Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic Biomarkers of Renal Cell Carcinoma for Liquid Biopsy Tests

Renal cell carcinomas (RCC) account for 2–3% of the global cancer burden and are characterized by the highest mortality rate among all genitourinary cancers. However, excluding conventional imagining approaches, there are no reliable diagnostic and prognostic tools available for clinical use at present. Liquid biopsies, such as urine, serum, and plasma, contain a significant amount of tumor-derived nucleic acids, which may serve as non-invasive biomarkers that are particularly useful for early cancer detection, follow-up, and personalization of treatment. Changes in epigenetic phenomena, such as DNA methylation level, expression of microRNAs (miRNAs), and long noncoding RNAs (lncRNAs), are observed early during cancer development and are easily detectable in biofluids when morphological changes are still undetermined by conventional diagnostic tools. Here, we reviewed recent advances made in the development of liquid biopsy-derived DNA methylation-, miRNAs- and lncRNAs-based biomarkers for RCC, with an emphasis on the performance characteristics. In the last two decades, a mass of circulating epigenetic biomarkers of RCC were suggested, however, most of the studies done thus far analyzed biomarkers selected from the literature, used relatively miniature, local, and heterogeneous cohorts, and suffered from a lack of sufficient validations. In summary, for improved translation into the clinical setting, there is considerable demand for the validation of the existing pool of RCC biomarkers and the discovery of novel ones with better performance and clinical utility.
Generation, Characterization, and Application of Inducible Proliferative Adult Human Epicardium-Derived Cells

Rationale: In recent decades, the great potential of human epicardium-derived cells (EPDCs) as an endogenous cell source for cardiac regeneration has been recognized. The limited availability and low proliferation capacity of primary human EPDCs and phenotypic differences between EPDCs obtained from different individuals hampers their reproducible use for experimental studies. Aim: To generate and characterize inducible proliferative adult human EPDCs for use in fundamental and applied research. Methods and results: Inducible proliferation of human EPDCs was achieved by doxycycline-controlled expression of simian virus 40 large T antigen (LT) with a repressor-based lentiviral Tet-On system. In the presence of doxycycline, these inducible EPDCs (iEPDCs) displayed high and long-term proliferation capacity. After doxycycline removal, LT expression ceased and the iEPDCs regained their cuboidal epithelial morphology. Similar to primary EPDCs, iEPDCs underwent an epithelial-to-mesenchymal transition (EMT) after stimulation with transforming growth factor β3. This was confirmed by reverse transcription-quantitative polymerase chain reaction analysis of epithelial and mesenchymal marker gene expression and (immuno) cytochemical staining. Collagen gel-based cell invasion assays demonstrated that mesenchymal iEPDCs, like primary EPDCs, possess increased invasion and migration capacities as compared to their epithelial counterparts. Mesenchymal iEPDCs co-cultured with sympathetic ganglia stimulated neurite outgrowth similarly to primary EPDCs. Conclusion: Using an inducible LT expression system, inducible proliferative adult human EPDCs were generated displaying high proliferative capacity in the presence of doxycycline. These iEPDCs maintain essential epicardial characteristics with respect to morphology, EMT ability, and paracrine signaling following doxycycline removal. This renders iEPDCs a highly useful new in vitro model for studying human epicardial properties.
Drug Repurposing, an Attractive Strategy in Pancreatic Cancer Treatment: Preclinical and Clinical Updates

Simple Summary The purpose of this review is to provide an update on some of the most promising non-oncology drugs that are already approved and that could be useful also in the treatment of pancreatic cancer, one of the deadliest malignancies worldwide. Current chemotherapy options are unsatisfactory in this cancer and there is an urgent need for more effective and less toxic drugs to improve the dismal pancreatic cancer therapy. The use in cancer therapy of drugs approved for other indications (drug repurposing) is an attractive approach that has the potential to overcome several issues associated with de novo drug discovery, such as dose-finding and safety profiles, accelerating their clinical adoption. In this review, we report proposed mechanisms of action and biological targets of drugs that are candidates for repurposing in pancreatic cancer therapy, focusing on targets that appear to be relevant for their anticancer action. Finally, considering that cancer immunotherapy provides remarkable long-term remission in some responsive tumors and that this strategy is mostly ineffective in pancreatic cancer patients, we discuss recent developments regarding the ability of some repurposing drug candidates to activate anti-tumor immune response, which may be particularly relevant for their clinical effectiveness. Abstract Pancreatic cancer (PC) is one of the deadliest malignancies worldwide, since patients rarely display symptoms until an advanced and unresectable stage of the disease. Current chemotherapy options are unsatisfactory and there is an urgent need for more effective and less toxic drugs to improve the dismal PC therapy. Repurposing of non-oncology drugs in PC treatment represents a very promising therapeutic option and different compounds are currently being considered as candidates for repurposing in the treatment of this tumor. In this review, we provide an update on some of the most promising FDA-approved, non-oncology, repurposed drug candidates that show prominent clinical and preclinical data in pancreatic cancer. We also focus on proposed mechanisms of action and known molecular targets that they modulate in PC. Furthermore, we provide an explorative bioinformatic analysis, which suggests that some of the PC repurposed drug candidates have additional, unexplored, oncology-relevant targets. Finally, we discuss recent developments regarding the immunomodulatory role displayed by some of these drugs, which may expand their potential application in synergy with approved anticancer immunomodulatory agents that are mostly ineffective as single agents in PC.
Integrated Metabolomic and Transcriptomic Analysis Reveals the Flavonoid Regulatory Network by Eutrema EsMYB90

Flavonoids are representative secondary metabolites with different metabolic functions in plants. Previous study found that ectopic expression of EsMYB90 from Eutrema salsugineum could strongly increase anthocyanin content in transgenic tobacco via regulating the expression of anthocyanin biosynthesis genes. In the present research, metabolome analysis showed that there existed 130 significantly differential metabolites, of which 23 metabolites enhanced more than 1000 times in EsMYB90 transgenic tobacco leaves relative to the control, and the top 10 of the increased metabolites included caffeic acid, cyanidin O-syringic acid, myricetin and naringin. A total of 50 markedly differential flavonoids including flavones (14), flavonols (13), flavone C-glycosides (9), flavanones (7), catechin derivatives (5), anthocyanins (1) and isoflavone (1) were identified, of which 46 metabolites were at a significantly enhanced level. Integrated analysis of metabolome and transcriptome revealed that ectopic expression of EsMYB90 in transgenic tobacco leaves is highly associated with the prominent up-regulation of 16 flavonoid metabolites and the corresponding 42 flavonoid biosynthesis structure genes in phenylpropanoid/flavonoid pathways. Dual luciferase assay documented that EsMYB90 strongly activated the transcription of NtANS and NtDFR genes via improving their promoter activity in transiently expressed tobacco leaves, suggesting that EsMYB90 functions as a key regulator on anthocyanin and flavonoid biosynthesis. Taken together, the crucial regulatory role of EsMYB90 on enhancing many flavonoid metabolite levels is clearly demonstrated via modulating flavonoid biosynthesis gene expression in the leaves of transgenic tobacco, which extends our understanding of the regulating mechanism of MYB transcription factor in the phenylpropanoid/flavonoid pathways and provides a new clue and tool for further investigation and genetic engineering of flavonoid metabolism in plants.
The Fatty Acid and Protein Profiles of Circulating CD81-Positive Small Extracellular Vesicles Are Associated with Disease Stage in Melanoma Patients

Simple Summary Early detection of cutaneous melanoma is the key to increasing survival and proper therapeutic adjustment, especially in stages II–IV. We investigated whether the fatty acid (FA) and protein compositions of small extracellular vesicles (sEV) expressing CD81, derived from the plasma of stage 0–I, II and III–IV melanoma patients, could reflect disease stage. Results showed a higher content of FA and differences in C18:0/C18:1 ratio, a marker of cell membrane fluidity, that distinguished patients’ CD81sEV from those of healthy donors (HD). By proteomic analysis (identifier PXD024434) we identified significant increases in CD14, PON1, PON3 and APOA5 in stage II CD81sEV compared to HD. In stage III–IV, CD81sEV’ RAP1B expression was decreased. These stage-related signatures may support the potential of sEV to provide information for early diagnosis, prediction of metastatic behavior, treatment and follow-up of melanoma patients. Abstract The early detection of cutaneous melanoma, a potentially lethal cancer with rising incidence, is fundamental to increasing survival and therapeutic adjustment. In stages II–IV especially, additional indications for adjuvant therapy purposes after resection and for treatment of metastatic patients are urgently needed. We investigated whether the fatty acid (FA) and protein compositions of small extracellular vesicles (sEV) derived from the plasma of stage 0–I, II and III–IV melanoma patients (n = 38) could reflect disease stage. The subpopulation of sEV expressing CD81 EV marker (CD81sEV) was captured by an ad hoc immune affinity technique from plasma depleted of large EV. Biological macromolecules were investigated by gas chromatography and mass spectrometry in CD81sEV. A higher content of FA was detectable in patients with respect to healthy donors (HD). Moreover, a higher C18:0/C18:1 ratio, as a marker of cell membrane fluidity, distinguished early (stage 0–I) from late (III–IV) stages’ CD81sEV. Proteomics detected increases in CD14, PON1, PON3 and APOA5 exclusively in stage II CD81sEV, and RAP1B was decreased in stage III–IV CD81sEV, in comparison to HD. Our results suggest that stage dependent alterations in CD81sEV’ FA and protein composition may occur early after disease onset, strengthening the potential of circulating sEV as a source of discriminatory information for early diagnosis, prediction of metastatic behavior and following up of melanoma patients.
Identification of 24-O-β-d-Glycosides and 7-Deoxy-Analogues of Okadaic Acid and Dinophysistoxin-1 and -2 in Extracts from Dinophysis Blooms, Dinophysis and Prorocentrum Cultures, and Shellfish in Europe, North America and Australasia

Two high-mass polar compounds were observed in aqueous side-fractions from the purification of okadaic acid (1) and dinophysistoxin-2 (2) from Dinophysis blooms in Spain and Norway. These were isolated and shown to be 24-O-β-d-glucosides of 1 and 2 (4 and 5, respectively) by nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and enzymatic hydrolysis. These, together with standards of 1, 2, dinophysistoxin-1 (3), and a synthetic specimen of 7-deoxy-1 (7), combined with an understanding of their mass spectrometric fragmentation patterns, were then used to identify 1–5, the 24-O-β-d-glucoside of dinophysistoxin-1 (6), 7, 7-deoxy-2 (8), and 7-deoxy-3 (9) in a range of extracts from Dinophysis blooms, Dinophysis cultures, and contaminated shellfish from Spain, Norway, Ireland, Canada, and New Zealand. A range of Prorocentrum lima cultures was also examined by liquid chromatography–high resolution tandem mass spectrometry (LC–HRMS/MS) and was found to contain 1, 3, 7, and 9. However, although 4–6 were not detected in these cultures, low levels of putative glycosides with the same exact masses as 4 and 6 were present. The potential implications of these findings for the toxicology, metabolism, and biosynthesis of the okadaic acid group of marine biotoxins are briefly discussed.
Muscle Synergy of Lower Limb Motion in Subjects with and without Knee Pathology

Surface electromyography (sEMG) has great potential in investigating the neuromuscular mechanism for knee pathology. However, due to the complex nature of neural control in lower limb motions and the divergences in subjects’ health and habits, it is difficult to directly use the raw sEMG signals to establish a robust sEMG analysis system. To solve this, muscle synergy analysis based on non-negative matrix factorization (NMF) of sEMG is carried out in this manuscript. The similarities of muscle synergy of subjects with and without knee pathology performing three different lower limb motions are calculated. Based on that, we have designed a classification method for motion recognition and knee pathology diagnosis. First, raw sEMG segments are preprocessed and then decomposed to muscle synergy matrices by NMF. Then, a two-stage feature selection method is executed to reduce the dimension of feature sets extracted from aforementioned matrices. Finally, the random forest classifier is adopted to identify motions or diagnose knee pathology. The study was conducted on an open dataset of 11 healthy subjects and 11 patients. Results show that the NMF-based sEMG classifier can achieve good performance in lower limb motion recognition, and is also an attractive solution for clinical application of knee pathology diagnosis.
Development of Nervilia fordii Extract-Loaded Electrospun PVA/PVP Nanocomposite for Antioxidant Packaging

An ethyl acetate extract from of Nervilia fordii (NFE) with considerable suppression activity on lipid peroxidation (LPO) was first obtained with total phenolic and flavonoid contents and anti-LPO activity (IC50) of 86.67 ± 2.5 mg GAE/g sample, 334.56 ± 4.7 mg RE/g extract and 0.307 mg/mL, respectively. In order to improve its stability and expand its application in antioxidant packaging, the nano-encapsulation of NFE within poly(vinyl alcohol) (PVA) and polyvinyl(pyrrolidone) (PVP) bio-composite film was then successfully developed using electrospinning. SEM analysis revealed that the NFE-loaded fibers exhibited similar morphology to the neat PVA/PVP fibers with a bead-free and smooth morphology. The encapsulation efficiency of NFE was higher than 90% and the encapsulated NFE still retained its antioxidant capacity. Fourier transform infrared spectroscopy (FTIR) and X-ray powder diffraction (XRD) analysis confirmed the successful encapsulation of NFE into fibers and their compatibility, and the thermal stability of which was also improved due to the intermolecular interaction demonstrated by thermo gravimetric analysis (TGA). The ability to preserve the fish oil’s oxidation and extend its shelf-life was also demonstrated, suggesting the obtained PVA/PVP/NFE fiber mat has the potential as a promising antioxidant food packaging material.
A Review of Adsorbents for Heavy Metal Decontamination: Growing Approach to Wastewater Treatment

Heavy metal is released from many industries into water. Before the industrial wastewater is discharged, the contamination level should be reduced to meet the recommended level as prescribed by the local laws of a country. They may be poisonous or cancerous in origin. Their presence does not only damage people, but also animals and vegetation because of their mobility, toxicity, and non-biodegradability into aquatic ecosystems. The review comprehensively discusses the progress made by various adsorbents such as natural materials, synthetic, agricultural, biopolymers, and commercial for extraction of the metal ions such as Ni2+, Cu2+, Pb2+, Cd2+, As2+ and Zn2+ along with their adsorption mechanisms. The adsorption isotherm indicates the relation between the amount adsorbed by the adsorbent and the concentration. The Freundlich isotherm explains the effective physical adsorption of the solute particle from the solution on the adsorbent and Langmuir isotherm gives an idea about the effect of various factors on the adsorption process. The adsorption kinetics data provide valuable insights into the reaction pathways, the mechanism of the sorption reaction, and solute uptake. The pseudo-first-order and pseudo-second-order models were applied to describe the sorption kinetics. The presented information can be used for the development of bio-based water treatment strategies.
Combined Effects of Metabolic Abnormalities and Obesity on Cardiovascular Diseases among Korean Postmenopausal Women

Combined effects of metabolic abnormalities, including metabolic syndrome and obesity, should be identified to screen postmenopausal women at risk of developing cardiovascular diseases. The purpose of this study was to identify the combined effects of metabolic abnormalities and obesity on cardiovascular diseases among postmenopausal Korean women (aged 40–83 years). Data of 5959 postmenopausal women from the Korean National Health and Nutrition Examination Survey (2015–2018) were secondarily analyzed. Using complex simple analysis procedures, logistic regression analysis was performed to identify the combined effect of metabolic abnormalities and obesity on cardiovascular diseases among postmenopausal Korean women. In combination, metabolic syndrome (more than three metabolic abnormalities) and obesity (overweight [≥23 kg/m2 and <25 kg/m2 in body mass index] and obese [>25 kg/m2 in body mass index]) increased the likelihood of developing cardiovascular diseases but combining more than one metabolic abnormality and obesity did not. Combining metabolic syndrome and non-obesity (underweight and normal weight) increased the likelihood of the prevalence of cardiovascular diseases but combining more than one metabolic abnormality and non-obesity did not. Increased cardiovascular diseases in postmenopausal women may be more commonly associated with metabolic syndrome having multiple metabolic abnormalities, but not obesity. Thus, instead of simple weight control, early management of metabolic syndrome is recommended to prevent cardiovascular disease among postmenopausal Korean women.
Transcription-Replication Collisions—A Series of Unfortunate Events

Transcription-replication interactions occur when DNA replication encounters genomic regions undergoing transcription. Both replication and transcription are essential for life and use the same DNA template making conflicts unavoidable. R-loops, DNA supercoiling, DNA secondary structure, and chromatin-binding proteins are all potential obstacles for processive replication or transcription and pose an even more potent threat to genome integrity when these processes co-occur. It is critical to maintaining high fidelity and processivity of transcription and replication while navigating through a complex chromatin environment, highlighting the importance of defining cellular pathways regulating transcription-replication interaction formation, evasion, and resolution. Here we discuss how transcription influences replication fork stability, and the safeguards that have evolved to navigate transcription-replication interactions and maintain genome integrity in mammalian cells.
MEM: An Algorithm for the Reliable Detection of Microsatellite Instability (MSI) on a Small NGS Panel in Colorectal Cancer

Simple Summary Microsatellite instability (MSI) assessment has become a major issue in the management of colorectal cancer, with the recent approval of anti-PD1 immunotherapies in MSI-metastatic colorectal cancer. The reference PCR method (MSI-PCR) can be costly, time and tissue-consuming. However, NGS could facilitate the assessment of MSI status while simultaneously screening for targetable oncogenic mutations (KRAS, NRAS, BRAF) for any colorectal cancer, but the algorithms developed to date use a large number of microsatellites that have not been approved by international guidelines and which are generally incompatible with small NGS panels. We present the MEM algorithm, which mimics the interpretation of MSI-PCR data by a human operator to reliably assess MSI status using only five validated microsatellites (BAT-25, BAT-26, NR-21, NR-24 and NR-27). We demonstrated that the MEM algorithm was in perfect agreement with MSI-PCR results, in terms of both MSI status and individual microsatellite status, in a cohort of 146 patients. Abstract Purpose: MEM is an NGS algorithm that uses Expectation-Maximisation to detect the presence of unstable alleles from the NGS sequences of five microsatellites (BAT-25, BAT-26, NR-21, NR-24 and NR-27). The purpose of this study was to compare the MEM algorithm with a reference PCR method (MSI-PCR) and MisMatch Repair protein immunohistochemistry (MMR-IHC). Methods: FFPE colorectal cancer samples from 146 patients were analysed in parallel by MSI-PCR and NGS using the MEM algorithm. MMR-IHC results were available for 133 samples. Serial dilutions of an MSI positive control were performed to estimate the limit of detection. Results: the MEM algorithm was able to detect unstable alleles of each microsatellite with up to a 5% allelic fraction. Of the 146 samples, 28 (19.2%) were MSI in MSI-PCR. MEM algorithm results were in perfect agreement with those of MSI-PCR, at both MSI status and individual microsatellite level (Cohen’s kappa = 1). A high level of agreement was noted between MSI-PCR/MEM algorithm results and MMR-IHC results (Cohen’s kappa = 0.931). Conclusion: the MEM algorithm can determine the MSI status of colorectal cancer samples on a small NGS panel, using only five microsatellites approved by international guidelines, and can be combined with screening for targetable mutations.
Antioxidant and Immunostimulatory Activities of a Submerged Culture of Cordyceps sinensis Using Spent Coffee

Spent coffee grounds (SCG) are inexpensive materials that have been used as a source of antioxidants and polysaccharides with immunostimulatory activity. In this study, we performed a microbial fermentation of SCG using Cordyceps sinensis and investigated the radical scavenging and immunostimulatory activity of fermented SCG. SCG fermentation using C. sinensis was performed at 25 °C for 8 d. The polyphenol content of the fermented SCG increased from 1022.4 to 1562.0 μg/mL. The glucosamine content of the mycelia also continuously increased during fermentation. The main polyphenol compounds of fermented SCG were chlorogenic acid and p-coumaric acid, which were increased by fermentation. Fermented SCG also showed significantly higher content of chlorogenic acid isomers than unfermented SCG. The fermented SCG exhibited significantly higher 2,2-diphenyl-2-picrylhydrazyl hydrate (half maximal inhibitory concentration: IC50, 0.37 mg/mL) and 2,2-azinobis (3-ethylbenzothiazoline-6-sulfonic acid) (IC50, 0.93 mg/mL) radical scavenging activities than those of the control (0.54 mg/mL and 1.20 mg/mL, respectively; p < 0.05). The fermented SCG stimulated macrophages and promoted the production of various immunostimulatory cytokines (IL-12, IL-6, and TNF-α) compared to control; therefore, microbial fermentation of SCG using C. sinensis is an effective means of generating antioxidant and immunostimulatory materials.