bluuebunny/crossref_metadata_2025 huggingface dataset:
Empirical Comparison and Analysis of Artificial Intelligence-Based Methods for Identifying Phosphorylation Sites of SARS-CoV-2 Infection
Authors: Lai Hongyan , Zhu Tao , Xie Sijia , Luo Xinwei , Hong Feitong , Luo Diyu , Dao Fuying , Lin Hao , Shu Kunxian , Lv Hao
Published: December 2024

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a member of the large coronavirus family with high infectivity and pathogenicity and is the primary pathogen causing the global pandemic of coronavirus disease 2019 (COVID-19). Phosphorylation is a major type of protein post-translational modification that plays an essential role in the process of SARS-CoV-2–host interactions. The precise identification of phosphorylation sites in host cells infected with SARS-CoV-2 will be of great importance to investigate potential antiviral responses and mechanisms and exploit novel targets for therapeutic development. Numerous computational tools have been developed on the basis of phosphoproteomic data generated by mass spectrometry-based experimental techniques, with which phosphorylation sites can be accurately ascertained across the whole SARS-CoV-2-infected proteomes. In this work, we have comprehensively reviewed several major aspects of the construction strategies and availability of these predictors, including benchmark dataset preparation, feature extraction and refinement methods, machine learning algorithms and deep learning architectures, model evaluation approaches and metrics, and publicly available web servers and packages. We have highlighted and compared the prediction performance of each tool on the independent serine/threonine (S/T) and tyrosine (Y) phosphorylation datasets and discussed the overall limitations of current existing predictors. In summary, this review would provide pertinent insights into the exploitation of new powerful phosphorylation site identification tools, facilitate the localization of more suitable target molecules for experimental verification, and contribute to the development of antiviral therapies.
Therapeutic Significance of NLRP3 Inflammasome in Cancer: Friend or Foe?
Authors: Jalali Aliea M. , Mitchell Kenyon J. , Pompoco Christian , Poludasu Sudeep , Tran Sabrina , Ramana Kota V.
Published: December 2024

Besides various infectious and inflammatory complications, recent studies also indicated the significance of NLRP3 inflammasome in cancer progression and therapy. NLRP3-mediated immune response and pyroptosis could be helpful or harmful in the progression of cancer, and also depend on the nature of the tumor microenvironment. The activation of NLRP3 inflammasome could increase immune surveillance and the efficacy of immunotherapy. It can also lead to the removal of tumor cells by the recruitment of phagocytic macrophages, T-lymphocytes, and other immune cells to the tumor site. On the other hand, NLRP3 activation can also be harmful, as chronic inflammation driven by NLRP3 supports tumor progression by creating an environment that facilitates cancer cell proliferation, migration, invasion, and metastasis. The release of pro-inflammatory cytokines such as IL-1β and IL-18 can promote tumor growth and angiogenesis, while sustained inflammation may lead to immune suppression, hindering effective anti-tumor responses. In this review article, we discuss the role of NLRP3 inflammasome-mediated inflammatory response in the pathophysiology of various cancer types; understanding this role is essential for the development of innovative therapeutic strategies for cancer growth and spread.
Inhibiting the Cholesterol Storage Enzyme ACAT1/SOAT1 in Aging Apolipoprotein E4 Mice Alters Their Brains’ Inflammatory Profiles
Authors: Huynh Thao N. , Fikse Emma N. , De La Torre Adrianna L. , Havrda Matthew C. , Chang Catherine C. Y. , Chang Ta Yuan
Published: December 2024

Aging and apolipoprotein E4 (APOE4) are the two most significant risk factors for late-onset Alzheimer’s disease (LOAD). Compared to APOE3, APOE4 disrupts cholesterol homeostasis, increases cholesteryl esters (CEs), and exacerbates neuroinflammation in brain cells, including microglia. Targeting CEs and neuroinflammation could be a novel strategy to ameliorate APOE4-dependent phenotypes. Toll-like receptor 4 (TLR4) is a key macromolecule in inflammation, and its regulation is associated with the cholesterol content of lipid rafts in cell membranes. We previously demonstrated that in normal microglia expressing APOE3, inhibiting the cholesterol storage enzyme acyl-CoA:cholesterol acyltransferase 1 (ACAT1/SOAT1) reduces CEs, dampened neuroinflammation via modulating the fate of TLR4. We also showed that treating myelin debris-loaded normal microglia with ACAT inhibitor F12511 reduced cellular CEs and activated ABC transporter 1 (ABCA1) for cholesterol efflux. This study found that treating primary microglia expressing APOE4 with F12511 also reduces CEs, activates ABCA1, and dampens LPS-dependent NFκB activation. In vivo, two-week injections of nanoparticle F12511, which consists of DSPE-PEG2000, phosphatidylcholine, and F12511, to aged female APOE4 mice reduced TLR4 protein content and decreased proinflammatory cytokines, including IL-1β in mice brains. Overall, our work suggests nanoparticle F12511 is a novel agent to ameliorate LOAD.
EWSR1::ATF1 Translocation: A Common Tumor Driver of Distinct Human Neoplasms
Authors: Bianco Julia Raffaella , Li YiJing , Petranyi Agota , Fabian Zsolt
Published: December 2024

Cancer is among the leading causes of mortality in developed countries due to limited available therapeutic modalities and high rate of morbidity. Although malignancies might show individual genetic landscapes, recurring aberrations in the neoplastic genome have been identified in the wide range of transformed cells. These include translocations of frequently affected loci of the human genetic material like the Ewing sarcoma breakpoint region 1 (EWSR1) of chromosome 22 that results in malignancies with mesodermal origin. These cytogenetic defects frequently result in the genesis of fusion genes involving EWSR1 and a number of genes from partner loci. One of these chromosomal rearrangements is the reciprocal translocation between the q13 and q12 loci of chromosome 12 and 22, respectively, that is believed to initiate cancer formation by the genesis of a novel, chimeric transcription factor provoking dysregulated gene expression. Since soft-tissue neoplasms carrying t(12;22)(q13;q12) have very poor prognosis and clinical modalities specifically targeting t(12;22)(q13;q12)-harboring cells are not available to date, understanding this DNA aberration is not only timely but urgent. Here, we review our current knowledge of human malignancies carrying the specific subset of EWSR1 rearrangements that leads to the expression of the EWSR1::ATF1 tumor-driver chimeric protein.
Antiviral Activity of Ecklonia cava Extracts and Dieckol Against Zika Virus
Authors: Kim Eun-A , Kang Nalae , Heo Jun-Ho , Park Areumi , Heo Seong-Yeong , Kim Hyun-Soo , Heo Soo-Jin
Published: December 2024

Ecklonia cava and its major compound dieckol, both natural marine products, possess antioxidant, anti-inflammatory, and metabolic-regulating effects. Zika virus (ZIKV), an arbovirus from the Flaviviridae family, is transmitted by mosquitoes and causes serious illnesses in humans. This study aimed to evaluate the anti-ZIKV potential of Ecklonia cava and dieckol. The antiviral activity of Ecklonia cava extract (ECE), prepared with 80% ethanol, was assessed in ZIKV-infected Vero E6 cells through MTT assay, plaque assay, and quantitative polymerase chain reaction (qPCR), demonstrating no cytotoxicity and a significant reduction in viral titers and ZIKV mRNA levels. In addition, ECE decreased the expression of tumor necrosis factor-α and interferon-induced protein with tetratricopeptide repeats in the ZIKV-infected cells. Dieckol, the primary active compound in ECE, exhibited potent anti-ZIKV activity, with a half maximal inhibitory concentration (IC50), value of 4.8 µM. In silico molecular docking analysis revealed that dieckol forms stable complexes with key ZIKV proteins, including the envelope, NS2B/NS3, and RNA-dependent RNA polymerase (RdRp) protein, exhibiting high binding energies of −438.09 kcal/mol, −1040.51 kcal/mol, and −1043.40 kcal/mol, respectively. Overall, our findings suggest that ECE and dieckol are promising candidates for the development of anti-ZIKV agents.
Microbubble-Protected Oncolytic Virotherapy Targeted by Sonoporation Induces Tumor Necrosis and T-Lymphocyte Infiltration in Humanized Mice Bearing Triple-Negative Breast Cancer
Authors: Sitta Juliana , De Carlo Flavia , Kirven Imani , Tackett John H. , Penfornis Patrice , Dobbins George Clement , Barbier Mallory , Del Valle Luis , Larsen Clayton T. , Schutt Ernest G. , Li Rhodemann , Howard Candace M. , Claudio Pier Paolo
Published: December 2024

Oncolytic virotherapy has shown great promise in mediating targeted tumor destruction through tumor-selective replication and induction of anti-tumor immunity; however, obstacles remain for virus candidates to reach the clinic. These include avoiding neutralizing antibodies, preventing stimulation of the adaptive immune response during intravenous administration, and inducing sufficient apoptosis and immune activation so that the body’s defense can work to eradicate systemic disease. We have developed a co-formulation of oncolytic viruses (OVs) with Imagent® lipid-encapsulated, perfluorocarbon microbubbles (MBs) to protect the OVs from the innate and adaptive immune system. Once inside the MB, the viral particles become acoustically active such that external ultrasound can target the delivery of the virus locally within the tumor. Humanized NSG female mice (Hu-CD34+ NSG-SGM3) engrafted in their flanks with MDA-MB-231-Luc triple-negative breast cancer (TNBC) cells were transduced with MB/OVs, with or without adjuvant Pembrolizumab treatment, and tumor sizes and tumor necrosis were assessed. The presence of CD8+ (cytotoxic T-cells), CD4+ (helper T-cells), and CD25+ (Tregs) tumor-infiltrating lymphocytes (TILs) was quantified in the tumor samples by immunohistochemistry. In an in vivo model of humanized mice engrafted with a human immune system, we observed significantly greater tumor necrosis and smaller tumor mass in human TNBC xenografts systemically treated with MB/OV complexes in the presence or absence of pembrolizumab adjuvant treatment, compared to controls. Additionally, we observed a low ratio of CD4+/CD8+ TILs and a high ratio of CD8+/CD25+ TILs in the MDA-MB-231 xenografts treated with MB/OVs complexes with or without pembrolizumab adjuvant treatment, compared to controls. Our study demonstrated the feasibility of using MBs to target OVs to TNBC through diagnostic ultrasound, which decreased tumor mass by increasing tumor necrosis and stimulated a local and systemic antitumoral immune response by increasing intratumoral CD8+ T-cytotoxic lymphocyte infiltration and decreasing CD25+ Treg cells.
Childhood-Onset ANCA-Associated Vasculitis: From Genetic Studies to Advances in Pathogenesis, Classification and Novel Therapeutic Approaches
Authors: Yeo Liching , Naheed Asma , Richards Chantelle , Ciurtin Coziana
Published: December 2024

Childhood-onset antineutrophil cytoplasmic antibodies (ANCA)-associated vasculitis (AAV) represents a heterogeneous group of multi-system autoimmune conditions associated with chronic inflammation, characteristically affecting small blood vessels, leading to various organ and system manifestations. Although rare in paediatric populations, AAV poses challenges in early recognition, diagnosis and management of refractory cases. This review highlights the characteristics of clinical presentation and outcomes of AAV in children, as well as its current classification and progress achieved in understanding the disease pathogenesis, with a focus on adult and paediatric genetic studies. Furthermore, we discuss the management of AAV in children, as well as new emerging therapies and future research needs, while proposing a potential algorithm for a childhood-onset-AAV therapeutic approach based on the disease phenotype.
Advancements in the Application of scRNA-Seq in Breast Research: A Review
Authors: Zhang Zhenyu , Ma Xiaoming , La Yongfu , Guo Xian , Chu Min , Bao Pengjia , Yan Ping , Wu Xiaoyun , Liang Chunnian
Published: December 2024

Single-cell sequencing technology provides apparent advantages in cell population heterogeneity, allowing individuals to better comprehend tissues and organs. Sequencing technology is currently moving beyond the standard transcriptome to the single-cell level, which is likely to bring new insights into the function of breast cells. In this study, we examine the primary cell types involved in breast development, as well as achievements in the study of scRNA-seq in the microenvironment, stressing the finding of novel cell subsets using single-cell approaches and analyzing the problems and solutions to scRNA-seq. Furthermore, we are excited about the field’s promising future.
Phytochemical Profile and In Vitro Cytotoxic, Genotoxic, and Antigenotoxic Evaluation of Cistus monspeliensis L. Leaf Extract
Authors: Al-Naqeb Ghanya , Zorzi Gianluca , Oldani Amanda , Azzalin Alberto , Avesani Linda , Guzzo Flavia , Pascale Alessia , De Giuseppe Rachele , Cena Hellas
Published: December 2024

Cistus monspeliensis L. (C. monspeliensis) is used in Italian folk medicine. This study was performed to determine genotoxic and antigenotoxic effects of C. monspeliensis leaf extract against mitomycin C (MMC) using an in vitro cytokinesis-block micronucleus assay (CBMN) in the Chinese Hamster Ovarian K1 (CHO-K1) cell line. The phytochemical composition of C. monspeliensis extract was evaluated using an untargeted metabolomic approach by employing UPLC-PDA-ESI/MS. The automated in vitro CBMN assay was carried out using image analysis systems with a widefield fluorescence microscope and the ImageStreamX imaging flow cytometer. The phytochemical profile of C. monspeliensis extract showed, as the most abundant metabolites, punicalagin, myricetin, gallocathechin, and a labdane-type diterpene. C. monspeliensis, at the tested concentrations of 50, 100, and 200 μg/mL, did not induce significant micronuclei frequency, thus indicating the absence of a genotoxic potential. When testing the C. monspeliensis extract for antigenotoxicity in the presence of MMC, we observed a hormetic concentration-dependent effect, where low concentrations resulted in a significant protective effect against MMC-induced micronuclei frequency, and higher concentrations resulted in no effect. In conclusion, our findings demonstrate that C. monspeliensis extract is not genotoxic and, at low concentration, exhibits an antigenotoxic effect. In relation to this final point, C. monspeliensis may act as a potential chemo-preventive against genotoxic agents.
Exploring the Impact of IL-33 Gene Polymorphism (rs1929992) on Susceptibility to Chronic Spontaneous Urticaria and Its Association with Serum Interleukin-33 Levels
Authors: Dobrican-Băruța Carmen-Teodora , Deleanu Diana Mihaela , Iancu Mihaela , Muntean Ioana Adriana , Nedelea Irena , Bălan Radu-Gheorghe , Procopciuc Lucia Maria , Filip Gabriela Adriana
Published: December 2024

Urticaria is a debilitating skin condition affecting up to 20% of the global population, characterized by erythematous, maculopapular lesions and significant quality of life impairment. This study focused on the role of interleukin 33 (IL-33) and its polymorphisms, particularly SNP rs1929992, in chronic spontaneous urticaria (CSU). Using demographic, clinical, and laboratory data from CSU patients and controls, we estimated allele and genotype frequencies, Hardy–Weinberg equilibrium condition, and serum IL-33 levels, using unconditional binomial logistic regression for association analysis. Results revealed that CSU patients had significantly higher frequencies of the minor allele of IL-33 rs1929992 compared to controls (31.25% vs. 17.35%, p = 0.024), and carriers of the GA genotype exhibited increased odds of CSU (adjusted OR = 2.208, p ≤ 0.001). Additionally, serum IL-33 levels were markedly elevated in CSU patients, particularly those with the GA genotype. The findings suggest that the IL-33 SNP is associated with an increased susceptibility to CSU, emphasizing its potential as a diagnostic and therapeutic biomarker. This study underscores the genetic and immunological underpinnings of CSU, paving the way for personalized treatment approaches.
Finerenone in Heart Failure—A Novel Therapeutic Approach
Authors: Holst-Hansen Amalie , Grimm Daniela , Wehland Markus
Published: December 2024

This review will discuss heart failure, introduce a new drug finerenone, and discuss clinical studies with a focus on its effects on heart failure. Heart failure is a condition or syndrome characterized by an impairment of the pumping ability of the heart, thus no longer keeping up with the demands of the body. There are several types of heart failure; among them are heart failure with reduced ejection fraction, with mildly reduced ejection fraction and with preserved ejection fraction. Heart failure can be caused by several factors including lifestyle factors and diseases such as hypertension, type 2 diabetes mellitus and other cardiovascular diseases. Chronic kidney disease is also a risk factor of heart failure, as it leads to a state of inflammation that can impair the cardiovascular system over time. The novel nonsteroidal mineralocorticoid receptor antagonist finerenone antagonizes the mineralocorticoid receptor and thereby decreases the amount of fibrosis and inflammation that is observed in many heart failure patients. It shows an equal tissue distribution among heart and kidney, a high affinity and selectivity for the mineralocorticoid receptor and little risk of hyperkalemia and feminization. It also exhibits a reduction in the incidence of cardiovascular outcomes among patients with chronic kidney disease and type 2 diabetes mellitus. Therefore, finerenone has been proposed as a beneficial medication for reducing heart failure, especially in patients with diabetes and chronic kidney disease. Further studies are to be conducted to clarify the effects of finerenone alone and in combination with other drugs.
Altered Protein Kinase A-Dependent Phosphorylation of Cav1.2 in Left Ventricular Myocardium from Cacna1c Haploinsufficient Rat Hearts
Authors: Königstein David , Fender Hauke , Plačkić Jelena , Kisko Theresa M. , Wöhr Markus , Kockskämper Jens
Published: December 2024

CACNA1C encodes the α1c subunit of the L-type Ca2+ channel, Cav1.2. Ventricular myocytes from haploinsufficient Cacna1c (Cacna1c+/−) rats exhibited reduced expression of Cav1.2 but an apparently normal sarcolemmal Ca2+ influx with an impaired response to sympathetic stress. We tested the hypothesis that the altered phosphorylation of Cav1.2 might underlie the sarcolemmal Ca2+ influx phenotype in Cacna1c+/− myocytes using immunoblotting of the left ventricular (LV) tissue from Cacna1c+/− versus wildtype (WT) hearts. Activation of cAMP-dependent protein kinase A (PKA) increases L-type Ca2+ current and phosphorylates Cav1.2 at serine-1928. Using an antibody directed against this phosphorylation site, we observed elevated phosphorylation of Cav1.2 at serine-1928 in LV myocardium from Cacna1c+/− rats under basal conditions (+110% versus WT). Sympathetic stress was simulated by isoprenaline (100 nM) in Langendorff-perfused hearts. Isoprenaline increased the phosphorylation of serine-1928 in Cacna1c+/− LV myocardium by ≈410%, but the increase was significantly smaller than in WT myocardium (≈650%). In conclusion, our study reveals altered PKA-dependent phosphorylation of Cav1.2 with elevated phosphorylation of serine-1928 under basal conditions and a diminished phosphorylation reserve during β-adrenergic stimulation. These alterations in the phosphorylation of Cav1.2 may explain the apparently normal sarcolemmal Ca2+ influx in Cacna1c+/− myocytes under basal conditions as well as the impaired response to sympathetic stimulation.
MET Exon 14 Skipping and Novel Actionable Variants: Diagnostic and Therapeutic Implications in Latin American Non-Small-Cell Lung Cancer Patients
Authors: Rivas Solange , Sepúlveda Romina V. , Tapia Ignacio , Estay Catalina , Soto Vicente , Blanco Alejandro , González Evelin , Armisen Ricardo
Published: December 2024

Targeted therapy indications for actionable variants in non-small-cell lung cancer (NSCLC) have primarily been studied in Caucasian populations, with limited data on Latin American patients. This study utilized a 52-genes next-generation sequencing (NGS) panel to analyze 1560 tumor biopsies from NSCLC patients in Chile, Brazil, and Peru. The RNA sequencing reads and DNA coverage were correlated to improve the detection of the actionable MET exon 14 skipping variant (METex14). The pathogenicity of MET variants of uncertain significance (VUSs) was assessed using bioinformatic methods, based on their predicted driver potential. The effects of the predicted drivers VUS T992I and H1094Y on c-MET signaling activation, proliferation, and migration were evaluated in HEK293T, BEAS-2B, and H1993 cell lines. Subsequently, c-Met inhibitors were tested in 2D and 3D cell cultures, and drug affinity was determined using 3D structure simulations. The prevalence of MET variants in the South American cohort was 8%, and RNA-based diagnosis detected 27% more cases of METex14 than DNA-based methods. Notably, 20% of METex14 cases with RNA reads below the detection threshold were confirmed using DNA analysis. The novel actionable T992I and H1094Y variants induced proliferation and migration through c-Met/Akt signaling. Both variants showed sensitivity to crizotinib and savolitinib, but the H1094Y variant exhibited reduced sensitivity to capmatinib. These findings highlight the importance of RNA-based METex14 diagnosis and reveal the drug sensitivity profiles of novel actionable MET variants from an understudied patient population.
Jeju Citrus (Citrus unshiu) Leaf Extract and Hesperidin Inhibit Small Intestinal α-Glucosidase Activities In Vitro and Postprandial Hyperglycemia in Animal Model
Authors: Kim Gi-Jung , Jang Yelim , Kwon Kyoung-Tae , Kim Jae-Won , Kang Seong-IL , Ko Hee-Chul , Lee Jung-Yun , Apostolidis Emmanouil , Kwon Young-In
Published: December 2024

Citrus fruits are widely distributed in East Asia, and tea made from citrus peels has demonstrated health benefits, such as a reduction in fever, inflammation, and high blood pressure. However, citrus leaves have not been evaluated extensively for their possible health benefits. In this study, the α-glucosidase-inhibitory activity of Jeju citrus hot-water (CW) and ethyl alcohol (CE) extracts, along with hesperidin (HP) (a bioactive compound in citrus leaf extracts), was investigated, and furthermore, their effect on postprandial blood glucose reduction in an animal model was determined. The hesperidin contents of CW and CE were 15.80 ± 0.18 and 39.17 ± 0.07 mg/g-extract, respectively. Hesperidin inhibited α-glucosidase (IC50, 4.39), sucrase (0.50), and CE (2.62) and demonstrated higher α-glucosidase inhibitory activity when compared to CW (4.99 mg/mL). When using an SD rat model, during sucrose and starch loading tests with CE (p < 0.01) and HP (p < 0.01), a significant postprandial blood glucose reduction effect was observed when compared to the control. The maximum blood glucose levels (Cmax) of the CE administration group decreased by about 15% (from 229.3 ± 14.5 to 194.0 ± 7.4, p < 0.01) and 11% (from 225.1 ± 13.8 to 201.1 ± 7.2 hr·mg/dL, p < 0.05) in the sucrose and starch loading tests, respectively. Our findings suggest that citrus leaf extracts standardized to hesperidin may reduce postprandial blood glucose levels through the observed inhibitory effect against sucrase, which results in delayed carbohydrate absorption. Our findings provide a biochemical rationale for further evaluating the benefits of citrus leaves.
The Emerging Role of Schwann Cells in the Tumor Immune Microenvironment and Its Potential Clinical Application
Authors: Zhang Shan , Chen Jing , Cheng Fanjun , Zheng Fang
Published: December 2024

As the primary glial cells in the peripheral nervous system (PNS), Schwann cells (SCs) have been proven to influence the behavior of cancer cells profoundly and are involved in cancer progression through extensive interactions with cancer cells and other stromal cells. Indeed, the tumor microenvironment (TME) is a critical factor that can significantly limit the efficacy of immunotherapeutic approaches. The TME promotes tumor progression in part by reshaping an immunosuppressive state. The immunosuppressive TME is the result of the crosstalk between the tumor cells and the different immune cell subsets, including macrophages, natural killer (NK) cells, dendritic cells (DCs), lymphocytes, myeloid-derived suppressor cells (MDSCs), etc. They are closely related to the anti-tumor immune status and the clinical prognosis of cancer patients. Increasing research demonstrates that SCs influence these immune cells and reshape the formation of the immunosuppressive TME via the secretion of various cytokines, chemokines, and other effector molecules, eventually facilitating immune evasion and tumor progression. In this review, we summarize the SC reprogramming in TME, the emerging role of SCs in tumor immune microenvironment, and the underlying mechanisms involved. We also discuss the possible therapeutic strategies to selectively target SCs, providing insights and perspectives for future research and clinical studies involving SC-targeted treatment.
Mode of Metal Ligation Governs Inhibition of Carboxypeptidase A
Authors: Amador Balderas Jorge Antonio , Beierlein Frank , Horn Anselm H. C. , Volkenandt Senta , Völcker Leon , Mokhtari Nikoo , Ndongue Jules Cesar Epee , Imhof Petra
Published: December 2024

Carboxypeptidase is a Zn-dependent protease that specifically recognises and hydrolyses peptides with a hydrophobic side chain at the C-terminal residue. According to hydrolysis mechanisms proposed in the literature, catalysis requires a water molecule to be close to the Zn ion so as to be activated as a nucleophile. Among small molecules that resemble the slowly hydrolysed Gly-Tyr peptide, which have been previously designed as inhibitors and characterised structurally, a variant with the terminal amino acid in a D-configuration has been the most effective. Our molecular dynamics simulations of carboxypeptidase complexed with different variants of those inhibitor ligands as well as variants of the Gly-Tyr peptide show that the strength of the inhibitory effect is not related to the binding strength of the ligand. Our data rather support an earlier notion that the inhibition is, at least partially, due to blocking a coordination site at the Zn ion by the ligand coordinating the metal ion in a bidentate fashion.
The Impact of Calcium Overload on Cellular Processes: Exploring Calcicoptosis and Its Therapeutic Potential in Cancer
Authors: Gielecińska Adrianna , Kciuk Mateusz , Kontek Renata
Published: December 2024

The key role of calcium in various physiological and pathological processes includes its involvement in various forms of regulated cell death (RCD). The concept of ‘calcicoptosis’ has been introduced as a calcium-induced phenomenon associated with oxidative stress and cellular damage. However, its definition remains controversial within the research community, with some considering it a general form of calcium overload stress, while others view it as a tumor-specific calcium-induced cell death. This review examines ‘calcicoptosis’ in the context of established RCD mechanisms such as apoptosis, necroptosis, ferroptosis, and others. It further analyzes the intricate relationship between calcium dysregulation and oxidative stress, emphasizing that while calcium overload often triggers cell death, it may not represent an entirely new type of RCD but rather an extension of known pathways. The purpose of this paper is to discuss the implications of this perspective for cancer therapy focusing on calcium-based nanoparticles. By investigating the connections between calcium dynamics and cell death pathways, this review contributes to the advancement of our understanding of calcicoptosis and its possible therapeutic uses.
A Potent Antibacterial Peptide (P6) from the De Novo Transcriptome of the Microalga Aureococcus anophagefferens
Authors: Zhang Kexin , Yin Xiaoting , Huang Yu , Liu Chao , Zhang Qingchun , Liu Qing , Wang Senyu , Fei Wenwu , Shi Qiong , Qiu Limei
Published: December 2024

Marine microalgae are a rich source of natural products, and their amino acid-based antimicrobial agents are usually obtained by enzymatic hydrolysis, which is inefficient and limits the research on antimicrobial peptides (AMPs) from microalgae. In this study, Aureococcus anophagefferens is used as a model to predict antimicrobial peptides through high-throughput methods, and 471 putative peptides are identified based on the de novo transcriptome technique. Among them, three short peptides, P1, P6, and P7 were found to have antimicrobial activity against Escherichia coli, Staphylococcus aureus, Micro1coccus luteus, and yeast Pichia pastoris, and they showed no hemolytic activity even at higher concentrations up to 10 mg/mL. Especially P6, a 12-amino acid peptide with three positive charges, which exhibited the most significant microbicidal effect with the lowest MIC of 31.25 μg/mL against E. coli, and electron microscope observations showed the surface of P6 treated E. coli with granular protrusions and ruptures, suggesting that it likely caused cell death by directly destroying the bacterial cell membrane. This study may enrich the database of microalgal AMPs and demonstrate an efficient process for searching and validating microalgal source AMPs by combining computer analysis with bioactivity experiments.
Correction: Dłuski et al. Circular RNA hsa_circ_0002268 (PHACTR1) Is Specific to Gestational Diabetes Mellitus in a Polish Pregnant Population. Int. J. Mol. Sci. 2024, 25, 7040
Authors: Dłuski Dominik Franciszek , Cieśla Marek , Darmochwał-Kolarz Dorota
Published: December 2024

In the original publication [...]
RTL4, a Retrovirus-Derived Gene Implicated in Autism Spectrum Disorder, Is a Microglial Gene That Responds to Noradrenaline in the Postnatal Brain
Authors: Ishino Fumitoshi , Itoh Johbu , Matsuzawa Ayumi , Irie Masahito , Suzuki Toru , Hiraoka Yuichi , Yoshikawa Masanobu , Kaneko-Ishino Tomoko
Published: December 2024

Retrotransposon Gag-like 4 (RTL4), a gene acquired from a retrovirus, is a causative gene in autism spectrum disorder. Its knockout mice exhibit increased impulsivity, impaired short-term spatial memory, failure to adapt to novel environments, and delayed noradrenaline (NA) recovery in the frontal cortex. However, due to its very low expression in the brain, it remains unknown which brain cells express RTL4 and its dynamics in relation to NA. We addressed these issues using knock-in mice carrying endogenous Rtl4 fused to Venus, which encodes a fluorescent protein. The RTL4-Venus fusion protein was detected as a secreted protein in the midbrain, hypothalamus, hippocampus and amygdala in the postnatal brain. Its signal intensity was high during critical periods of neonatal adaptation to novel environments. It was upregulated by various stimuli, including isoproterenol administration, whereas it was decreased by anesthesia but was maintained by milnacipran administration, suggesting its highly sensitive response to stressors, possible dependence on the arousal state and involvement in the NA reuptake process. In vitro mixed glial culture experiments demonstrated that Rtl4 is a microglial gene and suggested that RTL4 secretion responds rapidly to isoproterenol. Microglial RTL4 plays an important role in the NA response and possibly in the development of the NAergic neuronal network in the brain.
Metabolic Biomarkers of Liver Failure in Cell Models and Patient Sera: Toward Liver Damage Evaluation In Vitro
Authors: Rentschler Simone , Doss Sandra , Kaiser Lars , Weinschrott Helga , Kohl Matthias , Deigner Hans-Peter , Sauer Martin
Published: December 2024

Recent research has concentrated on the development of suitable in vitro cell models for the early identification of hepatotoxicity during drug development in order to reduce the number of animal models and to obtain a better predictability for hepatotoxic reactions in humans. The aim of the presented study was to identify translational biomarkers for acute liver injury in human patients that can serve as biomarkers for hepatocellular injury in vivo and in vitro in simple cell models. Therefore, 188 different metabolites from patients with acute-on-chronic liver failure before and after liver transplantation were analyzed with mass spectrometry. The identified potential metabolic biomarker set, including acylcarnitines, phosphatidylcholines and sphingomyelins, was used to screen primary and permanent hepatocyte culture models for their ability to model hepatotoxic responses caused by different drugs with known and unknown hepatotoxic potential. The results obtained suggest that simple in vitro cell models have the capability to display metabolic responses in biomarkers for liver cell damage in course of the treatment with different drugs and therefore can serve as a basis for in vitro models for metabolic analysis in drug toxicity testing. The identified metabolites should further be evaluated for their potential to serve as a metabolic biomarker set indicating hepatocellular injury in vitro as well as in vivo.
The Therapeutic Potential of Physical Exercise in Cancer: The Role of Chemokines
Authors: Buzaglo Glenda B. B. , Telles Guilherme D. , Araújo Rafaela B. , Junior Gilmar D. S. , Ruberti Olivia M. , Ferreira Marina L. V. , Derchain Sophie F. M. , Vechin Felipe C. , Conceição Miguel S.
Published: December 2024

The global increase in cancer cases and mortality has been associated with inflammatory processes, in which chemokines play crucial roles. These molecules, a subfamily of cytokines, are essential for the migration, adhesion, interaction, and positioning of immune cells throughout the body. Chemokines primarily originate in response to pathogenic stimuli and inflammatory cytokines. They are expressed by lymphocytes in the bloodstream and are divided into four classes (CC, CXC, XC, and CX3C), playing multifaceted roles in the tumor environment (TME). In the TME, chemokines regulate immune behavior by recruiting cells such as tumor-associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs), which promote tumor survival. Additionally, they directly influence tumor behavior, promoting pathological angiogenesis, invasion, and metastasis. On the other hand, chemokines can also induce antitumor responses by mobilizing CD8+ T cells and natural killer (NK) cells to the tumor, reducing pro-inflammatory chemokines and enhancing essential antitumor responses. Given the complex interaction between chemokines, the immune system, angiogenic factors, and metastasis, it becomes evident how important it is to target these pathways in therapeutic interventions to counteract cancer progression. In this context, physical exercise emerges as a promising strategy due to its role modulating the expression of anti-inflammatory chemokines and enhancing the antitumor response. Aerobic and resistance exercises have been associated with a beneficial inflammatory profile in cancer, increased infiltration of CD8+ T cells in the TME, and improvement of intratumoral vasculature. This creates an environment less favorable to tumor growth and supports the circulation of antitumor immune cells and chemokines. Therefore, understanding the impact of exercise on the expression of chemokines can provide valuable insights for therapeutic interventions in cancer treatment and prevention.
Optimizing Yeast Homologous Recombination for Splicing Large Coronavirus Genome Fragments
Authors: Xiong Guoqing , Huang Xuan , Hu Ao , Meng Zhixin , Cui Jiazhen , Feng Yuzhong , Chen Zhili , Lu Yuanyuan , Yang Qi , Liu Gang
Published: December 2024

Reverse genetics is a useful tool for studying viruses and developing vaccines for coronaviruses. However, constructing and manipulating the coronavirus genome in Escherichia coli can be time-consuming and challenging due to its large size and instability. Homologous recombination, a genetic manipulation mechanism found in organisms, is essential for DNA repair, gene recombination, and genetic engineering. In yeast, particularly Saccharomyces cerevisiae, homologous recombination technology is commonly used for constructing gene expression plasmids and genome editing. In this study, we successfully split and spliced a 30 kb viral genome fragment using yeast homologous recombination. By optimizing the program parameters, such as homologous arm lengths and fragment-to-vector ratios, we achieved a splicing efficiency of up to 97.9%. The optimal parameters selected were a 60 bp homologous sequence size and a vector fragment ratio of 1:2:2:2:2:2 for yeast homologous recombination of large DNA fragments.
Vertiport Infrastructure Location Optimization for Equitable Access to Urban Air Mobility
Authors: Volakakis Vasileios , Mahmassani Hani S.
Published: December 2024

Urban air mobility (UAM) has recently emerged as a promising new transportation mode, with various potential use cases. Facility location problems are well studied and of significant importance for various transportation modes. This work introduces a vertiport location identification framework, focusing on demand coverage and infrastructure accessibility. An Agglomerative Hierarchical Clustering (AHC) model was utilized for the identification of candidate vertiport locations, along with a k-means algorithm, for comparison and validation purposes, based on an estimated UAM demand pattern. A genetic algorithm (GA) was then formulated, for the solution of the proposed Uncapacitated and Capacitated Vertiport Location Problems (UVLP and CVLP, respectively), variations of the Uncapacitated and Capacitated Facility Location Problems. To evaluate and compare the introduced methodology, different existing facility location problems (FLPs) were considered and solved exactly using integer and linear programming. These are the Location Set Covering Problem (LSCP), the Maximal Coverage Location Problem (MCLP), and the p-median problem. The p-center problem was also considered and solved via a heuristic approach. The proposed framework is illustrated through applications in the Chicago Metropolitan Area, with the demand estimated on the basis of existing taxi and Transportation Network Company (TNC) data.
Antimicrobial Activity of Compounds Isolated from the Nest Material of Crematogaster rogenhoferi (Mayr) (Hymenoptera: Formicidae)
Authors: Bai Weihui , Chen Baihe , Chen Huimei , Nie Lei , Liang Mingrong , Xu Yijuan , Lu Yongyue , Wang Lei
Published: December 2024

Ants as social insects live in groups, which increases the risk of contagious diseases. In response to the threat of pathogens, ants have evolved a variety of defense mechanisms, including incorporating antimicrobial chemicals into nest material for nest hygiene. Crematogaster rogenhoferi is an arboreal ant, building its nest using plant tissues. It is still unclear how C. rogenhoferi is protected against pathogens in its nest. Two main chemicals, 2,2′-methylenebis[6-(1,1-dimethylethyl)-4-methyl-phenol] (MP) and lup-20(29)-en-3-one (LP), isolated from nest materials of C. rogenhoferi were used to investigate ants’ anti-pathogenic activity against the entomopathogenic fungus Beauveria bassiana and the entomopathogenic bacteria Serratia marcescens. The results showed that MP and LP can inhibit the growth of B. bassiana through direct contact and fumigation. However, neither MP nor LP had any negative effect on S. marcescens growth. Subsequent analysis showed that MP was found in both the abdomen part and the head part of C. rogenhoferi workers, and LP was not detected in C. rogenhoferi workers. Since LP is a common plant secondary metabolite, it is implied that LP may originate from the plant tissue of C. rogenhoferi nest materials. Our results showed that C. rogenhoferi capitalizes on its own antimicrobial chemicals and probably the chemical defenses which have evolved in plants to protect itself against pathogens.
Real-World Efficacy and Safety of Atezolizumab for Advanced Non-Small Cell Lung Cancer in Japan: A Retrospective Multicenter Analysis
Authors: Okada Masahiko , Ohgino Keiko , Horiuchi Kohei , Sayama Koichi , Arai Daisuke , Watase Mayuko , Kobayashi Keigo , Terashima Takeshi , Ishioka Kota , Miyawaki Masayoshi , Sakamaki Fumio , Masuzawa Keita , Terai Hideki , Yasuda Hiroyuki , Soejima Kenzo , Fukunaga Koichi
Published: December 2024

Background/Objectives: Atezolizumab, an immune checkpoint inhibitor (ICI), was used in a phase III clinical trial, i.e., the OAK trial, of previously treated patients with non-small cell lung cancer. We aimed to evaluate the real-world efficacy and safety of atezolizumab in a non-selected population and identify the clinical characteristics that influence its efficacy. Methods: This was a multicenter, retrospective, single-arm observational study. Seventy-four patients with advanced non-small cell lung cancer, who received atezolizumab monotherapy at Keio University and affiliated hospitals in Japan between April 2018 and March 2019, were enrolled. The follow-up period was until 28 February 2024. The efficacy of treatment and adverse events were reviewed retrospectively. Statistical analyses using Pearson’s χ2 test, Fisher’s exact test, log-rank test, and Student’s t-test were performed. Results: The median age of patients was 70 (range, 45–85) years. The overall survival duration was 7.54 (95% confidence interval [CI], 5.14–11.3) months, and the median time to treatment failure (TTF) was 2.00 (95% CI, 1.75–2.54) months. Patients treated with atezolizumab as their first ICI had a longer TTF than those treated with atezolizumab as their second or subsequent ICI (p = 0.04). Conclusions: Atezolizumab may be more effective when used as the first ICI for previously treated patients and may be safely used in elderly patients with non-small cell lung cancer in real-world settings.
Conservative Treatment of Neonatal Brachial Plexus Palsy: A Narrative Review
Authors: Boetto Valentina , Markova Anna , Malgrati Federica , Bongiovanni Isabel , Bassetto Anna , Pavese Chiara , Nardone Antonio , Massazza Giuseppe , Colò Gabriele , Titolo Paolo
Published: December 2024

Neonatal brachial plexus palsy (NBPP) is a flaccid paralysis of the upper limbs that occurs in about 0.4 percent of live births. This condition can produce permanent disabilities; to date, there is no consensus on protocols to be applied for the rehabilitation of children with this condition. The aim of this article is to provide a concise overview of conservative treatment beyond traditional physical therapy for the management of the child with NBPP and to offer a number of useful options for creating the most comprehensive and functional rehabilitation treatment possible. We conducted a narrative review after analyzing articles from the past 50 years on PubMed, Cochrane Library, Scopus, and Web of Science with the following search string [(“neonatal brachial plexus palsy” OR “obstetric brachial plexus palsy” OR “birth brachial plexus palsy”) AND (“rehabilitation” OR “physiotherapy” OR “conservative treatment”)]. We identified a potential of 1275 articles, but only 11 were exclusively about conservative approaches. The most represented rehabilitation approaches in the literature were botulinum toxin, constraint-induced movement therapy (CIMT), virtual reality, neuromuscular electrical stimulation, and kinesiotaping. In conclusion, the various rehabilitation approaches for NBPP are promising, but none can be considered the best option when used alone. In light of the current evidence, a multimodal approach is needed.
Diabetic Nephropathy-Associated Impaired Aortic Function Is Not Mediated by Mean Arterial Pressure and Its Determinants
Authors: Hsu Hon-Chun , Mazibuko Makabongwe S’kholiwe , Robinson Chanel , Dlongolo Noluntu , Woodiwiss Angela , Teckie Gloria , Tade Grace , Dessein Patrick Hector
Published: December 2024

Objective: The study aimed to assess the potential impacts of mean arterial pressure (MAP) and its determinants (cardiac output and systemic vascular resistance) on diabetic nephropathy (DNP)-associated impaired aortic function. Methods: This multi-ethnic study included 115 chronic kidney disease (CKD) patients (67 non-dialysis and 48 dialysis). Six aortic function measures were evaluated by SpygmoCor. The stroke volume was determined by echocardiography. Results: Hypertensive nephropathy (HNP) (53.9%), DNP (32.2%), glomerulonephritis (19.1%), and HIV-associated nephropathy (7.8%) composed the major CKD etiologies. Concurrent HNP and DNP were present in 31.1% of the patients. Participants with compared with those without concurrent HNP and DNP experienced more frequent established cardiovascular disease (43.2% versus 14.9%, p = 0.01), a faster pulse wave velocity (p = 0.001), and smaller total arterial compliance as an indicator of proximal aortic stiffness (p = 0.03). DNP was associated with each aortic function measure (p < 0.001–0.02) independent of potential confounders and MAP, as well as its determinants. HNP was not related to aortic function (p > 0.05 for all relationships). MAP and its determinants did not mediate the potential impact of DNP on aortic function (−4.1–6.4% contribution). Covariates that were associated with impaired aortic function measures included MAP and its determinants (p < 0.001–0.01). Conclusions: Mean or distending arterial pressure and its determinants were associated with impaired aortic function in the overall CKD population. However, these hemodynamic factors did not mediate DNP-associated impaired aortic function. Our results suggest that blood pressure lowering can be anticipated to improve impaired aortic function in the overall CKD population but not when it is solely induced by DNP.
The Influence of Long COVID on the Cardiovascular System and Predictors of Long COVID in Females: Data from the Polish Long COVID Cardiovascular (PoLoCOV-CVD) Study
Authors: Bielecka-Dabrowa Agata , Kapusta Joanna , Sakowicz Agata , Banach Maciej , Jankowski Piotr , Chudzik Michał
Published: December 2024

Background/Objectives: Female sex is one of the Long COVID (LC) risk factors; however, the LC predictors in females have not been established. This study was conducted to assess the influence of LC on the cardiovascular system and to assess the age-independent predictors of LC in females. Methods: Patient information and the course of the disease with symptoms were collected in women at least 12 weeks after COVID-19 recovery. The study participants were followed for 12 months. ECG monitoring, 24 h ECG monitoring, 24 h blood pressure monitoring, echocardiography, and biochemical tests were performed. Results: We studied 1946 consecutive female patients (age 53.0 [43.0–63.0] vs. 52.5 [41.0–63.0], p = 0.25). A more frequent occurrence of LC was observed in females with a severe SARS-CoV-2 infection (p = 0.0001). Women with LC compared to the control group had higher body mass index (p = 0.001), lower level of HDL cholesterol (p = 0.015), higher level of TG (p < 0.001) and higher TG/HDL ratio (p < 0.001), more often myocardial damage (p < 0.001), and lower LVEF (p = 0.01). LC women had more often QRS fragmentation, longer QTcB, and one of the ECG abnormalities. In a multivariate analysis in younger females with BMI > 24.8 kg/m2, TG/HDL ratio > 1.89 and severe course of COVID-19 and in older females, TG/HDL ratio > 1.89, lower LVEF, and also severe course of infection were independent LC predictors. Conclusions: Independent predictors of LC occurrence in women, regardless of age, are severe course of COVID-19 and TG/HDL ratio > 1.89. The presence of comorbidities and lifestyle before COVID-19 had no impact on the occurrence of LC in females regardless of age.