bluuebunny/crossref_metadata_2025 huggingface dataset:
Cheminformatics and Machine Learning Approaches to Assess Aquatic Toxicity Profiles of Fullerene Derivatives
Authors: Fjodorova Natalja , Novič Marjana , Venko Katja , Rasulev Bakhtiyor , Türker Saçan Melek , Tugcu Gulcin , Sağ Erdem Safiye , Toropova Alla P. , Toropov Andrey A.
Published: September 2023

Fullerene derivatives (FDs) are widely used in nanomaterials production, the pharmaceutical industry and biomedicine. In the present study, we focused on the potential toxic effects of FDs on the aquatic environment. First, we analyzed the binding affinity of 169 FDs to 10 human proteins (1D6U, 1E3K, 1GOS, 1GS4, 1H82, 1OG5, 1UOM, 2F9Q, 2J0D, 3ERT) obtained from the Protein Data Bank (PDB) and showing high similarity to proteins from aquatic species. Then, the binding activity of 169 FDs to the enzyme acetylcholinesterase (AChE)—as a known target of toxins in fathead minnows and Daphnia magna, causing the inhibition of AChE—was analyzed. Finally, the structural aquatic toxicity alerts obtained from ToxAlert were used to confirm the possible mechanism of action. Machine learning and cheminformatics tools were used to analyze the data. Counter-propagation artificial neural network (CPANN) models were used to determine key binding properties of FDs to proteins associated with aquatic toxicity. Predicting the binding affinity of unknown FDs using quantitative structure–activity relationship (QSAR) models eliminates the need for complex and time-consuming calculations. The results of the study show which structural features of FDs have the greatest impact on aquatic organisms and help prioritize FDs and make manufacturing decisions.
Effect of Fetal Bovine Serum or Basic Fibroblast Growth Factor on Cell Survival and the Proliferation of Neural Stem Cells: The Influence of Homocysteine Treatment
Authors: Petrović Dražen Juraj , Jagečić Denis , Krasić Jure , Sinčić Nino , Mitrečić Dinko
Published: September 2023

In vitro cell culture is a routinely used method which is also applied for in vitro modeling of various neurological diseases. On the other hand, media used for cell culture are often not strictly standardized between laboratories, which hinders the comparison of the obtained results. Here, we compared the effects of homocysteine (Hcy), a molecule involved in neurodegeneration, on immature cells of the nervous system cultivated in basal medium or media supplemented by either fetal bovine serum or basic fibroblast growth factor. The number of cells in basal media supplemented with basic fibroblast growth factor (bFGF) was 2.5 times higher in comparison to the number of cells in basal media supplemented with fetal bovine serum (FBS). We also found that the neuron-specific β-3-tubulin protein expression dose dependently decreased with increasing Hcy exposure. Interestingly, bFGF exerts a protective effect on β-3-tubulin protein expression at a concentration of 1000 µM Hcy compared to FBS-treated neural stem cells on Day 7. Supplementation with bFGF increased SOX2 protein expression two-fold compared to FBS supplementation. GFAP protein expression increased five-fold on Day 3 in FBS-treated neural stem cells, whereas on Day 7, bFGF increased GFAP expression two-fold compared to FBS-treated neural stem cells. Here, we have clearly shown that the selection of culturing media significantly influences various cellular parameters, which, in turn, can lead to different conclusions in experiments based on in vitro models of pathological conditions.
Promotion Effect of Coexposure to a High-Fat Diet and Nano-Diethylnitrosamine on the Progression of Fatty Liver Malignant Transformation into Liver Cancer
Authors: Yin Xin , Li Yu-Sang , Ye Sha-Zhou , Zhang Ting , Zhang Yi-Wen , Xi Yang , Tang He-Bin
Published: September 2023

Overconsumption of high-fat foods increases the risk of fatty liver disease (FLD) and liver cancer with long pathogenic cycles. It is also known that the intake of the chemical poison nitrosamine and its nanopreparations can promote the development of liver injuries, such as FLD, and hepatic fibrosis, and significantly shorten the formation time of the liver cancer cycle. The present work confirmed that the coexposure of a high-fat diet (HFD) and nano-diethylnitrosamine (nano-DEN) altered the tumor microenvironment and studied the effect of this coexposure on the progression of fatty liver malignant transformation into liver cancer. Gene transcriptomics and immunostaining were used to evaluate the tumor promotion effect of the coexposure in mice. After coexposure treatment, tumor nodules were obviously increased, and inflammation levels were elevated. The liver transcriptomics analysis showed that the expression levels of inflammatory, fatty, and fibrosis-related factors in the coexposed group were increased in comparison with the nano-DEN- and high-fat-alone groups. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that coexposure aggravated the high expression of genes related to the carcinomatous pathway and accelerated the formation of the tumor microenvironment. The immunohistochemical staining results showed that the coexposure significantly increased the abnormal changes in proteins related to inflammation, proliferation, aging, and hypoxia in mouse liver tissues. The coexposure of high fat and nano-DEN aggravated the process of steatosis and carcinogenesis. In conclusion, the habitual consumption of pickled foods containing nitrosamines in a daily HFD significantly increases the risk of liver pathology lesions progressing from FLD to liver cancer.
The Diagnostic, Prognostic, and Therapeutic Potential of Cell-Free DNA with a Special Focus on COVID-19 and Other Viral Infections
Authors: Hovhannisyan Galina , Harutyunyan Tigran , Aroutiounian Rouben , Liehr Thomas
Published: September 2023

Cell-free DNA (cfDNA) in human blood serum, urine, and other body fluids recently became a commonly used diagnostic marker associated with various pathologies. This is because cfDNA enables a much higher sensitivity than standard biochemical parameters. The presence of and/or increased level of cfDNA has been reported for various diseases, including viral infections, including COVID-19. Here, we review cfDNA in general, how it has been identified, where it can derive from, its molecular features, and mechanisms of release and clearance. General suitability of cfDNA for diagnostic questions, possible shortcomings and future directions are discussed, with a special focus on coronavirus infection.
Red Blood Cell Fatty Acid Profiles Are Significantly Altered in South Australian Mild Cognitive Impairment and Alzheimer’s Disease Cases Compared to Matched Controls
Authors: Dhillon Varinderpal S. , Thomas Philip , Lee Sau L. , Deo Permal , Fenech Michael
Published: September 2023

Nutritional imbalances have been associated with a higher risk for cognitive impairment. This study determined the red blood cell (RBC) fatty acid profile of newly diagnosed mild cognitive impairment (MCI) and Alzheimer’s disease (AD) patients compared to age and gender-matched controls. There was a significant increase in palmitic acid (p < 0.00001) for both MCI and AD groups. Saturated fatty acids were significantly elevated in the MCI group, including stearic acid (p = 0.0001), arachidic acid (p = 0.003), behenic acid (p = 0.0002), tricosanoic acid (p = 0.007) and lignoceric acid (p = 0.001). n-6 polyunsaturated fatty acids (PUFAs) were significantly reduced in MCI, including linoleic acid (p = 0.001), γ-linolenic acid (p = 0.03), eicosatrienoic acid (p = 0.009) and arachidonic acid (p < 0.00004). The n-3 PUFAs, α-linolenic acid and docosahexaenoic acid, were both significantly reduced in MCI and AD (p = 0.0005 and p = 0.00003). A positive correlation was evident between the Mini-Mental State Examination score and nervonic acid in MCI (r = 0.54, p = 0.01) and a negative correlation with γ-linolenic acid in AD (r = −0.43, p = 0.05). Differences in fatty acid profiles may prove useful as potential biomarkers reflecting increased risk for dementia.
Identification of Two Flip-Over Genes in Grass Family as Potential Signature of C4 Photosynthesis Evolution
Authors: Wu Chao , Guo Dianjing
Published: September 2023

In flowering plants, C4 photosynthesis is superior to C3 type in carbon fixation efficiency and adaptation to extreme environmental conditions, but the mechanisms behind the assembly of C4 machinery remain elusive. This study attempts to dissect the evolutionary divergence from C3 to C4 photosynthesis in five photosynthetic model plants from the grass family, using a combined comparative transcriptomics and deep learning technology. By examining and comparing gene expression levels in bundle sheath and mesophyll cells of five model plants, we identified 16 differentially expressed signature genes showing cell-specific expression patterns in C3 and C4 plants. Among them, two showed distinctively opposite cell-specific expression patterns in C3 vs. C4 plants (named as FOGs). The in silico physicochemical analysis of the two FOGs illustrated that C3 homologous proteins of LHCA6 had low and stable pI values of ~6, while the pI values of LHCA6 homologs increased drastically in C4 plants Setaria viridis (7), Zea mays (8), and Sorghum bicolor (over 9), suggesting this protein may have different functions in C3 and C4 plants. Interestingly, based on pairwise protein sequence/structure similarities between each homologous FOG protein, one FOG PGRL1A showed local inconsistency between sequence similarity and structure similarity. To find more examples of the evolutionary characteristics of FOG proteins, we investigated the protein sequence/structure similarities of other FOGs (transcription factors) and found that FOG proteins have diversified incompatibility between sequence and structure similarities during grass family evolution. This raised an interesting question as to whether the sequence similarity is related to structure similarity during C4 photosynthesis evolution.
Quantitative Mass Spectrometry Characterizes Client Spectra of Components for Targeting of Membrane Proteins to and Their Insertion into the Membrane of the Human ER
Authors: Jung Martin , Zimmermann Richard
Published: September 2023

To elucidate the redundancy in the components for the targeting of membrane proteins to the endoplasmic reticulum (ER) and/or their insertion into the ER membrane under physiological conditions, we previously analyzed different human cells by label-free quantitative mass spectrometry. The HeLa and HEK293 cells had been depleted of a certain component by siRNA or CRISPR/Cas9 treatment or were deficient patient fibroblasts and compared to the respective control cells by differential protein abundance analysis. In addition to clients of the SRP and Sec61 complex, we identified membrane protein clients of components of the TRC/GET, SND, and PEX3 pathways for ER targeting, and Sec62, Sec63, TRAM1, and TRAP as putative auxiliary components of the Sec61 complex. Here, a comprehensive evaluation of these previously described differential protein abundance analyses, as well as similar analyses on the Sec61-co-operating EMC and the characteristics of the topogenic sequences of the various membrane protein clients, i.e., the client spectra of the components, are reported. As expected, the analysis characterized membrane protein precursors with cleavable amino-terminal signal peptides or amino-terminal transmembrane helices as predominant clients of SRP, as well as the Sec61 complex, while precursors with more central or even carboxy-terminal ones were found to dominate the client spectra of the SND and TRC/GET pathways for membrane targeting. For membrane protein insertion, the auxiliary Sec61 channel components indeed share the client spectra of the Sec61 complex to a large extent. However, we also detected some unexpected differences, particularly related to EMC, TRAP, and TRAM1. The possible mechanistic implications for membrane protein biogenesis at the human ER are discussed and can be expected to eventually advance our understanding of the mechanisms that are involved in the so-called Sec61-channelopathies, resulting from deficient ER protein import.
Genetic Variants Identified by Whole Exome Sequencing in a Large Italian Family with High Plasma Levels of Factor VIII and Von Willebrand Factor
Authors: Spena Silvia , Cairo Andrea , Gianniello Francesca , Pappalardo Emanuela , Mortarino Mimosa , Garagiola Isabella , Martinelli Ida , Peyvandi Flora
Published: September 2023

High plasma levels of factor VIII (FVIII) and von Willebrand factor (VWF) have been indicated as independent risk factors for venous thromboembolism. However, the genetic factors responsible for their increase remain poorly known. In a large Italian family with high FVIII/VWF levels and thrombotic episodes, whole exome sequencing (WES) was performed on 12 family members to identify variants/genes involved in FVIII/VWF increase. Twenty variants spread over a 8300 Kb region on chromosome 5 were identified in 12 genes, including the low frequency rs13158382, located upstream of the MIR143/145 genes, which might affect miR-143/145 transcription or processing. The expression of miR-143/145 and VWF mRNA were evaluated in the peripheral blood mononuclear cells of six family members. Members with the variant (n = 3) showed lower levels of both miRNAs and higher levels of VWF mRNA compared to members without the variant (n = 3). An analysis of genetic and expression data from a larger cohort of individuals from the 1000 Genomes and GEUVADIS project confirmed a statistically significant reduction (p-value = 0.023) in miR-143 in heterozygous (n = 35) compared to homozygous wild-type individuals (n = 386). This family-based study identified a new genetic variant potentially involved in VWF increase by affecting miR-143/145 expression.
A Comparison of the Fifth World Health Organization and the International Consensus Classifications of Mature T-Cell Lymphomas
Authors: Piccaluga Pier Paolo , Khattab Shaimaa S.
Published: September 2023

Peripheral T-cell lymphomas (PTCLs) are a rare subset of non-Hodgkin lymphomas that often carry significant difficulty in diagnosis and classification because of their rarity and biological complexity. Previous editions of the World Health Organization (WHO) classifications of hemopoietic neoplasms in 2001, 2008, and 2017 aimed to standardize hemopoietic neoplasm diagnosis in general. Since then, crucial clinico-pathological, immunophenotypic, and recent molecular discoveries have been made in the field of lymphomas, contributing to refining diagnostic criteria of several diseases, upgrading entities previously defined as provisional, and identifying new entities. In 2022, two different models were proposed to classify hematolymphoid neoplasms: the 5th edition of the WHO classification (WHO-HAEM5) and the International Consensus Classification (ICC). Of note, a common nosography is mandatory to ensure progress in health science and ensure the basis for a real precision medicine. In this article, the authors summarized the main differences with the previous fourth WHO edition and reviewed the main discrepancies between the two newest classifications, as far as PTCLs are concerned.
Special Issue “Latest Review Papers in Molecular Genetics and Genomics 2023”
Authors: Zaravinos Apostolos
Published: September 2023

In the rapidly evolving landscape of molecular genetics and genomics, this Special Issue brings together a collection of insightful review articles that delve into the forefront of scientific exploration [...]
Metabolic Responses of the Microalga Neochloris oleoabundans to Extracellular Self- and Nonself-DNA
Authors: Zárate-López Mónica A. , Quintana-Rodríguez Elizabeth , Orona-Tamayo Domancar , Aguilar-Hernández Víctor , Araujo-León Jesús A. , Brito-Argáez Ligia , Molina-Torres Jorge , Hernández-Flores José Luis , Loyola-Vargas Víctor M. , Lozoya-Pérez Nancy E. , Lozoya-Gloria Edmundo
Published: September 2023

Stressed organisms identify intracellular molecules released from damaged cells due to trauma or pathogen infection as components of the innate immune response. These molecules called DAMPs (Damage-Associated Molecular Patterns) are extracellular ATP, sugars, and extracellular DNA, among others. Animals and plants can recognize their own DNA applied externally (self-exDNA) as a DAMP with a high degree of specificity. However, little is known about the microalgae responses to damage when exposed to DAMPs and specifically to self-exDNAs. Here we compared the response of the oilseed microalgae Neochloris oleoabundans to self-exDNA, with the stress responses elicited by nonself-exDNA, methyl jasmonate (MeJA) and sodium bicarbonate (NaHCO3). We analyzed the peroxidase enzyme activity related to the production of reactive oxygen species (ROS), as well as the production of polyphenols, lipids, triacylglycerols, and phytohormones. After 5 min of addition, self-exDNA induced peroxidase enzyme activity higher than the other elicitors. Polyphenols and lipids were increased by self-exDNA at 48 and 24 h, respectively. Triacylglycerols were increased with all elicitors from addition and up to 48 h, except with nonself-exDNA. Regarding phytohormones, self-exDNA and MeJA increased gibberellic acid, isopentenyladenine, and benzylaminopurine at 24 h. Results show that Neochloris oleoabundans have self-exDNA specific responses.
New Insights in Immunometabolism in Neonatal Monocytes and Macrophages in Health and Disease
Authors: de Jong Renske , Tenbrock Klaus , Ohl Kim
Published: September 2023

It is well established that the neonatal immune system is different from the adult immune system. A major task of the neonatal immune system is to bridge the achievement of tolerance towards harmless antigens and commensal bacteria while providing protection against pathogens. This is highly important because neonates are immunologically challenged directly after birth by a rigorous change from a semi-allogeneic sterile environment into a world rich with microbes. A so called disease tolerogenic state is typical for neonates and is anticipated to prevent immunopathological damage potentially at the cost of uncontrolled pathogen proliferation. As a consequence, neonates are more susceptible than adults to life-threatening infections. At the basis of a well-functioning immune response, both for adults and neonates, innate immune cells such as monocytes and monocyte-derived macrophages play an essential role. A well-responsive monocyte will alter its cellular metabolism to subsequently induce certain immune effector function, a process which is called immunometabolism. Immunometabolism has received extensive attention in the last decade; however, it has not been broadly studied in neonates. This review focuses on carbohydrate metabolism in monocytes and macrophages in neonates. We will exhibit pathways involving glycolysis, the tricarboxylic acid (TCA) cycle and oxidative phosphorylation and their role in shaping neonates’ immune systems to a favorable tolerogenic state. More insight into these pathways will elucidate potential treatments targets in life-threatening conditions including neonatal sepsis or expose potential targets which can be used to induce tolerance in conditions where tolerance is harmfully impaired such as in autoimmune diseases.
Regulatory Roles of Long Non-Coding RNAs Relevant to Antioxidant Enzymes and Immune Responses of Apis cerana Larvae Following Ascosphaera apis Invasion
Authors: Guo Rui , Wang Siyi , Guo Sijia , Fan Xiaoxue , Zang He , Gao Xuze , Jing Xin , Liu Zhitan , Na Zhihao , Zou Peiyuan , Chen Dafu
Published: September 2023

Long non-coding RNAs (lncRNAs) play an essential part in controlling gene expression and a variety of biological processes such as immune defense and stress-response. However, whether and how lncRNAs regulate responses of Apis cerana larvae to Ascosphaera apis invasion has remained unclear until now. Here, the identification and structural analysis of lncRNAs in the guts of A. cerana worker larvae were conducted, and the expression profile of larval lncRNAs during the A. apis infection process was then analyzed, followed by an investigation of the regulatory roles of differentially expressed lncRNAs (DElncRNAs) in the host response. In total, 76 sense lncRNAs, 836 antisense lncRNAs, 184 intron lncRNAs, 362 bidirectional lncRNAs, and 2181 intron lncRNAs were discovered in the larval guts. Additionally, 30 known and 9 novel lncRNAs were potential precursors for 36 and 11 miRNAs, respectively. In the three comparison groups, 386, 351, and 272 DElncRNAs were respectively identified, indicating the change in the overall expression pattern of host lncRNAs following the A. apis invasion. Analysis of cis-acting effect showed that DElncRNAs in the 4-, 5-, and 6-day-old comparison groups putatively regulated 55, 30, and 20 up- and down-stream genes, respectively, which were involved in a series of crucial functional terms and pathways, such as MAPK signaling pathway, and cell process. Analysis showed that 31, 8, and 11 DElncRNAs as potential antisense lncRNAs may interact with 26, 8, and 9 sense-strand mRNAs. Moreover, investigation of the competing endogenous RNA (ceRNA) network indicated that 148, 283, and 257 DElncRNAs were putatively regulated. The expression of target genes by targeting corresponding DEmiRNAs included those associated with antioxidant enzymes and immune responses. These results suggested that DElncRNAs played a potential part in the larval guts responding to the A. apis infection through a cis-acting manner and ceRNA mechanisms. Our findings deepen our understanding of interactions between A. cerana larvae and A. apis and offer a basis for clarifying the DElncRNA-mediated mechanisms underlying the host response to fungal invasion.
The Cytotoxic Effect of Septic Plasma on Healthy RBCs: Is Eryptosis a New Mechanism for Sepsis?
Authors: Marcello Matteo , Virzì Grazia Maria , Marturano Davide , de Cal Massimo , Marchionna Nicola , Sgarabotto Luca , De Rosa Silvia , Ronco Claudio , Zanella Monica
Published: September 2023

Sepsis is a life-threatening multiple-organ dysfunction induced by infection and is one of the leading causes of mortality and critical illness worldwide. The pathogenesis of sepsis involves the alteration of several biochemical pathways such as immune response, coagulation, dysfunction of endothelium and tissue damage through cellular death and/or apoptosis. Recently, in vitro and in vivo studies reported changes in the morphology and in the shape of human red blood cells (RBCs) causing erythrocyte death (eryptosis) during sepsis. Characteristics of eryptosis include cell shrinkage, membrane blebbing, and surface exposure to phosphatidylserine (PS), which attract macrophages. The aim of this study was to evaluate the in vitro induction of eryptosis on healthy RBCs exposed to septic plasma at different time points. Furthermore, we preliminary investigated the in vivo levels of eryptosis in septic patients and its relationship with Endotoxin Activity Assay (EAA), mortality and other biological markers of inflammation and oxidative stress. We enrolled 16 septic patients and 16 healthy subjects (no systemic inflammation in the last 3 months) as a control group. At diagnosis, we measured Interleukin-6 (IL-6) and Myeloperoxidase (MPO). For in vitro study, healthy RBCs were exposed to the plasma of septic patients and CTR for 15 min, 1, 2, 4 and 24 h. Morphological markers of death and eryptosis were evaluated by flow cytometric analyses. The cytotoxic effect of septic plasma on RBCs was studied in vitro at 15 min, 1, 2, 4 and 24 h. Healthy RBCs incubated with plasma from septic patients went through significant morphological changes and eryptosis compared to those exposed to plasma from the control group at all time points (all, p < 0.001). IL-6 and MPO levels were significantly higher in septic patients than in controls (both, p < 0.001). The percentage of AnnexinV-binding RBCs was significantly higher in septic patients with EAA level ≥0.60 (positive EAA: 32.4%, IQR 27.6–36.2) compared to septic patients with EAA level <0.60 (negative EAA: 14.7%, IQR 5.7–30.7) (p = 0.04). Significant correlations were observed between eryptosis and EAA levels (Spearman rho2 = 0.50, p < 0.05), IL-6 (Spearman rho2 = 0.61, p < 0.05) and MPO (Spearman rho2 = 0.70, p < 0.05). In conclusion, we observed a quick and great cytotoxic effect of septic plasma on healthy RBCs and a strong correlation with other biomarkers of severity of sepsis. Based on these results, we confirmed the pathological role of eryptosis in sepsis and we hypothesized its use as a biomarker of sepsis, potentially helping physicians to face important treatment decisions.
Licochalcone A: A Potential Multitarget Drug for Alzheimer’s Disease Treatment
Authors: Olloquequi Jordi , Ettcheto Miren , Cano Amanda , Fortuna Ana , Bicker Joana , Sánchez-Lopez Elena , Paz Cristian , Ureña Jesús , Verdaguer Ester , Auladell Carme , Camins Antoni
Published: September 2023

Licochalcone A (Lico-A) is a flavonoid compound derived from the root of the Glycyrrhiza species, a plant commonly used in traditional Chinese medicine. While the Glycyrrhiza species has shown promise in treating various diseases such as cancer, obesity, and skin diseases due to its active compounds, the investigation of Licochalcone A’s effects on the central nervous system and its potential application in Alzheimer’s disease (AD) treatment have garnered significant interest. Studies have reported the neuroprotective effects of Lico-A, suggesting its potential as a multitarget compound. Lico-A acts as a PTP1B inhibitor, enhancing cognitive activity through the BDNF-TrkB pathway and exhibiting inhibitory effects on microglia activation, which enables mitigation of neuroinflammation. Moreover, Lico-A inhibits c-Jun N-terminal kinase 1, a key enzyme involved in tau phosphorylation, and modulates the brain insulin receptor, which plays a role in cognitive processes. Lico-A also acts as an acetylcholinesterase inhibitor, leading to increased levels of the neurotransmitter acetylcholine (Ach) in the brain. This mechanism enhances cognitive capacity in individuals with AD. Finally, Lico-A has shown the ability to reduce amyloid plaques, a hallmark of AD, and exhibits antioxidant properties by activating the nuclear factor erythroid 2-related factor 2 (Nrf2), a key regulator of antioxidant defense mechanisms. In the present review, we discuss the available findings analyzing the potential of Lico-A as a neuroprotective agent. Continued research on Lico-A holds promise for the development of novel treatments for cognitive disorders and neurodegenerative diseases, including AD. Further investigations into its multitarget action and elucidation of underlying mechanisms will contribute to our understanding of its therapeutic potential.
Identification of SH2 Domain-Containing Protein 3C as a Novel, Putative Interactor of Dipeptidyl Peptidase 3
Authors: Matovina Mihaela , Tomašić Paić Ana , Tomić Sanja , Brkić Hrvoje , Horvat Lucija , Barbarić Lea , Filić Vedrana , Pinterić Marija , Jurić Snježana , Kussayeva Akmaral
Published: September 2023

Dipeptidyl peptidase 3 (DPP3) is a zinc-dependent exopeptidase with broad specificity for four to eight amino acid residue substrates. It has a role in the regulation of oxidative stress response NRF2–KEAP1 pathway through the interaction with KEAP1. We have conducted stable isotope labeling by amino acids in a cell culture coupled to mass spectrometry (SILAC-MS) interactome analysis of TRex HEK293T cells using DPP3 as bait and identified SH2 Domain-Containing Protein 3C (SH2D3C) as prey. SH2D3C is one of three members of a family of proteins that contain both the SH2 domain and a domain similar to guanine nucleotide exchange factor domains of Ras family GTPases (Ras GEF-like domain), named novel SH2-containing proteins (NSP). NSPs, including SH2D3C (NSP3), are adaptor proteins involved in the regulation of adhesion, migration, tissue organization, and immune response. We have shown that SH2D3C binds to DPP3 through its C-terminal Ras GEF-like domain, detected the colocalization of the proteins in living cells, and confirmed direct interaction in the cytosol and membrane ruffles. Computational analysis also confirmed the binding of the C-terminal domain of SH2D3C to DPP3, but the exact model could not be discerned. This is the first indication that DPP3 and SH2D3C are interacting partners, and further studies to elucidate the physiological significance of this interaction are on the way.
Restoring Angiotensin Type 2 Receptor Function Reverses PFOS-Induced Vascular Hyper-Reactivity and Hypertension in Pregnancy
Authors: Dangudubiyyam Sri Vidya , Bosse Bradley , Yadav Pankaj , Song Ruolin , Hofmann Alissa , Mishra Jay S. , Kumar Sathish
Published: September 2023

Perfluorooctane sulfonic acid (PFOS) exposure during pregnancy induces hypertension with decreased vasodilatory angiotensin type-2 receptor (AT2R) expression and impaired vascular reactivity and fetal weights. We hypothesized that AT2R activation restores the AT1R/AT2R balance and reverses gestational hypertension by improving vascular mechanisms. Pregnant Sprague-Dawley rats were exposed to PFOS through drinking water (50 μg/mL) from gestation day (GD) 4–20. Controls received drinking water with no detectable PFOS. Control and PFOS-exposed rats were treated with AT2R agonist Compound 21 (C21; 0.3 mg/kg/day, SC) from GD 15–20. In PFOS dams, blood pressure was higher, blood flow in the uterine artery was reduced, and C21 reversed these to control levels. C21 mitigated the heightened contraction response to Ang II and enhanced endothelium-dependent vasorelaxation in uterine arteries of PFOS dams. The observed vascular effects of C21 were correlated with reduced AT1R levels and increased AT2R and eNOS protein levels. C21 also increased plasma bradykinin production in PFOS dams and attenuated the fetoplacental growth restriction. These data suggest that C21 improves the PFOS-induced maternal vascular dysfunction and blood flow to the fetoplacental unit, providing preclinical evidence to support that AT2R activation may be an important target for preventing or treating PFOS-induced adverse maternal and fetal outcomes.
Differential Sensitivity of Germline and Somatic BRCA Variants to PARP Inhibitor in High-Grade Serous Ovarian Cancer
Authors: Vendrell Julie A. , Ban Iulian O. , Solassol Isabelle , Audran Patricia , Cabello-Aguilar Simon , Topart Delphine , Lindet-Bourgeois Clothilde , Colombo Pierre-Emmanuel , Legouffe Eric , D’Hondt Véronique , Fabbro Michel , Solassol Jérôme
Published: September 2023

Purpose: The introduction of PARP inhibitors (PARPis) as a treatment option for patients with high-grade serous ovarian cancer (HGSOC) modified the approach of BRCA testing worldwide. In this study, we aim to evaluate the impact of BRCA1 and BRCA2 variants on treatment response and survival outcomes in patients diagnosed in our institution. Methods: A total of 805 HGSOC samples underwent BRCA1 and BRCA2 variant detection by using next-generation sequencing (NGS). Among them, a pathogenic alteration was detected in 104 specimens. Clinicopathological features and germline status were recovered, and alteration types were further characterized. The clinical significance of variant type in terms of response to chemotherapy and to PARPis as well as overall survival were evaluated using univariate analysis. Results: In our cohort, 13.2% of the HGSOC samples harbored a pathogenic BRCA1 or BRCA2 variant, among which 58.7% were inherited. No difference was observed between germline and somatic variants in terms of the gene altered. Interestingly, patients with somatic variants only (no germline) demonstrated better outcomes under PARPi treatment compared to those with germline ones. Conclusion: The determination of the inheritance or acquisition of BRCA1 and BRCA2 alterations could provide valuable information for improving management strategies and predicting the outcome of patients with HGSOC.
Modeling Myotonic Dystrophy Type 2 Using Drosophila melanogaster
Authors: Marzullo Marta , Coni Sonia , De Simone Assia , Canettieri Gianluca , Ciapponi Laura
Published: September 2023

Myotonic dystrophy 2 (DM2) is a genetic multi-systemic disease primarily affecting skeletal muscle. It is caused by CCTGn expansion in intron 1 of the CNBP gene, which encodes a zinc finger protein. DM2 disease has been successfully modeled in Drosophila melanogaster, allowing the identification and validation of new pathogenic mechanisms and potential therapeutic strategies. Here, we describe the principal tools used in Drosophila to study and dissect molecular pathways related to muscular dystrophies and summarize the main findings in DM2 pathogenesis based on DM2 Drosophila models. We also illustrate how Drosophila may be successfully used to generate a tractable animal model to identify novel genes able to affect and/or modify the pathogenic pathway and to discover new potential drugs.
Therapeutic Anti-KIR Antibody of 1–7F9 Attenuates the Antitumor Effects of Expanded and Activated Human Primary Natural Killer Cells on In Vitro Glioblastoma-like Cells and Orthotopic Tumors Derived Therefrom
Authors: Maeoka Ryosuke , Nakazawa Tsutomu , Matsuda Ryosuke , Morimoto Takayuki , Shida Yoichi , Yamada Shuichi , Nishimura Fumihiko , Nakamura Mitsutoshi , Nakagawa Ichiro , Park Young-Soo , Tsujimura Takahiro , Nakase Hiroyuki
Published: September 2023

Glioblastoma (GBM) is the leading malignant intracranial tumor, where prognosis for which has remained extremely poor for two decades. Immunotherapy has recently drawn attention as a cancer treatment, including for GBM. Natural killer (NK) cells are immune cells that attack cancer cells directly and produce antitumor immunity-related cytokines. The adoptive transfer of expanded and activated NK cells is expected to be a promising GBM immunotherapy. We previously established an efficient expansion method that produced highly purified, activated primary human NK cells, which we designated genuine induced NK cells (GiNKs). The GiNKs demonstrated antitumor effects in vitro and in vivo, which were less affected by blockade of the inhibitory checkpoint receptor programmed death 1 (PD-1). In the present study, we assessed the antitumor effects of GiNKs, both alone and combined with an antibody targeting killer Ig-like receptor 2DLs (KIR2DL1 and DL2/3, both inhibitory checkpoint receptors of NK cells) in vitro and in vivo with U87MG GBM-like cells and the T98G GBM cell line. Impedance-based real-time cell growth assays and apoptosis detection assays revealed that the GiNKs exhibited growth inhibitory effects on U87MG and T98G cells by inducing apoptosis. KIR2DL1 blockade attenuated the growth inhibition of the cell lines in vitro. The intracranial administration of GiNKs prolonged the overall survival of the U87MG-derived orthotopic xenograft brain tumor model. The KIR2DL1 blockade did not enhance the antitumor effects; rather, it attenuated it in the same manner as in the in vitro experiment. GiNK immunotherapy directly administered to the brain could be a promising immunotherapeutic alternative for patients with GBM. Furthermore, KIR2DL1 blockade appeared to require caution when used concomitantly with GiNKs.
Structural and Thermomagnetic Properties of Gallium Nanoferrites and Their Influence on Cells In Vitro
Authors: Orzechowska Marta , Rećko Katarzyna , Klekotka Urszula , Czerniecka Magdalena , Tylicki Adam , Satuła Dariusz , Soloviov Dmytro V. , Beskrovnyy Anatoly I. , Miaskowski Arkadiusz , Kalska-Szostko Beata
Published: September 2023

Magnetite and gallium substituted cuboferrites with a composition of GaxFe3−xO4 (0 ≤ x ≤ 1.4) were fabricated by thermal decomposition from acetylacetonate salts. The effect of Ga3+ cation substitution on the structural and thermomagnetic behavior of 4–12 nm sized core-shell particles was explored by X-ray and neutron diffraction, small angle neutron scattering, transmission electron microscopy, Mössbauer spectroscopy, and calorimetric measurements. Superparamagnetic (SPM) behavior and thermal capacity against increasing gallium concentration in nanoferrites were revealed. The highest heat capacity typical for Fe3O4@Ga0.6Fe2.4O4 and Ga0.6Fe2.4O4@Fe3O4 is accompanied by a slight stimulation of fibroblast culture growth and inhibition of HeLa cell growth. The observed effect is concentration dependent in the range of 0.01–0.1 mg/mL and particles of Ga0.6Fe2.4O4@Fe3O4 design have a greater effect on cells. Observed magnetic heat properties, as well as interactions with tumor and healthy cells, provide a basis for further biomedical research to use the proposed nanoparticle systems in cancer thermotherapy (magnetic hyperthermia).
Beyond the Umbrella: A Systematic Review of the Interventions for the Prevention of and Reduction in the Incidence and Severity of Ovarian Hyperstimulation Syndrome in Patients Who Undergo In Vitro Fertilization Treatments
Authors: Palomba Stefano , Costanzi Flavia , Nelson Scott M. , Besharat Aris , Caserta Donatella , Humaidan Peter
Published: September 2023

Ovarian hyperstimulation syndrome (OHSS) is the main severe complication of ovarian stimulation for in vitro fertilization (IVF) cycles. The aim of the current study was to identify the interventions for the prevention of and reduction in the incidence and severity of OHSS in patients who undergo IVF not included in systematic reviews with meta-analyses of randomized controlled trials (RCTs) and assess and grade their efficacy and evidence base. The best available evidence for each specific intervention was identified, analyzed in terms of safety/efficacy ratio and risk of bias, and graded using the Oxford Centre for Evidence-Based Medicine (CEBM) hierarchy of evidence. A total of 15 interventions to prevent OHSS were included in the final analysis. In the IVF population not at a high risk for OHSS, follitropin delta for ovarian stimulation may reduce the incidence of early OHSS and/or preventive interventions for early OHSS. In high-risk patients, inositol pretreatment, ovulation triggering with low doses of urinary hCG, and the luteal phase administration of a GnRH antagonist may reduce OHSS risk. In conclusion, even if not supported by systematic reviews with homogeneity of the RCTs, several treatments/strategies to reduce the incidence and severity of OHSS have been shown to be promising.
Base Excision Repair: Mechanisms and Impact in Biology, Disease, and Medicine
Authors: Gohil Dhara , Sarker Altaf H. , Roy Rabindra
Published: September 2023

Base excision repair (BER) corrects forms of oxidative, deamination, alkylation, and abasic single-base damage that appear to have minimal effects on the helix. Since its discovery in 1974, the field has grown in several facets: mechanisms, biology and physiology, understanding deficiencies and human disease, and using BER genes as potential inhibitory targets to develop therapeutics. Within its segregation of short nucleotide (SN-) and long patch (LP-), there are currently six known global mechanisms, with emerging work in transcription- and replication-associated BER. Knockouts (KOs) of BER genes in mouse models showed that single glycosylase knockout had minimal phenotypic impact, but the effects were clearly seen in double knockouts. However, KOs of downstream enzymes showed critical impact on the health and survival of mice. BER gene deficiency contributes to cancer, inflammation, aging, and neurodegenerative disorders. Medicinal targets are being developed for single or combinatorial therapies, but only PARP and APE1 have yet to reach the clinical stage.
Epigallocatechin Gallate Affects the Structure of Chromatosomes, Nucleosomes and Their Complexes with PARP1
Authors: Andreeva Tatiana V. , Maluchenko Natalya V. , Efremenko Anastasiya V. , Lyubitelev Alexander V. , Korovina Anna N. , Afonin Dmitry A. , Kirpichnikov Mikhail P. , Studitsky Vasily M. , Feofanov Alexey V.
Published: September 2023

The natural flavonoid epigallocatechin gallate has a wide range of biological activities, including being capable of binding to nucleic acids; however, the mechanisms of the interactions of epigallocatechin gallate with DNA organized in chromatin have not been systematically studied. In this work, the interactions of epigallocatechin gallate with chromatin in cells and with nucleosomes and chromatosomes in vitro were studied using fluorescent microscopy and single-particle Förster resonance energy transfer approaches, respectively. Epigallocatechin gallate effectively penetrates into the nuclei of living cells and binds to DNA there. The interaction of epigallocatechin gallate with nucleosomes in vitro induces a large-scale, reversible uncoiling of nucleosomal DNA that occurs without the dissociation of DNA or core histones at sub- and low-micromolar concentrations of epigallocatechin gallate. Epigallocatechin gallate does not reduce the catalytic activity of poly(ADP-ribose) polymerase 1, but causes the modulation of the structure of the enzyme–nucleosome complex. Epigallocatechin gallate significantly changes the structure of chromatosomes, but does not cause the dissociation of the linker histone. The reorganization of nucleosomes and chromatosomes through the use of epigallocatechin gallate could facilitate access to protein factors involved in DNA repair, replication and transcription to DNA and, thus, might contribute to the modulation of gene expression through the use of epigallocatechin gallate, which was reported earlier.
Investigating the Heterogeneity of Immune Cells in Triple-Negative Breast Cancer at the Single-Cell Level before and after Paclitaxel Chemotherapy
Authors: Zhao Heng , Lin Zhang , Zhang Yangfan , Liu Jingjing , Chen Qi
Published: September 2023

Despite the numerous treatments for triple-negative breast cancer (TNBC), chemotherapy is still one of the most effective methods. However, the impact of chemotherapy on immune cells is not yet clear. Therefore, this study aims to explore the different roles of immune cells and their relationship with treatment outcomes in the tumor and blood before and after paclitaxel therapy. We analyzed the single-cell sequencing data of immune cells in tumors and blood before and after paclitaxel treatment. We confirmed a high correlation between T cells, innate lymphoid cells (ILCs), and therapeutic efficacy. The differences in T cells were analyzed related to therapeutic outcomes before and after paclitaxel treatment. In the effective treatment group, post-treatment tumor-infiltrating CD8+ T cells were associated with elevated inflammation, cytokines, and Toll-like-receptor-related gene expression, which were expected to enhance anti-tumor capabilities in tumor immune cells. Moreover, we found that the expression of immune-checkpoint-related genes is also correlated with treatment outcomes. In addition, an ILC subgroup, b_ILC1-XCL1, in which the corresponding marker gene XCL1 was highly expressed, was mainly present in the effective treatment group and was also associated with higher patient survival rates. Overall, we found differences in gene expression in T cells across different groups and a correlation between the expression of immune checkpoint genes in T cells, the b_ILC1-XCL1 subgroup, and patient prognosis.
Anti-Tumor Immunogenicity of the Oncolytic Virus CF33-hNIS-antiPDL1 against Ex Vivo Peritoneal Cells from Gastric Cancer Patients
Authors: Zhang Zhifang , Yang Annie , Chaurasiya Shyambabu , Park Anthony K. , Kim Sang-In , Lu Jianming , Valencia Hannah , Fong Yuman , Woo Yanghee
Published: September 2023

We studied the immunotherapeutic potential of CF33-hNIS-antiPDL1 oncolytic virus (OV) against gastric cancer with peritoneal metastasis (GCPM). We collected fresh malignant ascites (MA) or peritoneal washings (PW) during routine paracenteses and diagnostic laparoscopies from GC patients (n = 27). Cells were analyzed for cancer cell markers and T cells, or treated with PBS, CF33-GFP, or CF33-hNIS-antiPDL1 (MOI = 3). We analyzed infectivity, replication, cytotoxicity, CD107α upregulation of CD8+ and CD4+ T cells, CD274 (PD-L1) blockade of cancer cells by virus-encoded anti-PD-L1 scFv, and the release of growth factors and cytokines. We observed higher CD45−/large-size cells and lower CD8+ T cell percentages in MA than PW. CD45−/large-size cells were morphologically malignant and expressed CD274 (PD-L1), CD252 (OX40L), and EGFR. CD4+ and CD8+ T cells did not express cell surface exhaustion markers. Virus infection and replication increased cancer cell death at 15 h and 48 h. CF33-hNIS-antiPDL1 treatment produced functional anti-PD-L1 scFv, which blocked surface PD-L1 binding of live cancer cells and increased CD8+CD107α+ and CD4+CD107α+ T cell percentages while decreasing EGF, PDGF, soluble anti-PD-L1, and IL-10. CF33-OVs infect, replicate in, express functional proteins, and kill ex vivo GCPM cells with immune-activating effects. CF33-hNIS-antiPDL1 displays real potential for intraperitoneal GCPM therapy.
Simplified Synthesis of the Amine-Functionalized Magnesium Ferrite Magnetic Nanoparticles and Their Application in DNA Purification Method
Authors: Ilosvai Ágnes M. , Gerzsenyi Tímea B. , Sikora Emőke , Harasztosi Lajos , Kristály Ferenc , Viskolcz Béla , Váradi Csaba , Szőri-Dorogházi Emma , Vanyorek László
Published: September 2023

For pathogens identification, the PCR test is a widely used method, which requires the isolation of nucleic acids from different samples. This extraction can be based on the principle of magnetic separation. In our work, amine-functionalized magnesium ferrite nanoparticles were synthesized for this application by the coprecipitation of ethanolamine in ethylene glycol from Mg(II) and Fe(II) precursors. The conventional synthesis method involves a reaction time of 12 h (MgFe2O4-H&R MNP); however, in our modified method, the reaction time could be significantly reduced to only 4 min by microwave-assisted synthesis (MgFe2O4-MW MNP). A comparison was made between the amine-functionalized MgFe2O4 samples prepared by two methods in terms of the DNA-binding capacity. The experimental results showed that the two types of amine-functionalized magnesium ferrite magnetic nanoparticles (MNPs) were equally effective in terms of their DNA extraction yield. Moreover, by using a few minutes-long microwave synthesis, we obtained the same quality magnesium ferrite particles as those made through the long and energy-intensive 12-h production method. This advancement has the potential to improve and expedite pathogen identification processes, helping to better prevent the spread of epidemics.
Butyrate Protects against SARS-CoV-2-Induced Tissue Damage in Golden Hamsters
Authors: Yu Huan , Yuan Lunzhi , Yan Zhigang , Zhou Ming , Ye Jianghui , Wu Kun , Chen Wenjia , Chen Rirong , Xia Ningshao , Guan Yi , Zhu Huachen
Published: September 2023

Butyrate, produced by gut microbe during dietary fiber fermentation, has anti-inflammatory and antioxidant effects on chronic inflammation diseases, yet it remains to be explored whether butyrate has protective effects against viral infections. Here, we demonstrated that butyrate alleviated tissue injury in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected golden hamsters supplemented with butyrate before and during the infection. Butyrate-treated hamsters showed augmentation of type I interferon (IFN) response and activation of endothelial cells without exaggerated inflammation. In addition, butyrate regulated redox homeostasis by enhancing the activity of superoxide dismutase (SOD) to inhibit excessive apoptotic cell death. Therefore, butyrate exhibited effective prevention against SARS-CoV-2 by upregulating antiviral immune responses and promoting cell survival.