 and EIF6 confirmed a significantly different expression at the protein level (p < 0.05). In conclusion, this work identifies the eukaryotic translation initiation factors EIF2S1 and EIF6 to be significantly upregulated in ITAC. As these factors have been described as promising therapeutic targets in other cancers, this work identifies candidate therapeutic targets in this rare but often deadly cancer.
Regulation of Adaptive Tumor Immunity by Non-Coding RNAs
Authors: Papaioannou Eleftheria , González-Molina María del Pilar , Prieto-Muñoz Ana M. , Gámez-Reche Laura , González-Martín Alicia
Published: November 2021

Cancer immunology research has mainly focused on the role of protein-coding genes in regulating immune responses to tumors. However, despite more than 70% of the human genome is transcribed, less than 2% encodes proteins. Many non-coding RNAs (ncRNAs), including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), have been identified as critical regulators of immune cell development and function, suggesting that they might play important roles in orchestrating immune responses against tumors. In this review, we summarize the scientific advances on the role of ncRNAs in regulating adaptive tumor immunity, and discuss their potential therapeutic value in the context of cancer immunotherapy.
The Effect of Intraocular Pressure-Lowering Medication on Metastatic Uveal Melanomas
Authors: Pals Jan , Mensink Hanneke W. , Brosens Erwin , Verdijk Robert M. , Naus Nicole C. , Paridaens Dion A. , Kilic Emine , Ramdas Wishal D.
Published: November 2021

Background: There has been speculation that IOP-lowering medication, which increases aqueous humor outflow, increases the risk of metastatic uveal melanoma (UM). This hypothesis has not been studied previously but is relevant for UM patients who use IOP-lowering medication. The aim of the current study is to assess the association between the use of intraocular pressure (IOP)-lowering medication and the risk of metastatic UM, and mortality. Methods: A retrospective cohort study, in which patients from the Rotterdam Ocular Melanoma Study were included from 1986 onwards. Medical records were evaluated for use of IOP-lowering medication at baseline (i.e., before diagnosis). For each IOP-lowering medication, we divided patients into two groups for comparison (e.g., patients with alpha2-agonist use and patients without alpha2-agonist use). All patients underwent regular ophthalmic examinations and routine screening for metastasis. Survival analyses were initiated to compare groups in each IOP-lowering medication group. In addition, secondary analyses were performed to examine the association between IOP and the development of metastatic UM, and mortality. Results: A total of 707 patients were included of whom 13 patients used prostaglandin or pilocarpine at baseline. For alpha2-agonist, beta-blocker, carbonic anhydrase inhibitor, and oral IOP-lowering medication these were 4, 14, 11, and 12 patients, respectively. The risk of metastatic UM (choroid and ciliary body melanoma) among the prostaglandin/pilocarpine users was significantly higher than controls (HR [95% CI]: 4.840 [1.452–16.133]). Mortality did not differ significantly among the IOP-lowering medications groups, except for the prostaglandin or pilocarpine group (HR [95% CI]: 7.528 [1.836–30.867]). If we combined all IOP-lowering medication that increase aqueous humor outflow, the risk (HR [95% CI]) of metastatic UM and mortality was 6.344 (1.615–24.918) and 9.743 (2.475–38.353), respectively. There was an association between IOP and mortality, but not for the onset of metastatic UM. Conclusion: The use of topical prostaglandin or pilocarpine may increase the risk of metastatic UM and mortality compared to patients without prostaglandin or pilocarpine use. Therefore, use of IOP-lowering medication which increases aqueous humor outflow, should be avoided in patients with (presumed) UM.
Accuracy and Safety of Ultrasound-Guided Core Needle Biopsy of Soft Tissue Tumors in an Outpatient Setting: A Sarcoma Center Analysis of 392 Consecutive Patients
Authors: Weigl Helene , Hohenberger Peter , Marx Alexander , Vassos Nikolaos , Jakob Jens , Galata Christian
Published: November 2021

Background: The aim of this study was to investigate diagnostic accuracy, safety and histologic results of ultrasound guided core needle biopsy (CNB) in patients with soft tissue lesions (STL) at a tertiary referral center. Methods: A retrospective analysis of all consecutive patients undergoing ultrasound guided CNB for STL at our sarcoma outpatient service between January 2015 and August 2020 was performed. Results: A total of 392 patients were identified. Main histologic entities were sarcomas, lipomas and desmoid tumors. Biopsy was performed in an outpatient setting in 87.6% of the cases. Conclusive biopsies were obtained in 88.5% of the cases. In patients who underwent surgical resection after CNB, the concordance of dignity, tumor entity and histopathological grading between biopsy and resection specimen were 97.2%, 92.7% and 92.5% respectively. The risk of inconclusive CNB was highest in intraabdominal or retroperitoneal tumors (19.5%) and lowest in lesions at the lower extremity (4.4%). Major complications after CNB occurred in three cases (0.8%). No case of biopsy tract seeding was observed during the study period. Conclusions: Ultrasound guided CNB for STL at first presentation in a dedicated surgical outpatient setting is a safe procedure and yields a high diagnostic accuracy.
Novel Biomarkers of Gastric Adenocarcinoma: Current Research and Future Perspectives
Authors: Niclauss Nadja , Gütgemann Ines , Dohmen Jonas , Kalff Jörg C. , Lingohr Philipp
Published: November 2021

Overall survival of gastric cancer remains low, as patients are often diagnosed with advanced stage disease. In this review, we give an overview of current research on biomarkers in gastric cancer and their implementation in treatment strategies. The HER2-targeting trastuzumab is the first molecular targeted agent approved for gastric cancer treatment. Other promising biomarkers for targeted therapies that have shown relevance in clinical trials are VEGF and Claudin 18.2. Expression of MET has been shown to be a negative prognostic factor in gastric cancer. Targeting the PD-1/PD-L1 pathway with immune checkpoint inhibitors has proven efficacy in advanced gastric cancer. Recent technology advances allow the detection of circulating tumor cells that may be used as diagnostic and prognostic indicators and for therapy monitoring in gastric cancer patients. Prognostic molecular subtypes of gastric cancer have been identified using genomic data. In addition, transcriptome profiling has allowed a comprehensive characterization of the immune and stromal microenvironment in gastric cancer and development of novel risk scores. These prognostic and predictive markers highlight the rapidly evolving field of research in gastric cancer, promising improved treatment stratification and identification of molecular targets for individualized treatment in gastric cancer.
Pimavanserin: A Novel Autophagy Modulator for Pancreatic Cancer Treatment
Authors: Ramachandran Sharavan , Kaushik Itishree S. , Srivastava Sanjay K.
Published: November 2021

Pancreatic tumors exhibit high basal autophagy compared to that of other cancers. Several studies including those from our laboratory reported that enhanced autophagy leads to apoptosis in cancer cells. In this study, we evaluated the autophagy and apoptosis inducing effects of Pimavanserin tartrate (PVT). Autophagic effects of PVT were determined by Acridine Orange assay and Transmission Electron Microscopy analysis. Clinical significance of ULK1 in normal and pancreatic cancer patients was evaluated by R2 and GEPIA cancer genomic databases. Modulation of proteins in autophagy signaling was assessed by Western blotting and Immunofluorescence. Apoptotic effects of PVT was evaluated by Annexin-V/APC assay. Subcutaneous xenograft pancreatic tumor model was used to evaluate the autophagy-mediated apoptotic effects of PVT in vivo. Autophagy was induced upon PVT treatment in pancreatic ducal adenocarcinoma (PDAC) cells. Pancreatic cancer patients exhibit reduced levels of autophagy initiator gene, ULK1, which correlated with reduced patient survival. Interestingly, PVT induced the expression of autophagy markers ULK1, FIP200, Atg101, Beclin-1, Atg5, LC3A/B, and cleavage of caspase-3, an indicator of apoptosis in several PDAC cells. ULK1 agonist LYN-1604 enhanced the autophagic and apoptotic effects of PVT. On the other hand, autophagy inhibitors chloroquine and bafilomycin blocked the autophagic and apoptotic effects of PVT in PDAC cells. Notably, chloroquine abrogated the growth suppressive effects of PVT by 25% in BxPC3 tumor xenografts in nude mice. Collectively, our results indicate that PVT mediated pancreatic tumor growth suppression was associated with induction of autophagy mediated apoptosis.
miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data
Authors: Glogovitis Ilias , Yahubyan Galina , Würdinger Thomas , Koppers-Lalic Danijela , Baev Vesselin
Published: November 2021

Tools for microRNA (miR) sequencing data analyses are broadly used in biomedical research. However, the complexity of computational approaches still remains a challenge for biologists with scarce experience in data analytics and bioinformatics. Here, we present miRGalaxy, a Galaxy-based framework for comprehensive analysis of miRs and their sequence variants—miR isoforms (isomiRs). Though isomiRs are commonly reported in deep-sequencing experiments, their detailed structure complexity and specific differential expression (DE) remain not fully examined by the majority of the available analysis tools. miRGalaxy encompasses biologist-user-friendly tools and workflows dedicated to the analysis of the isomiR-ome and its complex behavior in various biological samples. miRGalaxy is developed as a modular, accessible, redistributable, shareable, and user-friendly framework for scientists working with small RNA (sRNA)-seq data. Due to its modular workflow, advanced users can customize the steps and tools for their needs. In addition, the framework provides an analysis report where the significant output results are summarized in charts and visualizations. miRGalaxy can be accessed via preconfigured Docker image flavor and a Toolshed installation if the user already has a running Galaxy instance. Over the last decade, studies on the expression of miRs and isomiRs in normal and deregulated tissues have led to the discovery of their potential as diagnostic biomarkers. The detection of miRs in biofluids further expanded the exploration of the miR repertoire as a source of liquid biopsy biomarkers. Here we show the miRGalaxy framework application for in-depth analysis of the sRNA-seq data from two different biofluids, milk and plasma, to identify, annotate, and discover specific differentially expressed miRs and isomiRs.
The Classification of Myeloproliferative Neoplasms: Rationale, Historical Background and Future Perspectives with Focus on Unclassifiable Cases
Authors: Pizzi Marco , Croci Giorgio Alberto , Ruggeri Marco , Tabano Silvia , Dei Tos Angelo Paolo , Sabattini Elena , Gianelli Umberto
Published: November 2021

Myeloproliferative neoplasms (MPNs) are a heterogeneous group of clonal hematopoietic stem cell disorders, characterized by increased proliferation of one or more myeloid lineages in the bone marrow. The classification and diagnostic criteria of MPNs have undergone relevant changes over the years, reflecting the increased awareness on these conditions and a better understanding of their biological and clinical-pathological features. The current World Health Organization (WHO) Classification acknowledges four main sub-groups of MPNs: (i) Chronic Myeloid Leukemia; (ii) classical Philadelphia-negative MPNs (Polycythemia Vera; Essential Thrombocythemia; Primary Myelofibrosis); (iii) non-classical Philadelphia-negative MPNs (Chronic Neutrophilic Leukemia; Chronic Eosinophilic Leukemia); and (iv) MPNs, unclassifiable (MPN-U). The latter are currently defined as MPNs with clinical-pathological findings not fulfilling the diagnostic criteria for any other entity. The MPN-U spectrum traditionally encompasses early phase MPNs, terminal (i.e., advanced fibrotic) MPNs, and cases associated with inflammatory or neoplastic disorders that obscure the clinical-histological picture. Several lines of evidence and clinical practice suggest the existence of additional myeloid neoplasms that may expand the spectrum of MPN-U. To gain insight into such disorders, this review addresses the history of MPN classification, the evolution of their diagnostic criteria and the complex clinical-pathological and biological features of MPN-U.
Cannabidiol Suppresses Angiogenesis and Stemness of Breast Cancer Cells by Downregulation of Hypoxia-Inducible Factors-1α
Authors: Jo Min Jee , Kim Bu Gyeom , Kim Woo Young , Lee Dae-Hee , Yun Hye Kyeong , Jeong Soyeon , Park Seong Hye , Kim Bo Ram , Kim Jung Lim , Kim Dae Yeong , Lee Sun Il , Oh Sang Cheul
Published: November 2021

To assess the effect of Cannabidiol (CBD) on the angiogenesis and stemness of breast cancer cells as well as proliferation. Methods: mRNA level and the amount of protein of vascular endothelial growth factor (VEGF) were determined by qRT-PCR and ELISA. The angiogenic potential of breast cancer cells under hypoxic conditions was identified by the HUVEC tube formation assay. The degradation of HIF-1α by CBD and the Src/von Hippel–Lindau tumor suppressor protein (VHL) interaction were assessed by a co-immunoprecipitation assay and Western blotting. To identify the stemness of mamospheres, they were evaluated by the sphere-forming assay and flow cytometry. Results: CBD can suppress angiogenesis and stem cell-like properties of breast cancer through Src/VHL/HIF-1α signaling. CBD may potentially be utilized in the treatment of refractory or recurrent breast cancer.
The Transcription Factor FEZF1, a Direct Target of EWSR1-FLI1 in Ewing Sarcoma Cells, Regulates the Expression of Neural-Specific Genes
Authors: García-García Laura , Fernández-Tabanera Enrique , Cervera Saint T. , Melero-Fernández de Mera Raquel M. , Josa Santiago , González-González Laura , Rodríguez-Martín Carlos , Grünewald Thomas G. P. , Alonso Javier
Published: November 2021

Ewing sarcoma is a rare pediatric tumor characterized by chromosomal translocations that give rise to aberrant chimeric transcription factors (e.g., EWSR1-FLI1). EWSR1-FLI1 promotes a specific cellular transcriptional program. Therefore, the study of EWSR1-FLI1 target genes is important to identify critical pathways involved in Ewing sarcoma tumorigenesis. In this work, we focused on the transcription factors regulated by EWSR1-FLI1 in Ewing sarcoma. Transcriptomic analysis of the Ewing sarcoma cell line A673 indicated that one of the genes more strongly upregulated by EWSR1-FLI1 was FEZF1 (FEZ family zinc finger protein 1), a transcriptional repressor involved in neural cell identity. The functional characterization of FEZF1 was performed in three Ewing sarcoma cell lines (A673, SK-N-MC, SK-ES-1) through an shRNA-directed silencing approach. FEZF1 knockdown inhibited clonogenicity and cell proliferation. Finally, the analysis of the FEZF1-dependent expression profile in A673 cells showed several neural genes regulated by FEZF1 and concomitantly regulated by EWSR1-FLI1. In summary, FEZF1 is transcriptionally regulated by EWSR1-FLI1 in Ewing sarcoma cells and is involved in the regulation of neural-specific genes, which could explain the neural-like phenotype observed in several Ewing sarcoma tumors and cell lines.
Elucidating the Role of Extracellular Vesicles in Pancreatic Cancer
Authors: Marzan Akbar Lulu , Stewart Sarah Elizabeth
Published: November 2021

Pancreatic cancer is one of the deadliest cancers worldwide, with a 5-year survival rate of less than 10%. This dismal survival rate can be attributed to several factors including insufficient diagnostics, rapid metastasis and chemoresistance. To identify new treatment options for improved patient outcomes, it is crucial to investigate the underlying mechanisms that contribute to pancreatic cancer progression. Accumulating evidence suggests that extracellular vesicles, including exosomes and microvesicles, are critical players in pancreatic cancer progression and chemoresistance. In addition, extracellular vesicles also have the potential to serve as promising biomarkers, therapeutic targets and drug delivery tools for the treatment of pancreatic cancer. In this review, we aim to summarise the current knowledge on the role of extracellular vesicles in pancreatic cancer progression, metastasis, immunity, metabolic dysfunction and chemoresistance, and discuss their potential roles as biomarkers for early diagnosis and drug delivery vehicles for treatment of pancreatic cancer.
Machine Learning for Recurrence Prediction of Gynecologic Cancers Using Lynch Syndrome-Related Screening Markers
Authors: Kim Byung Wook , Choi Min Chul , Kim Min Kyu , Lee Jeong-Won , Kim Min Tae , Noh Joseph J. , Park Hyun , Jung Sang Geun , Joo Won Duk , Song Seung Hun , Lee Chan
Published: November 2021

To support the implementation of genome-based precision medicine, we developed machine learning models that predict the recurrence of patients with gynecologic cancer in using immune checkpoint inhibitors (ICI) based on clinical and pathologic characteristics, including Lynch syndrome-related screening markers such as immunohistochemistry (IHC) and microsatellite instability (MSI) tests. To accomplish our goal, we reviewed the patient demographics, clinical data, and pathological results from their medical records. Then we identified seven potential characteristics (four MMR IHC [MLH1, MSH2, MSH6, and PMS2], MSI, Age 60, and tumor size). Following that, predictive models were built based on these variables using six machine learning algorithms: logistic regression (LR), support vector machine (SVM), naive Bayes (NB), random forest (RF), gradient boosting (GB), and extreme gradient boosting (EGB) (XGBoost). The experimental results showed that the RF-based model performed best at predicting gynecologic cancer recurrence, with AUCs of 0.818 and 0.826 for the 5-fold cross-validation (CV) and 5-fold CV with 10 repetitions, respectively. This study provides novel and baseline results about predicting the recurrence of gynecologic cancer in patients using ICI by using machine learning methods based on Lynch syndrome-related screening markers.
Highly Sensitive and Selective Copper (II)-Catalyzed Dual-DNAzyme Colorimetric Biosensor Based on Exonuclease III-Mediated Cyclical Assembly
Authors: Zhai Baiqiang , Huang Kunlun , Wang Hongtao , Su Dongmin , Xu Yuancong
Published: November 2021

“Cu-DNAzyme” and “G4-DNAzyme” were used to develop a “turn-off” dual-DNAzyme colorimetric biosensor, which could be used to detect Cu2+ by employing exonuclease III-mediated cyclical assembly (EMCA). EMCA was based on the cleavage activity of Cu2+ to transfer the linkage sequences of the substrate strand and enzyme strand into the transition sequence. The horseradish peroxidase (HRP)-mimicking activity of the G4-DNAzyme was lost after binding with the complementary transition sequence and was hydrolyzed by Exo III. These results demonstrate that the proposed colorimetric biosensor was an effective method for ultradetection of trace metals in a high original signal background. Due to the high sensitivity of the biosensor, the limit of detection (LOD) of Cu2+ is 0.16 nM. This design offers a general purpose platform that could be applied for the detection of any metal ion target through adjustment of metal-dependent DNA-cleaving DNAzymes, which is of great significance for the rapid determination of food safety.
Modified Carbon Nanotubes: Surface Properties and Activity in Oxygen Reduction Reaction
Authors: Bogdanovskaya Vera , Vernigor Inna , Radina Marina , Sobolev Vladimir , Andreev Vladimir , Nikolskaya Nadezhda
Published: November 2021

In order to develop highly efficient and stable catalysts for oxygen reduction reaction (ORR) that do not contain precious metals, it is necessary to modify carbon nanotubes (CNT) and define the effect of the modification on their activity in the ORR. In this work, the modification of CNTs included functionalization by treatment in NaOH or HNO3 (soft and hard conditions, respectively) and subsequent doping with nitrogen (melamine was used as a precursor). The main parameters that determine the efficiency of modified CNT in ORR are composition and surface area (XPS, BET), hydrophilic–hydrophobic surface properties (method of standard contact porosimetry (MSP)) and zeta potential (dynamic light scattering method). The activity of CNT in ORR was assessed following half-wave potential, current density within kinetic potential range and the electrochemically active surface area (SEAS). The obtained results show that the modification of CNT with oxygen-containing groups leads to an increase in hydrophilicity and, consequently, SEAS, as well as the total (overall) current. Subsequent doping with nitrogen ensures further increase in SEAS, higher zeta potential and specific activity in ORR, reflected in the shift of the half-wave potential by 150 mV for CNTNaOH-N and 110 mV for CNTHNO3-N relative to CNTNaOH and CNTHNO3, respectively. Moreover, the introduction of N into the structure of CNTHNO3 increases their corrosion stability.
Hierarchical Mesoporous SSZ-13 Chabazite Zeolites for Carbon Dioxide Capture
Authors: Hillen Lucy , Degirmenci Volkan
Published: November 2021

Artificial carbon dioxide capture is an alternative method to remove the carbon dioxide already accumulated in the atmosphere as well as to stop its release at its large-scale emission points at the source, such as at power plants. However, new adsorbents are needed to make the approach feasible. For this purpose, in this study, hierarchical mesoporous-microporous chabazite-type zeolites were synthesised by applying a dual-templating method. The microporous zeolite structure-directing agent N,N,N-trimethyl-1-adamantanammonium hydroxide was combined with an organosilane mesopore-generating template, 3-(trimethoxysilyl)propyl octadecyl dimethyl ammonium chloride. Materials were characterised for their structural and textural properties and tested for their carbon dioxide capture capacity both in their original sodium form and in their proton-exchanged form by means of breakthrough curve analysis and sorption isotherms. The influence of template ratios on their structure, carbon dioxide capture, and capacity have been identified. All mesoporous materials showed fast adsorption-desorption kinetics due to a reduction in the steric limitations via the introduction of a meso range network of pores. The hierarchical zeolites are recyclable with a negligible loss in crystallinity and carbon dioxide capture capacity, which makes them potential materials for larger-scale application.
Trans Influence of Boryl Ligands in CO2 Hydrogenation on Ruthenium Complexes: Theoretical Prediction of Highly Active Catalysts for CO2 Reduction
Authors: Liu Tian , Liu Zhangyong , Tang Lipeng , Li Jun , Yang Zhuhong
Published: November 2021

In this work, we study the trans influence of boryl ligands and other commonly used non-boryl ligands in order to search for a more active catalyst than the ruthenium dihydride complex Ru(PNP)(CO)H2 for the hydrogenation of CO2. The theoretical calculation results show that only the B ligands exhibit a stronger trans influence than the hydride ligand and are along increasing order of trans influence as follows: –H < –BBr2 < –BCl2 ≈ –B(OCH)2 < –Bcat < –B(OCH2)2 ≈ –B(OH)2 < –Bpin < –B(NHCH2)2 < –B(OCH3)2 < –B(CH3)2 < –BH2. The computed activation free energy for the direct hydride addition to CO2 and the NBO analysis of the property of the Ru–H bond indicate that the activity of the hydride can be enhanced by the strong trans influence of the B ligands through the change in the Ru–H bond property. The function of the strong trans influence of B ligands is to decrease the d orbital component of Ru in the Ru–H bond. The design of a more active catalyst than the Ru(PNP)(CO)H2 complex is possible.
Simplified Method to Optimize Enzymatic Esters Syntheses in Solvent-Free Systems: Validation Using Literature and Experimental Data
Authors: Sousa Ronaldo Rodrigues de , Silva Ayla Sant’Ana da , Fernandez-Lafuente Roberto , Ferreira-Leitão Viridiana Santana
Published: November 2021

The adoption of biocatalysis in solvent-free systems is an alternative to establish a greener esters production. An interesting correlation between the acid:alcohol molar ratio and biocatalyst (immobilized lipase) loading in the optimization of ester syntheses in solvent-free systems had been observed and explored. A simple mathematical tool named Substrate-Enzyme Relation (SER) has been developed, indicating a range of reaction conditions that resulted in high conversions. Here, SER utility has been validated using data from the literature and experimental assays, totalizing 39 different examples of solvent-free enzymatic esterifications. We found a good correlation between the SER trends and reaction conditions that promoted high conversions on the syntheses of short, mid, or long-chain esters. Moreover, the predictions obtained with SER are coherent with thermodynamic and kinetics aspects of enzymatic esterification in solvent-free systems. SER is an easy-to-handle tool to predict the reaction behavior, allowing obtaining optimum reaction conditions with a reduced number of experiments, including the adoption of reduced biocatalysts loadings.
Impact of Design on the Activity of ZrO2 Catalysts in Cellulose Hydrolysis-Dehydration to Glucose and 5-Hydroxymethylfurfural
Authors: Medvedeva Tatiana B. , Ogorodnikova Olga L. , Yakovleva Irina S. , Isupova Lyubov A. , Taran Oxana P. , Gromov Nikolay V. , Parmon Valentin N.
Published: November 2021

The one-pot hydrolysis-dehydration of activated microcrystalline cellulose was studied in pure hydrothermal water at 453 K over ZrO2 catalysts produced by thermodegradation, microwave treatment, mechanical activation, and sol–gel methods and spent without any co-catalyst. ZrO2 prepared by microwave treatment was more active compared to ones derived by other methods. The catalyst calcination temperature also impacted reactivity. The cellulose conversion increased simultaneously with acidity and SBET, which in turn were set by the preparation method and calcination temperature. Phase composition did not affect the activity. Yields of glucose and 5-HMF reaching 18 and 15%, respectively, were over the most promising ZrO2 prepared by microwave treatment at 593 K. To our knowledge, this ZrO2 sample provided the highest activity in terms of TOF values (15.1 mmol g−1 h−1) compared to the pure ZrO2 systems reported elsewhere. High stability of ZrO2 derived by microwave irradiation was shown in five reaction runs.
Study on the Mechanism of SO2 Poisoning of MnOx/PG for Lower Temperature SCR by Simple Washing Regeneration
Authors: Zhang Xianlong , Liu Shiwen , Ma Kang , Chen Yazhong , Jin Shi , Wang Xinyu , Wu Xueping
Published: November 2021

Manganese oxide-supported palygorskite (MnOx/PG) catalysts are considered highly efficient for low-temperature SCR of NOx. However, the MnOx/PG catalyst tends to be poisoned by SO2. The effect of SO2 on activity of the SO2-pretreated poisoning catalysts under ammonia-free conditions was explored. It was determined that the MnOx/PG catalyst tends to be considerably deactivated by SO2 in the absence of ammonia and that water-washed regeneration can completely recover activity of the deactivated catalyst. Based on these results and characterizations of the catalysts, a reasonable mechanism for the deactivation of MnOx/PG catalyst by SO2 was proposed in this study. SO2 easily oxidized to SO3 on the surface of the catalyst, leading to the formation of polysulfuric acid, wrapping of the active component and blocking the micropores. The deactivation of the MnOx/PG catalyst is initially caused by the formation of polysulfuric rather than the deposition of ammonia sulfate, which occurs later.
Sesquiterpene Cyclases from the Basidiomycete Cerrena unicolor
Authors: Püth Nils , Ersoy Franziska , Krings Ulrich , Berger Ralf G.
Published: November 2021

Hundreds of terpenoids have been isolated from Basidiomycota, among them are volatile mono- and sesquiterpenes with amazing sensory qualities, representing a promising alternative to essential oils from endangered plant species. Sesquiterpene synthases (STS) appear to be an abundant class of enzymes in these fungi. The basidiomycete Cerrena unicolor, a known sesquiterpene producer, was in silico screened for sesquiterpene cyclases via homology Basic Local Alignment Search Tool searches. Cyclase genes identified were cloned and heterologously expressed in Escherichia coli Bl21 using pCOLD I as the expression vector. Ten cyclases were successfully produced and purified, and their identity was confirmed using amino acid sequencing of tryptic peptides by nano-liquid chromatography-high resolution-electrospray ionization-tandem mass spectrometry. Gas chromatography/mass spectrometry analysis was applied to characterize these cyclases according to the formation of sesquiterpene hydrocarbons and oxidized terpenoids. Bioinformatic characterization and phylogenetic determination allowed for the classification of these diverse fungal enzymes. A representative single and a multi-product STS, respectively, were further analyzed for their dependency from divalent metal cations as a cofactor for the catalytic activity.
Direct Interaction of ATP7B and LC3B Proteins Suggests a Cooperative Role of Copper Transportation and Autophagy
Authors: Pantoom Supansa , Pomorski Adam , Huth Katharina , Hund Christina , Petters Janine , Krężel Artur , Hermann Andreas , Lukas Jan
Published: November 2021

Macroautophagy/autophagy plays an important role in cellular copper clearance. The means by which the copper metabolism and autophagy pathways interact mechanistically is vastly unexplored. Dysfunctional ATP7B, a copper-transporting ATPase, is involved in the development of monogenic Wilson disease, a disorder characterized by disturbed copper transport. Using in silico prediction, we found that ATP7B contains a number of potential binding sites for LC3, a central protein in the autophagy pathway, the so-called LC3 interaction regions (LIRs). The conserved LIR3, located at the C-terminal end of ATP7B, was found to directly interact with LC3B in vitro. Replacing the two conserved hydrophobic residues W1452 and L1455 of LIR3 significantly reduced interaction. Furthermore, autophagy was induced in normal human hepatocellular carcinoma cells (HepG2) leading to enhanced colocalization of ATP7B and LC3B on the autophagosome membranes. By contrast, HepG2 cells deficient of ATP7B (HepG2 ATP7B−/−) showed autophagy deficiency at elevated copper condition. This phenotype was complemented by heterologous ATP7B expression. These findings suggest a cooperative role of ATP7B and LC3B in autophagy-mediated copper clearance.
Controlled Growth Factor Delivery and Cyclic Stretch Induces a Smooth Muscle Cell-like Phenotype in Adipose-Derived Stem Cells
Authors: Walters Brandan , Turner Paul A. , Rolauffs Bernd , Hart Melanie L. , Stegemann Jan P.
Published: November 2021

Adipose-derived stem cells (ASCs) are an abundant and easily accessible multipotent stem cell source with potential application in smooth muscle regeneration strategies. In 3D collagen hydrogels, we investigated whether sustained release of growth factors (GF) PDGF-AB and TGF-β1 from GF-loaded microspheres could induce a smooth muscle cell (SMC) phenotype in ASCs, and if the addition of uniaxial cyclic stretch could enhance the differentiation level. This study demonstrated that the combination of cyclic stretch and GF release over time from loaded microspheres potentiated the differentiation of ASCs, as quantified by protein expression of early to late SMC differentiation markers (SMA, TGLN and smooth muscle MHC). The delivery of GFs via microspheres produced large ASCs with a spindle-shaped, elongated SMC-like morphology. Cyclic strain produced the largest, longest, and most spindle-shaped cells regardless of the presence or absence of growth factors or the growth factor delivery method. Protein expression and cell morphology data confirmed that the sustained release of GFs from GF-loaded microspheres can be used to promote the differentiation of ASCs into SMCs and that the addition of uniaxial cyclic stretch significantly enhances the differentiation level, as quantified by intermediate and late SMC markers and a SMC-like elongated cell morphology.
Activation Mechanisms of the VPS34 Complexes
Authors: Ohashi Yohei
Published: November 2021

Phosphatidylinositol-3-phosphate (PtdIns(3)P) is essential for cell survival, and its intracellular synthesis is spatially and temporally regulated. It has major roles in two distinctive cellular pathways, namely, the autophagy and endocytic pathways. PtdIns(3)P is synthesized from phosphatidylinositol (PtdIns) by PIK3C3C/VPS34 in mammals or Vps34 in yeast. Pathway-specific VPS34/Vps34 activity is the consequence of the enzyme being incorporated into two mutually exclusive complexes: complex I for autophagy, composed of VPS34/Vps34–Vps15/Vps15-Beclin 1/Vps30-ATG14L/Atg14 (mammals/yeast), and complex II for endocytic pathways, in which ATG14L/Atg14 is replaced with UVRAG/Vps38 (mammals/yeast). Because of its involvement in autophagy, defects in which are closely associated with human diseases such as cancer and neurodegenerative diseases, developing highly selective drugs that target specific VPS34/Vps34 complexes is an essential goal in the autophagy field. Recent studies on the activation mechanisms of VPS34/Vps34 complexes have revealed that a variety of factors, including conformational changes, lipid physicochemical parameters, upstream regulators, and downstream effectors, greatly influence the activity of these complexes. This review summarizes and highlights each of these influences as well as clarifying key questions remaining in the field and outlining future perspectives.
Diurnal Response of Photosystem I to Fluctuating Light Is Affected by Stomatal Conductance
Authors: Li Ting-Yu , Shi Qi , Sun Hu , Yue Ming , Zhang Shi-Bao , Huang Wei
Published: November 2021

Upon a sudden transition from low to high light, electrons transported from photosystem II (PSII) to PSI should be rapidly consumed by downstream sinks to avoid the over-reduction of PSI. However, the over-reduction of PSI under fluctuating light might be accelerated if primary metabolism is restricted by low stomatal conductance. To test this hypothesis, we measured the effect of diurnal changes in stomatal conductance on photosynthetic regulation under fluctuating light in tomato (Solanum lycopersicum) and common mulberry (Morus alba). Under conditions of high stomatal conductance, we observed PSI over-reduction within the first 10 s after transition from low to high light. Lower stomatal conductance limited the activity of the Calvin–Benson–Bassham cycle and aggravated PSI over-reduction within 10 s after the light transition. We also observed PSI over-reduction after transition from low to high light for 30 s at the low stomatal conductance typical of the late afternoon, indicating that low stomatal conductance extends the period of PSI over-reduction under fluctuating light. Therefore, diurnal changes in stomatal conductance significantly affect the PSI redox state under fluctuating light. Moreover, our analysis revealed an unexpected inhibition of cyclic electron flow by the severe over-reduction of PSI seen at low stomatal conductance. In conclusion, stomatal conductance can have a large effect on thylakoid reactions under fluctuating light.
The TRPA1 Channel Amplifies the Oxidative Stress Signal in Melanoma
Authors: De Logu Francesco , Souza Monteiro de Araujo Daniel , Ugolini Filippo , Iannone Luigi Francesco , Vannucchi Margherita , Portelli Francesca , Landini Lorenzo , Titiz Mustafa , De Giorgi Vincenzo , Geppetti Pierangelo , Massi Daniela , Nassini Romina
Published: November 2021

Macrophages (MΦs) and reactive oxygen species (ROS) are implicated in carcinogenesis. The oxidative stress sensor, transient receptor potential ankyrin 1 (TRPA1), activated by ROS, appears to contribute to lung and breast cancer progression. Although TRPA1 expression has been reported in melanoma cell lines, and oxidative stress has been associated with melanocytic transformation, their role in melanoma remains poorly known. Here, we localized MΦs, the final end-product of oxidative stress, 4-hydroxynonenal (4-HNE), and TRPA1 in tissue samples of human common dermal melanocytic nevi, dysplastic nevi, and thin (pT1) and thick (pT4) cutaneous melanomas. The number (amount) of intratumoral and peritumoral M2 MΦs and 4-HNE staining progressively increased with tumor severity, while TRPA1 expression was similar in all samples. Hydrogen peroxide (H2O2) evoked a TRPA1-dependent calcium response in two distinct melanoma cell lines (SK-MEL-28 and WM266-4). Furthermore, H2O2 induced a TRPA1-dependent H2O2 release that was prevented by the TRPA1 antagonist, A967079, or Trpa1 gene silencing (siRNA). ROS release from infiltrating M2 MΦs may target TRPA1-expressing melanoma cells to amplify the oxidative stress signal that affects tumor cell survival and proliferation.