Current Issues in Molecular Biology

17 pages, 8068 KiB

Open AccessArticle

1,2-¹³C₂-Glucose Tracing Approach to Assess Metabolic Alterations of Human Monocytes under Neuroinflammatory Conditions

by Ginevra Giacomello, Carolin Otto, Josef Priller, Klemens Ruprecht, Chotima Böttcher and Maria Kristina Parr

Curr. Issues Mol. Biol. 2023, 45(1), 765-781; https://doi.org/10.3390/cimb45010051 - 16 Jan 2023

Cited by 3 | Viewed by 2682

Abstract

Neuroinflammation is one of the common features in most neurological diseases including multiple sclerosis (MScl) and neurodegenerative diseases such as Alzheimer’s disease (AD). It is associated with local brain inflammation, microglial activation, and infiltration of peripheral immune cells into cerebrospinal fluid (CSF) and [...] Read more.

Neuroinflammation is one of the common features in most neurological diseases including multiple sclerosis (MScl) and neurodegenerative diseases such as Alzheimer’s disease (AD). It is associated with local brain inflammation, microglial activation, and infiltration of peripheral immune cells into cerebrospinal fluid (CSF) and the central nervous system (CNS). It has been shown that the diversity of phenotypic changes in monocytes in CSF relates to neuroinflammation. It remains to be investigated whether these phenotypic changes are associated with functional or metabolic alteration, which may give a hint to their function or changes in cell states, e.g., cell activation. In this article, we investigate whether major metabolic pathways of blood monocytes alter after exposure to CSF of healthy individuals or patients with AD or MScl. Our findings show a significant alteration of the metabolism of monocytes treated with CSF from patients and healthy donors, including higher production of citric acid and glutamine, suggesting a more active glycolysis and tricarboxylic acid (TCA) cycle and reduced production of glycine and serine. These alterations suggest metabolic reprogramming of monocytes, possibly related to the change of compartment (from blood to CSF) and/or disease-related. Moreover, the levels of serine differ between AD and MScl, suggesting different phenotypic alterations between diseases. Full article

(This article belongs to the Special Issue Signaling Pathways, Development, and Biomarkers in Neuropathy)

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13 pages, 2019 KiB

Open AccessArticle

Identification of the Interaction between Minichromosome Maintenance Proteins and the Core Protein of Hepatitis B Virus

by Kaili Du, Eriko Ohsaki, Masami Wada and Keiji Ueda

Curr. Issues Mol. Biol. 2023, 45(1), 752-764; https://doi.org/10.3390/cimb45010050 - 16 Jan 2023

Cited by 1 | Viewed by 2511

Abstract

Chronic HBV infection is a major cause of cirrhosis and hepatocellular carcinoma. Finding host factors involved in the viral life cycle and elucidating their mechanisms is essential for developing innovative strategies for treating HBV. The HBV core protein has pleiotropic roles in HBV [...] Read more.

Chronic HBV infection is a major cause of cirrhosis and hepatocellular carcinoma. Finding host factors involved in the viral life cycle and elucidating their mechanisms is essential for developing innovative strategies for treating HBV. The HBV core protein has pleiotropic roles in HBV replication; thus, finding the interactions between the core protein and host factors is important in clarifying the mechanism of viral infection and proliferation. Recent studies have revealed that core proteins are involved in cccDNA formation, transcriptional regulation, and RNA metabolism, in addition to their primary functions of capsid formation and pgRNA packaging. Here, we report the interaction of the core protein with MCMs, which have an essential role in host DNA replication. The knockdown of MCM2 led to increased viral replication during infection, suggesting that MCM2 serves as a restriction factor for HBV proliferation. This study opens the possibility of elucidating the relationship between core proteins and host factors and their function in viral proliferation. Full article

(This article belongs to the Topic Clinical, Translational and Basic Research on Liver Diseases, 2nd Volume)

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14 pages, 2019 KiB

Open AccessArticle

The Effect of Different Anesthetic Techniques on Proliferation, Apoptosis, and Gene Expression in Colon Cancer Cells: A Pilot In Vitro Study

by Alexandru Leonard Alexa, Ancuta Jurj, Ciprian Tomuleasa, Adrian Bogdan Tigu, Raluca-Miorita Hategan and Daniela Ionescu

Curr. Issues Mol. Biol. 2023, 45(1), 738-751; https://doi.org/10.3390/cimb45010049 - 14 Jan 2023

Cited by 2 | Viewed by 2373

Abstract

Background: Colorectal cancer is highly common and causes high mortality rates. Treatment for colorectal cancer is multidisciplinary, but in most cases the main option remains surgery. Intriguingly, in recent years, a number of studies have shown that a patient’s postoperative outcome may be [...] Read more.

Background: Colorectal cancer is highly common and causes high mortality rates. Treatment for colorectal cancer is multidisciplinary, but in most cases the main option remains surgery. Intriguingly, in recent years, a number of studies have shown that a patient’s postoperative outcome may be influenced by certain anesthetic drugs. Our main objective was to compare the effect of propofol–total intravenous anesthesia (TIVA) with sevoflurane anesthesia and to investigate the potential role of intravenous lidocaine on colon cancer cell functions. We tested the effects of serum from colorectal cancer patients undergoing TIVA vs. sevoflurane anesthesia with or without lidocaine on HCT 116 cell lines; on proliferation, apoptosis, migration, and cell cycles; and on cancer-related gene expressions. Methods: 60 patients who were scheduled for colorectal cancer surgery were randomized into four different groups (two groups with TIVA and two groups with sevoflurane anesthesia with or without intravenous lidocaine). Blood samples were collected at the start and at the end of surgery. HCT 116 cells were exposed to the patients’ serum. Results: 15 patients were included in each of the study groups. We did not find any significant difference on cell viability or apoptosis between the study groups. However, there was an increased apoptosis in propofol groups, but this result was not statistically significant. A significant increase in the expression profile of the TP53 gene in the propofol group was registered (p = 0.029), while in the other study groups, no significant differences were reported. BCL2 and CASP3 expressions increased in the sevoflurane–lidocaine group without statistical significance. Conclusions: In our study, serum from patients receiving different anesthetic techniques did not significantly influence the apoptosis, migration, and cell cycle of HCT-116 colorectal carcinoma cells. Viability was also not significantly influenced by the anesthetic technique, except the sevoflurane–lidocaine group where it was increased. The gene expression of TP53 was significantly increased in the propofol group, which is consistent with the results of similar in vitro studies and may be one of the mechanisms by which anesthetic agents may influence the biology of cancer cells. Further studies that investigate the effects of propofol and lidocaine in different plasma concentrations on different colon cancer cell lines and assess the impacts of these findings on the clinical outcome are much needed. Full article

(This article belongs to the Special Issue Advances in Molecular Pathogenesis Regulation in Cancer)

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17 pages, 1532 KiB

Open AccessArticle

Genetic and Epigenetic Regulation of MEFV Gene and Their Impact on Clinical Outcome in Auto-Inflammatory Familial Mediterranean Fever Patients

by May E. Zekry, Al-Aliaa M. Sallam, Sherihan G. AbdelHamid, Waheba A. Zarouk, Hala T. El-Bassyouni and Hala O. El-Mesallamy

Curr. Issues Mol. Biol. 2023, 45(1), 721-737; https://doi.org/10.3390/cimb45010048 - 13 Jan 2023

Cited by 3 | Viewed by 3455

Abstract

Epigenetic modifications play a pivotal role in autoimmune/inflammatory disorders and could establish a bridge between personalized medicine and disease epidemiological contexts. We sought to investigate the role of epigenetic modifications beside genetic alterations in the MEFV gene in familial Mediterranean fever (FMF). The [...] Read more.

Epigenetic modifications play a pivotal role in autoimmune/inflammatory disorders and could establish a bridge between personalized medicine and disease epidemiological contexts. We sought to investigate the role of epigenetic modifications beside genetic alterations in the MEFV gene in familial Mediterranean fever (FMF). The study comprised 63 FMF patients diagnosed according to the Tel Hashomer criteria: 37 (58.7%) colchicine-responders, 26 (41.3%) non-responders, and 19 matched healthy controls. MEFV mutations were detected using a CE/IVD-labeled 4-230 FMF strip assay. DNA methylation of MEFV gene exon 2 was measured using bisulfite modification and related to pyrin level, phenotypic picture, MEFV mutations, disease severity, serum amyloid A (SAA), CRP, ESR, disease severity, and colchicine response. Our results showed that FMF patients exhibited significantly higher methylation percentage (p < 0.001) and lower pyrin levels (p < 0.001) compared to the control. The MEFV gene M694I mutation was the most commonly reported mutation (p < 0.004). High methylation percentage of the MEFV exon 2 and low pyrin concentration were correlated with disease severity, high SAA, ESR levels, H-pylori, and renal calculi. In conclusion, this study highlights the relation between high methylation percentage, reduced pyrin level, and different biomarkers in FMF, which underscores their role in the pathogenesis of FMF and could be considered as potential therapeutic targets. Full article

(This article belongs to the Special Issue Complex Molecular Mechanism of Monogenic Diseases)

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22 pages, 3527 KiB

Open AccessArticle

Transcriptomic Analysis of Yunwu Tribute Tea Leaves under Cold Stress

by Ying Wang, Cheng Wan, Leijia Li, Zhun Xiang, Jihong Wang, Yan Li and Degang Zhao

Curr. Issues Mol. Biol. 2023, 45(1), 699-720; https://doi.org/10.3390/cimb45010047 - 13 Jan 2023

Cited by 4 | Viewed by 1985

Abstract

Background: Cold stress usually occurs in winter and is one of the most significant environmental factors restricting the growth of the tea plant as well as its geographical distribution. Objective: It is necessary to identify the physiological and molecular mechanisms of plants under [...] Read more.

Background: Cold stress usually occurs in winter and is one of the most significant environmental factors restricting the growth of the tea plant as well as its geographical distribution. Objective: It is necessary to identify the physiological and molecular mechanisms of plants under cold stress so that cold-tolerant crop varieties can be cultivated to limit production losses. At the same time, this would allow the crop planting area to be expanded, hence improving the economic benefits. Methods: In this study, the transcriptome data of Yunwu Tribute Tea under cold conditions were obtained using the Illumina HiSeq platform. By analyzing changes in transcriptome data associated with the antioxidant enzyme system, plant hormone signal transduction, proline and tyrosine metabolism pathways, and transcription factors, the molecular mechanisms involved in Yunwu Tribute Tea under cold stress were investigated. Results: In this study, Illumina HiSeq technology was applied to investigate the cold-tolerance mechanism. For this purpose, cDNA libraries were obtained from two groups of samples, namely the cold-treated group (DW) and the control group (CK). A total of 185,973 unigenes were produced from 511,987 assembled transcripts; among these, 16,020 differentially expressed genes (DEGs) (corrected p-value < 0.01, |log2(fold change)| >3), including 9606 up-regulated and 6414 down-regulated genes, were obtained. Moreover, the antioxidant enzyme system, plant hormone signal transduction, proline and tyrosine metabolism pathways, and transcription factors were analyzed; based on these results, a series of candidate genes related to cold stress were screened out and discussed. The physiological indexes related to the low-temperature response were tested, along with five DEGs which were validated by quantitative real-time PCR. Conclusions: Differential gene expression analysis has confirmed that substantial cold-responsive genes are related to the antioxidant enzyme system, plant hormone signal transduction, proline metabolism pathway, tyrosine metabolism pathway, and transcription factors. Full article

(This article belongs to the Special Issue Stress and Signal Transduction in Plants)

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14 pages, 1311 KiB

Open AccessReview

Garlic (Allium sativum L.) as an Ally in the Treatment of Inflammatory Bowel Diseases

by Silvana Zugaro, Elisabetta Benedetti and Giulia Caioni

Curr. Issues Mol. Biol. 2023, 45(1), 685-698; https://doi.org/10.3390/cimb45010046 - 11 Jan 2023

Cited by 16 | Viewed by 9176

Abstract

For centuries, garlic (Allium sativum) has been used both as a traditional remedy for most health-related ailments and for culinary purposes. Current preclinical investigations have suggested that dietary garlic intake has beneficial health effects, such as antioxidant, anti-inflammatory, antitumor, antiobesity, antidiabetic, [...] Read more.

For centuries, garlic (Allium sativum) has been used both as a traditional remedy for most health-related ailments and for culinary purposes. Current preclinical investigations have suggested that dietary garlic intake has beneficial health effects, such as antioxidant, anti-inflammatory, antitumor, antiobesity, antidiabetic, antiallergic, cardioprotective, and hepatoprotective effects. Its therapeutic potential is influenced by the methods of use, preparation, and extraction. Of particular importance is the Aged Garlic Extract (AGE). During the aging process, the odorous, sour, and irritating compounds in fresh raw garlic, such as allicin, are naturally converted into stable and safe compounds that have significantly greater therapeutic effects than fresh garlic. In AGE, S-allylcysteine (SAC) and S-allylmercaptocysteine (SAMC) are the major water-soluble organosulfurized compounds (OSCs). SAC has been extensively studied, demonstrating remarkable antioxidant, anti-inflammatory, and immunomodulatory capacities. Recently, AGE has been suggested as a promising candidate for the maintenance of immune system homeostasis through modulation of cytokine secretion, promotion of phagocytosis, and activation of macrophages. Since immune dysfunction plays an important role in the development and progress of various diseases, given the therapeutic effects of AGE, it can be thought of exploiting its immunoregulatory capacity to contribute to the treatment and prevention of chronic inflammatory bowel diseases (IBD). Full article

(This article belongs to the Special Issue Bioactives and Inflammation)

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8 pages, 364 KiB

Open AccessArticle

In Vitro Antiviral Evaluations of Coldmix^®: An Essential Oil Blend against SARS-CoV-2

by Kemal Hüsnü Can Başer, Ayşe Esra Karadağ, Sevde Nur Biltekin, Murat Ertürk and Fatih Demirci

Curr. Issues Mol. Biol. 2023, 45(1), 677-684; https://doi.org/10.3390/cimb45010045 - 11 Jan 2023

Viewed by 2467

Abstract

Coldmix^® is a commercially available Eucalyptus aetheroleum and, Abies aetheroleum blend for medicinal applications. In this present study, the in vitro antiviral potential of Coldmix^®, and its major constituents 1,8-cineole and α-pinene were evaluated by using the in vitro ACE2 [...] Read more.

Coldmix^® is a commercially available Eucalyptus aetheroleum and, Abies aetheroleum blend for medicinal applications. In this present study, the in vitro antiviral potential of Coldmix^®, and its major constituents 1,8-cineole and α-pinene were evaluated by using the in vitro ACE2 enzyme inhibition assay as well as the direct contact test against SARS-CoV-2. The observed ACE2 enzyme inhibitory activity of Coldmix^®, 1,8-cineole, and α-pinene were 72%, 88%, and 80%, respectively; whereas in the direct contact test in the vapor phase, the destruction of the virus was 79.9% within 5 min and 93.2% in the 30th min, respectively. In a similar Coldmix^® vapor phase setup using the in vitro cytotoxicity cell assay, E6 VERO healthy cells were experimentally not affected by toxicity. According to the promising initial antiviral results of Coldmix^® and the individually tested constituents, detailed further in vivo evaluation using different virus classes is suggested. Full article

(This article belongs to the Collection Application of Natural and Pseudo Natural Products in Drug Discovery and Development)

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14 pages, 1431 KiB

Open AccessArticle

Mapping QTLs for Super-Earliness and Agro-Morphological Traits in RILs Population Derived from Interspecific Crosses between Pisum sativum × P. fulvum

by Hatice Sari, Tuba Eker, Hilal Sule Tosun, Nedim Mutlu, Ibrahim Celik and Cengiz Toker

Curr. Issues Mol. Biol. 2023, 45(1), 663-676; https://doi.org/10.3390/cimb45010044 - 11 Jan 2023

Cited by 6 | Viewed by 2169

Abstract

Earliness in crop plants has a vital role in prevention of heat-induced drought stress and in combating global warming, which is predicted to exacerbate in the near future. Furthermore, earliness may expand production into northern areas or higher altitudes, having relatively shorter growing [...] Read more.

Earliness in crop plants has a vital role in prevention of heat-induced drought stress and in combating global warming, which is predicted to exacerbate in the near future. Furthermore, earliness may expand production into northern areas or higher altitudes, having relatively shorter growing season and may also expand arable lands to meet global food demands. The primary objective of the present study was to investigate quantitative trait loci (QTLs) for super-earliness and important agro-morphological traits in a recombinant inbred line (RIL) population derived from an interspecific cross. A population of 114 RILs developed through single-seed descent from an interspecific cross involving Pisum sativum L. and P. fulvum Sibth. et Sm. was evaluated to identify QTLs for super-earliness and important agro-morphological traits. A genetic map was constructed with 44 SSRs markers representing seven chromosomes with a total length of 262.6 cM. Of the 14 QTLs identified, two were for super-earliness on LG2, one for plant height on LG3, six for number of pods per plant on LG2, LG4, LG5 and LG6, one for number of seeds per pod on LG6, one for pod length on LG4 and three for harvest index on LG3, LG5, and LG6. AA205 and AA372-1 flanking markers for super-earliness QTLs were suggested for marker-assisted selection (MAS) in pea breeding programs due to high heritability of the trait. This is the first study to map QTLs originating from P. sativum and P. fulvum recently identified species with super-earliness character and the markers (AA205 and AA372-1) linked to QTLs were valuable molecular tools for pea breeding. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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14 pages, 2673 KiB

Open AccessReview

Molecular Mechanisms Underlying CRISPR/Cas-Based Assays for Nucleic Acid Detection

by Denis N. Antropov and Grigory A. Stepanov

Curr. Issues Mol. Biol. 2023, 45(1), 649-662; https://doi.org/10.3390/cimb45010043 - 10 Jan 2023

Cited by 4 | Viewed by 2919

Abstract

Applied to investigate specific sequences, nucleic acid detection assays can help identify novel bacterial and viral infections. Most up-to-date systems combine isothermal amplification with Cas-mediated detection. They surpass standard PCR methods in detection time and sensitivity, which is crucial for rapid diagnostics. The [...] Read more.

Applied to investigate specific sequences, nucleic acid detection assays can help identify novel bacterial and viral infections. Most up-to-date systems combine isothermal amplification with Cas-mediated detection. They surpass standard PCR methods in detection time and sensitivity, which is crucial for rapid diagnostics. The first part of this review covers the variety of isothermal amplification methods and describes their reaction mechanisms. Isothermal amplification enables fast multiplication of a target nucleic acid sequence without expensive laboratory equipment. However, researchers aim for more reliable results, which cannot be achieved solely by amplification because it is also a source of non-specific products. This motivated the development of Cas-based assays that use Cas9, Cas12, or Cas13 proteins to detect nucleic acids and their fragments in biological specimens with high specificity. Isothermal amplification yields a high enough concentration of target nucleic acids for the specific signal to be detected via Cas protein activity. The second part of the review discusses combinations of different Cas-mediated reactions and isothermal amplification methods and presents signal detection techniques adopted in each assay. Understanding the features of Cas-based assays could inform the choice of an optimal protocol to detect different nucleic acids. Full article

(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)

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21 pages, 4087 KiB

Open AccessArticle

Investigation of the Molecular Evolution of Treg Suppression Mechanisms Indicates a Convergent Origin

by Suniti Bhaumik, Marzena Łazarczyk, Norwin Kubick, Pavel Klimovich, Agata Gurba, Justyna Paszkiewicz, Patrycja Teodorowicz, Tomasz Kocki, Jarosław Olav Horbańczuk, Gina Manda, Mariusz Sacharczuk and Michel-Edwar Mickael

Curr. Issues Mol. Biol. 2023, 45(1), 628-648; https://doi.org/10.3390/cimb45010042 - 9 Jan 2023

Cited by 7 | Viewed by 2152

Abstract

Regulatory T cell (Treg) suppression of conventional T cells is a central mechanism that ensures immune system homeostasis. The exact time point of Treg emergence is still disputed. Furthermore, the time of Treg-mediated suppression mechanisms’ emergence has not been identified. It is not [...] Read more.

Regulatory T cell (Treg) suppression of conventional T cells is a central mechanism that ensures immune system homeostasis. The exact time point of Treg emergence is still disputed. Furthermore, the time of Treg-mediated suppression mechanisms’ emergence has not been identified. It is not yet known whether Treg suppression mechanisms diverged from a single pathway or converged from several sources. We investigated the evolutionary history of Treg suppression pathways using various phylogenetic analysis tools. To ensure the conservation of function for investigated proteins, we augmented our study using nonhomology-based methods to predict protein functions among various investigated species and mined the literature for experimental evidence of functional convergence. Our results indicate that a minority of Treg suppressor mechanisms could be homologs of ancient conserved pathways. For example, CD73, an enzymatic pathway known to play an essential role in invertebrates, is highly conserved between invertebrates and vertebrates, with no evidence of positive selection (w = 0.48, p-value < 0.00001). Our findings indicate that Tregs utilize homologs of proteins that diverged in early vertebrates. However, our findings do not exclude the possibility of a more evolutionary pattern following the duplication degeneration–complementation (DDC) model. Ancestral sequence reconstruction showed that Treg suppression mechanism proteins do not belong to one family; rather, their emergence seems to follow a convergent evolutionary pattern. Full article

(This article belongs to the Collection Feature Papers in Current Issues in Molecular Biology)

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14 pages, 3121 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of the Heat-Shock Protein Gene in L. edodes and Expression Pattern Analysis under Heat Shock

by Xu Zhao, Kaiyong Yin, Rencai Feng, Renyun Miao, Junbin Lin, Luping Cao, Yanqing Ni, Wensheng Li and Qin Zhang

Curr. Issues Mol. Biol. 2023, 45(1), 614-627; https://doi.org/10.3390/cimb45010041 - 9 Jan 2023

Cited by 6 | Viewed by 2366

Abstract

Lentinula edodes (L. edodes), one of the most popular edible mushrooms in China, is adversely affected by high temperature. Heat shock proteins (HSPs) play a crucial role in regulating the defense responses against the abiotic stresses in L. edodes. Some [...] Read more.

Lentinula edodes (L. edodes), one of the most popular edible mushrooms in China, is adversely affected by high temperature. Heat shock proteins (HSPs) play a crucial role in regulating the defense responses against the abiotic stresses in L. edodes. Some HSPs in L. edodes have been described previously, but a genome-wide analysis of these proteins is still lacking. Here, the HSP genes across the entire genome of the L. edodes mushroom were identified. The 34 LeHSP genes were subsequently classified into six subfamilies according to their molecular weights and the phylogenetic analysis. Sequence analysis showed that LeHSP proteins from the same subfamily have conserved domains and one to five similar motifs. Except for Chr 5 and 9, 34 LeHSPs genes were distributed on the other eight chromosomes. Three pairs of paralogs were identified because of sequence alignment and were confirmed as arising from segmental duplication. In LeHSPs’ promoters, different numbers of heat shock elements (HSEs) were predicted. The expression profiles of LeHSPs in 18N44 and 18 suggested that the thermo-tolerance of strain 18N44 might be related to high levels of LeHSPs transcript in response to heat stress. The quantitative real-time PCR (qRT-PCR) analysis of the 16 LeHSP genes in strains Le015 and Le027 verified their stress-inducible expression patterns under heat stress. Therefore, these comprehensive findings provide useful in-depth information on the evolution and function of LeHSPs and lay a theoretical foundation in breeding thermotolerant L. edodes varieties. Full article

(This article belongs to the Special Issue Microbial Engineering: Gene Expression Regulation and Its Application)

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10 pages, 1829 KiB

Open AccessCommunication

“Losing the Brakes”—Suppressed Inhibitors Triggering Uncontrolled Wnt/ß-Catenin Signaling May Provide a Potential Therapeutic Target in Elderly Acute Myeloid Leukemia

by Ghaleb Elyamany, Hassan Rizwan, Ariz Akhter, Mansour S. Aljabry, Sultan Alotaibi, Mohammad A. Hameed Albalawi, Meer-Taher Shabani-Rad, Tariq Mahmood Roshan and Adnan Mansoor

Curr. Issues Mol. Biol. 2023, 45(1), 604-613; https://doi.org/10.3390/cimb45010040 - 9 Jan 2023

Viewed by 2752

Abstract

Dysregulated Wnt/β-catenin signal transduction is implicated in initiation, propagation, and poor prognosis in AML. Epigenetic inactivation is central to Wnt/β-catenin hyperactivity, and Wnt/β-catenin inhibitors are being investigated as targeted therapy. Dysregulated Wnt/β-catenin signaling has also [...] Read more.

Dysregulated Wnt/β-catenin signal transduction is implicated in initiation, propagation, and poor prognosis in AML. Epigenetic inactivation is central to Wnt/β-catenin hyperactivity, and Wnt/β-catenin inhibitors are being investigated as targeted therapy. Dysregulated Wnt/β-catenin signaling has also been linked to accelerated aging. Since AML is a disease of old age (>60 yrs), we hypothesized age-related differential activity of Wnt/β-catenin signaling in AML patients. We probed Wnt/β-catenin expression in a series of AML in the elderly (>60 yrs) and compared it to a cohort of pediatric AML (<18 yrs). RNA from diagnostic bone marrow biopsies (n = 101) were evaluated for key Wnt/β-catenin molecule expression utilizing the NanoString platform. Differential expression of significance was defined as >2.5-fold difference (p < 0.01). A total of 36 pediatric AML (<18 yrs) and 36 elderly AML (>60 yrs) were identified in this cohort. Normal bone marrows (n = 10) were employed as controls. Wnt/β-catenin target genes (MYC, MYB, and RUNX1) showed upregulation, while Wnt/β-catenin inhibitors (CXXR, DKK1-4, SFRP1-4, SOST, and WIFI) were suppressed in elderly AML compared to pediatric AML and controls. Our data denote that suppressed inhibitor expression (through mutation or hypermethylation) is an additional contributing factor in Wnt/β-catenin hyperactivity in elderly AML, thus supporting Wnt/β-catenin inhibitors as potential targeted therapy. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Leukemia)

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11 pages, 2030 KiB

Open AccessArticle

Cooperative Binding of SRSF3 to Structured 3’ss-α Exon RNA during α Exon Inclusion in the ZO-1 mRNA

by Tea Anastasia Ruiz-Luis, Carlos Ortuño-Pineda, José Manuel Galindo-Rosales, Odila Saucedo-Cárdenas and Jesús Valdés

Curr. Issues Mol. Biol. 2023, 45(1), 593-603; https://doi.org/10.3390/cimb45010039 - 9 Jan 2023

Viewed by 2010

Abstract

ZO-1α+ and ZO-1α− proteins are expressed in hermetic and leaky tight junctions, respectively. Two cis-acting distant exonic elements partly activate the 240 nucleotide-long α exon producing the ZO-1α+ isoform. However, the elements within and around the α exon and their respective factors involved [...] Read more.

ZO-1α+ and ZO-1α− proteins are expressed in hermetic and leaky tight junctions, respectively. Two cis-acting distant exonic elements partly activate the 240 nucleotide-long α exon producing the ZO-1α+ isoform. However, the elements within and around the α exon and their respective factors involved in its splicing are unknown. To study the dynamic interaction between SRSF3 and its bioinformatically predicted target sites around the 3’ss upstream of the α exon during its activation, we performed EMSA, crosslinking, and in vivo splicing assays by ZO-1 minigene expression and siRNA-mediated silencing in transfected cells. Using V1 RNase, we probed the possible formation of a hairpin RNA structure between the intronic and proximal exonic SRSF3 binding sites. The hairpin sufficed for complex formations in the EMSA. The interaction of SRSF3 with the intronic site promoted the cooperative binding of SRSF3 to the exonic site. Finally, SRSF3 restored α exon activation in SRSF3 knockdown transfectants. Altogether, our results show that SRSF3–hairpin RNA interaction is crucial in the early recognition of 3’ss for α exon activation. It remains to be explored whether SRSF3 recruits or stabilizes the binding of other factors or brings separate splice sites into proximity. Full article

(This article belongs to the Special Issue Studying the Function of RNAs Using Omics Approaches)

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22 pages, 3690 KiB

Open AccessArticle

Cytochalasin B-Induced Membrane Vesicles from TRAIL-Overexpressing Mesenchymal Stem Cells Induce Extrinsic Pathway of Apoptosis in Breast Cancer Mouse Model

by Daria S. Chulpanova, Tamara V. Pukhalskaia, Zarema E. Gilazieva, Yuliya V. Filina, Milana N. Mansurova, Albert A. Rizvanov and Valeriya V. Solovyeva

Curr. Issues Mol. Biol. 2023, 45(1), 571-592; https://doi.org/10.3390/cimb45010038 - 9 Jan 2023

Cited by 4 | Viewed by 3444

Abstract

Tumor-necrosis-factor-associated apoptosis-inducing ligand (TRAIL) is one of the most promising therapeutic cytokines that selectively induce apoptosis in tumor cells. It is known that membrane vesicles (MVs) can carry the surface markers of parental cells. Therefore, MVs are of interest as a tool for [...] Read more.

Tumor-necrosis-factor-associated apoptosis-inducing ligand (TRAIL) is one of the most promising therapeutic cytokines that selectively induce apoptosis in tumor cells. It is known that membrane vesicles (MVs) can carry the surface markers of parental cells. Therefore, MVs are of interest as a tool for cell-free cancer therapy. In this study, membrane vesicles were isolated from TRAIL-overexpressing mesenchymal stem cells using cytochalasin B treatment (CIMVs). To evaluate the antitumor effect of CIMVs-TRAIL in vivo, a breast cancer mouse model was produced. The animals were intratumorally injected with 50 µg of native CIMVs or CIMVs-TRAIL for 12 days with an interval of two days. Then, tumor growth rate, tumor necrotic area, the expression of the apoptosis-related genes CASP8, BCL-2, and BAX and the level of CASP8 protein were analyzed. A 1.8-fold increase in the CAS8 gene mRNA and a 1.7-fold increase in the CASP8 protein level were observed in the tumors injected with CIMVs-TRAIL. The expression of the anti-apoptotic BCL-2 gene in the CIMV-TRAIL group remained unchanged, while the mRNA level of the pro-apoptotic BAX gene was increased by 1.4 times, which indicated apoptosis activation in the tumor tissue. Thus, CIMVs-TRAIL were able to activate the extrinsic apoptosis pathway and induce tumor cell death in the breast cancer mouse model. Full article

(This article belongs to the Special Issue Mesenchymal Stem Cells (MSC), Exosomes, and Other MSC Products in Research and Clinics)

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16 pages, 10172 KiB

Open AccessArticle

Deciphering the Mechanism of Wogonin, a Natural Flavonoid, on the Proliferation of Pulmonary Arterial Smooth Muscle Cells by Integrating Network Pharmacology and In Vitro Validation

by Lidan Cui, Zuomei Zeng, Xinyue Wang, Tianyi Yuan, Can Wang, Dianlong Liu, Jian Guo and Yucai Chen

Curr. Issues Mol. Biol. 2023, 45(1), 555-570; https://doi.org/10.3390/cimb45010037 - 8 Jan 2023

Cited by 3 | Viewed by 2861

Abstract

Wogonin is one of the main active components of Scutellaria baicalensis, which has anti-inflammatory, anti-angiogenesis, and anti-fibrosis effects. Nevertheless, the effect of wogonin on pulmonary hypertension (PH) still lacks systematic research. This study aims to elucidate the potential mechanism of wogonin against [...] Read more.

Wogonin is one of the main active components of Scutellaria baicalensis, which has anti-inflammatory, anti-angiogenesis, and anti-fibrosis effects. Nevertheless, the effect of wogonin on pulmonary hypertension (PH) still lacks systematic research. This study aims to elucidate the potential mechanism of wogonin against PH through network pharmacology and further verify it through biological experiments in pulmonary arterial smooth muscle cells (PASMCs). The potential targets and pathways of wogonin against PH were predicted and analyzed by network pharmacology methods and molecular docking technology. Subsequently, the proliferation of PASMCs was induced by platelet-derived growth factor-BB (PDGF-BB). Cell viability and migration ability were examined. The method of Western blot was adopted to analyze the changes in related signaling pathways. Forty potential targets related to the effect of wogonin against PH were obtained. Based on the protein–protein interaction (PPI) network, gene-ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment, and molecular docking, it was shown that the effect of wogonin against PH is closely related to the proliferation of PASMCs and the hypoxia-inducible factor-1α (HIF-1α) pathway. A variety of results from biological experiments verified that wogonin can effectively inhibit the proliferation, migration, and phenotypic transformation of PDGF-BB-mediated PASMCs. In addition, the anti-proliferation effect of wogonin may be achieved by regulating HIF-1/ NADPH oxidase 4 (NOX4) pathway. Full article

(This article belongs to the Collection Application of Natural and Pseudo Natural Products in Drug Discovery and Development)

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17 pages, 4527 KiB

Open AccessArticle

Magnolia kobus Extract Inhibits Periodontitis-Inducing Mediators in Porphyromonas gingivalis Lipopolysaccharide-Activated RAW 264.7 Cells

by Hae-Jin Lee, So-Jung Lee, Sung-Kwon Lee, Bong-Keun Choi and Dong-Ryung Lee

Curr. Issues Mol. Biol. 2023, 45(1), 538-554; https://doi.org/10.3390/cimb45010036 - 6 Jan 2023

Cited by 4 | Viewed by 2260

Abstract

Periodontitis, a disease caused by inflammation of oral bacteria, contributes to the loss of alveolar bone and destruction of connective tissues. Porphyromonas gingivalis, a Gram-negative bacterium, is known to possess important pathogenic factors for periodontal disease. In this study, we investigated the [...] Read more.

Periodontitis, a disease caused by inflammation of oral bacteria, contributes to the loss of alveolar bone and destruction of connective tissues. Porphyromonas gingivalis, a Gram-negative bacterium, is known to possess important pathogenic factors for periodontal disease. In this study, we investigated the anti-periodontitis effects of Magnolia kobus extract (MKE) and magnolin as a component of Magnolia kobus (MK) in murine macrophage RAW 264.7 cells stimulated with Porphyromonas gingivalis lipopolysaccharide (LPS). Effects of MKE and magnolin on the mechanism of RAW 264.7 cellular inflammation were determined by analyzing nitric oxide (NO) production and Western blot protein expression (n = 3). MKE/magnolin inhibited NO production without affecting cell survival. MKE/magnolin treatment inhibited LPS-induced pro-inflammatory cytokines, expression levels of matrix metalloproteinases (MMPs such as MMP-1, 3, 8, 9, and 13), and protein levels of inflammatory mediators (such as TNF-α, IL-1β, and mPGES-1). MKE/magnolin also suppressed NF-κB activation by inhibiting the TLR4 signaling pathway. These findings suggest that MKE has a therapeutic effect on inflammatory periodontal disease caused by oral bacterium P. gingivalis and that magnolin is a major functional component in the anti-inflammatory effect of MKE. Full article

(This article belongs to the Special Issue Advances in Research on Molecular Oral Microorganisms)

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14 pages, 3026 KiB

Open AccessArticle

Single Prolonged Stress Decreases the Level of Adult Hippocampal Neurogenesis in C57BL/6, but Not in House Mice

by Ekaterina Kurilova, Maria Sidorova and Oksana Tuchina

Curr. Issues Mol. Biol. 2023, 45(1), 524-537; https://doi.org/10.3390/cimb45010035 - 6 Jan 2023

Cited by 7 | Viewed by 2990

Abstract

Many people experience traumatic events during their lives, but not all of them develop severe mental pathologies, characterized by high levels of anxiety that persists for more than a month after psychological trauma, such as posttraumatic stress disorder (PTSD). We used a single [...] Read more.

Many people experience traumatic events during their lives, but not all of them develop severe mental pathologies, characterized by high levels of anxiety that persists for more than a month after psychological trauma, such as posttraumatic stress disorder (PTSD). We used a single prolonged stress protocol in order to model PTSD in long-inbred C57BL/6 and wild-derived (house) female mice. The susceptibility of mice to single prolonged stress was assessed by behavior phenotyping in the Open Field and Elevated Plus Maze, the level of neuroinflammation in the hippocampus was estimated by real-time PCR to TNFα, IL-1β, IL-6, IL-10, Iba1 and GFAP, as well as immunohistochemical analysis of microglial morphology and mean fluorescence intensity for GFAP+ cells. The level of neurogenesis was analyzed by real-time PCR to Ki67, Sox2 and DCX as well as immunohistochemistry to Ki67. We showed that long-inbread C57BL/6 mice are more susceptible to a single prolonged stress protocol compared to wild-derived (house) mice. Stressed C57BL/6 mice demonstrated elevated expression levels of proinflammatory cytokines TNFα, IL-1β, and IL-6 in the hippocampus, while in house mice no differences in cytokine expression were detected. Expression levels of Iba1 in the hippocampus did not change significantly after single prolonged stress, however GFAP expression increased substantially in stressed C57BL/6 mice. The number of Iba+ cells in the dentate gyrus also did not change after stress, but the morphology of Iba+ microglia in C57BL/6 animals allowed us to suggest that it was activated; house mice also had significantly more microglia than C57BL/6 animals. We suppose that decreased microglia levels in the hippocampus of C57BL/6 compared to house mice might be one of the reasons for their sensitivity to a single prolonged stress. Single prolonged stress reduced the number of Ki67+ proliferating cells in the dentate gyrus of the hippocampus but only in C57BL/6 mice, not in house mice, with the majority of cells detected in the dorsal (septal) hippocampus in both. The increase in the expression level of DCX might be a compensatory reaction to stress; however, it does not necessarily mean that these immature neurons will be functionally integrated, and this issue needs to be investigated further. Full article

(This article belongs to the Section Molecular Medicine)

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12 pages, 2305 KiB

Open AccessArticle

Semi-Site-Specific Primer PCR: A Simple but Reliable Genome-Walking Tool

by Cheng Wei, Zhiyu Lin, Jinfeng Pei, Hao Pan and Haixing Li

Curr. Issues Mol. Biol. 2023, 45(1), 512-523; https://doi.org/10.3390/cimb45010034 - 5 Jan 2023

Cited by 8 | Viewed by 2521

Abstract

Genome-walking has been frequently applied to molecular biology and related areas. Herein, a simple but reliable genome-walking technique, termed semi-site-specific primer PCR (3SP-PCR), is presented. The key to 3SP-PCR is the use of a semi-site-specific primer in secondary PCR that partially overlaps its [...] Read more.

Genome-walking has been frequently applied to molecular biology and related areas. Herein, a simple but reliable genome-walking technique, termed semi-site-specific primer PCR (3SP-PCR), is presented. The key to 3SP-PCR is the use of a semi-site-specific primer in secondary PCR that partially overlaps its corresponding primary site-specific primer. A 3SP-PCR set comprises two rounds of nested amplification reactions. In each round of reaction, any primer is allowed to partially anneal to the DNA template once only in the single relaxed-stringency cycle, creating a pool of single-stranded DNAs. The target single-stranded DNA can be converted into a double-stranded molecule directed by the site-specific primer, and thus can be exponentially amplified by the subsequent high-stringency cycles. The non-target one cannot be converted into a double-strand due to the lack of a perfect binding site to any primer, and thus fails to be amplified. We validated the 3SP-PCR method by using it to probe the unknown DNA regions of rice hygromycin genes and Levilactobacillus brevis CD0817 glutamic acid decarboxylase genes. Full article

(This article belongs to the Collection Feature Papers in Current Issues in Molecular Biology)

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11 pages, 2242 KiB

Open AccessArticle

Bridging PCR: An Efficient and Reliable Scheme Implemented for Genome-Walking

by Zhiyu Lin, Cheng Wei, Jinfeng Pei and Haixing Li

Curr. Issues Mol. Biol. 2023, 45(1), 501-511; https://doi.org/10.3390/cimb45010033 - 5 Jan 2023

Cited by 8 | Viewed by 2323

Abstract

The efficacy of the available genome-walking methods is restricted by low specificity, high background, or composite operations. We herein conceived bridging PCR, an efficient genome-walking approach. Three primers with random sequences, inner walker primer (IWP), bridging primer (BP), and outer walker primer (OWP), [...] Read more.

The efficacy of the available genome-walking methods is restricted by low specificity, high background, or composite operations. We herein conceived bridging PCR, an efficient genome-walking approach. Three primers with random sequences, inner walker primer (IWP), bridging primer (BP), and outer walker primer (OWP), are involved in bridging PCR. The BP is fabricated by splicing OWP to the 5′-end of IWP’s 5′-part. A bridging PCR set is constituted by three rounds of amplification reactions, sequentially performed by IWP, BP plus OWP, and OWP, respectively pairing with three nested sequence-specific primers (SSP). A non-target product arising from IWP alone undergoes end-lengthening mediated by BP. This modified non-target product is a preferentially formed hairpin between the lengthened ends, instead of binding with shorter OWP. Meanwhile, a non-target product, triggered by SSP alone or SSP plus IWP, is removed by nested SSP. As a result, only the target DNA is accumulated. The efficacy of bridging PCR was validated by walking the gadA/R genes of Levilactobacillus brevis CD0817 and the hyg gene of rice. Full article

(This article belongs to the Collection Feature Papers in Current Issues in Molecular Biology)

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11 pages, 3103 KiB

Open AccessArticle

The Expression of Testin, Ki-67 and p16 in Cervical Cancer Diagnostics

by Aneta Popiel-Kopaczyk, Jedrzej Grzegrzolka, Aleksandra Piotrowska, Mateusz Olbromski, Beata Smolarz, Hanna Romanowicz, Agnieszka Rusak, Monika Mrozowska, Piotr Dziegiel, Marzenna Podhorska-Okolow and Christopher Kobierzycki

Curr. Issues Mol. Biol. 2023, 45(1), 490-500; https://doi.org/10.3390/cimb45010032 - 5 Jan 2023

Cited by 8 | Viewed by 3283

Abstract

Testin is a protein expressed in normal human tissues, being responsible, with other cytoskeleton proteins, for the proper functioning of cell–cell junction areas and focal adhesion plaques. It takes part in the regulation of actin filament changes during cell spreading and motility. Loss [...] Read more.

Testin is a protein expressed in normal human tissues, being responsible, with other cytoskeleton proteins, for the proper functioning of cell–cell junction areas and focal adhesion plaques. It takes part in the regulation of actin filament changes during cell spreading and motility. Loss of heterozygosity in the testin-encoding gene results in altered protein expression in many malignancies, as partly described for cervical cancer. The aim of our study was the assessment of the immunohistochemical (IHC) expression of testin in cervical cancer and its analysis in regard to clinical data as well the expression of the Ki-67 antigen and p16 protein. Moreover, testin expression was assessed by Western blot (WB) in commercially available cell lines. The IHC analysis disclosed that the expression of testin inversely correlated with p16 (r = −0.2104, p < 0.0465) and Ki-67 expression (r = −0.2359, p < 0.0278). Moreover, weaker testin expression was observed in cancer cases vs. control ones (p < 0.0113). The WB analysis of testin expression in the cervical cancer cell lines corresponded to the IHC results and showed a weaker expression compared to that in the control cell line. When we compared the expression of testin in cervical cancer cell lines, we found a weaker expression in HPV-negative cell lines. In summary, we found that the intensity of testin expression and the number of positive cells inversely correlated with the expression of Ki-67 (a marker of proliferation) and p16 (a marker of cell cycle dysregulation). This study shows that the combined assessment of testin, Ki-67 and p16 expression may improve cervical cancer diagnostics. Full article

(This article belongs to the Special Issue Molecular Studies of Female Pregnancy Disorders)

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11 pages, 839 KiB

Open AccessArticle

Protective Effect of Vitamin D against Hepatic Molecular Apoptosis Caused by a High-Fat Diet in Rats

by Huda F. Alshaibi, Sherin Bakhashab, Asma Almuhammadi, Yusuf S. Althobaiti, Mohammed A. Baghdadi and Khadeejah Alsolami

Curr. Issues Mol. Biol. 2023, 45(1), 479-489; https://doi.org/10.3390/cimb45010031 - 5 Jan 2023

Cited by 3 | Viewed by 2343

Abstract

The protective effects of vitamin D (VitD) in different diseases were studied. The liver is of great interest, especially with the presence of VitD receptors. A high-fat diet (HFD) is associated with many diseases, including liver injury. Consumption of saturated fatty acids triggers [...] Read more.

The protective effects of vitamin D (VitD) in different diseases were studied. The liver is of great interest, especially with the presence of VitD receptors. A high-fat diet (HFD) is associated with many diseases, including liver injury. Consumption of saturated fatty acids triggers hepatic apoptosis and is associated with increased inflammation. We aimed in this study to investigate the protective effects of VitD on hepatic molecular apoptotic changes in response to an HFD in rats. Forty male Wistar albino rats were used and divided into four groups: control, HFD, control + VitD, and VitD-supplemented HFD (HFD + VitD) groups. After six months, the rats were sacrificed, and the livers were removed. RNA was extracted from liver tissues and used for the quantitative real-time RT-PCR of different genes: B-cell lymphoma/leukemia-2 (BCL2), BCL-2-associated X protein (Bax), Fas cell surface death receptor (FAS), FAS ligand (FASL), and tumor necrosis factor α (TNF-α). The results showed that an HFD increased the expression of the pro-apoptotic genes Bax, FAS, and FASL, and reduced the expression of the anti-apoptotic gene BCL2. Interestingly, a VitD-supplemented HFD significantly increased the BCL2 expression and decreased the expression of all pro-apoptotic genes and TNFα. In conclusion, VitD has a protective role against hepatic molecular apoptotic changes in response to an HFD. Full article

(This article belongs to the Special Issue Metabolic Reprogramming of Immune Cells in Tumor Microenvironment)

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14 pages, 751 KiB

Open AccessArticle

OPA1 Dominant Optic Atrophy: Diagnostic Approach in the Pediatric Population

by Natalia Arruti, Patricia Rodríguez-Solana, María Nieves-Moreno, Marta Guerrero-Carretero, Ángela del Pozo, Victoria E. F. Montaño, Fernando Santos-Simarro, Emi Rikeros-Orozco, Luna Delgado-Mora, Elena Vallespín and Susana Noval

Curr. Issues Mol. Biol. 2023, 45(1), 465-478; https://doi.org/10.3390/cimb45010030 - 5 Jan 2023

Cited by 1 | Viewed by 2764

Abstract

A clinical and genetic study was conducted with pediatric patients and their relatives with optic atrophy 1 (OPA1) mutations to establish whether there is a genotype–phenotype correlation among the variants detected within and between families. Eleven children with a confirmed OPA1 mutation [...] Read more.

A clinical and genetic study was conducted with pediatric patients and their relatives with optic atrophy 1 (OPA1) mutations to establish whether there is a genotype–phenotype correlation among the variants detected within and between families. Eleven children with a confirmed OPA1 mutation were identified during the study period. The main initial complaint was reduced visual acuity (VA), present in eight patients of the cohort. Eight of eleven patients had a positive family history of optic atrophy. The mean visual acuity at the start of the study was 0.40 and 0.44 LogMAR in the right and left eye, respectively. At the end of the study, the mean visual acuity was unchanged. Optical coherence tomography during the first visit showed a mean retinal nerve fiber layer thickness of 81.6 microns and 80.5 microns in the right and left eye, respectively; a mean ganglion cell layer of 52.5 and 52.4 microns, respectively, and a mean central macular thickness of 229.5 and 233.5 microns, respectively. The most common visual field defect was a centrocecal scotoma, and nine out of eleven patients showed bilateral temporal disc pallor at baseline. Sequencing of OPA1 showed seven different mutations in the eleven patients, one of which, NM_130837.3: c.1406_1407del (p.Thr469LysfsTer16), has not been previously reported. Early diagnosis of dominant optic atrophy is crucial, both for avoiding unnecessary consultations and/or treatments and for appropriate genetic counseling. Full article

(This article belongs to the Special Issue Complex Molecular Mechanism of Monogenic Diseases)

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31 pages, 6376 KiB

Open AccessArticle

Lung Cancer Gene Regulatory Network of Transcription Factors Related to the Hallmarks of Cancer

by Beatriz Andrea Otálora-Otálora, Liliana López-Kleine and Adriana Rojas

Curr. Issues Mol. Biol. 2023, 45(1), 434-464; https://doi.org/10.3390/cimb45010029 - 5 Jan 2023

Cited by 8 | Viewed by 3354

Abstract

The transcriptomic analysis of microarray and RNA-Seq datasets followed our own bioinformatic pipeline to identify a transcriptional regulatory network of lung cancer. Twenty-six transcription factors are dysregulated and co-expressed in most of the lung cancer and pulmonary arterial hypertension datasets, which makes them [...] Read more.

The transcriptomic analysis of microarray and RNA-Seq datasets followed our own bioinformatic pipeline to identify a transcriptional regulatory network of lung cancer. Twenty-six transcription factors are dysregulated and co-expressed in most of the lung cancer and pulmonary arterial hypertension datasets, which makes them the most frequently dysregulated transcription factors. Co-expression, gene regulatory, coregulatory, and transcriptional regulatory networks, along with fibration symmetries, were constructed to identify common connection patterns, alignments, main regulators, and target genes in order to analyze transcription factor complex formation, as well as its synchronized co-expression patterns in every type of lung cancer. The regulatory function of the most frequently dysregulated transcription factors over lung cancer deregulated genes was validated with ChEA3 enrichment analysis. A Kaplan–Meier plotter analysis linked the dysregulation of the top transcription factors with lung cancer patients’ survival. Our results indicate that lung cancer has unique and common deregulated genes and transcription factors with pulmonary arterial hypertension, co-expressed and regulated in a coordinated and cooperative manner by the transcriptional regulatory network that might be associated with critical biological processes and signaling pathways related to the acquisition of the hallmarks of cancer, making them potentially relevant tumor biomarkers for lung cancer early diagnosis and targets for the development of personalized therapies against lung cancer. Full article

(This article belongs to the Special Issue Molecular Research in Lung Cancer)

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34 pages, 9248 KiB

Open AccessReview

A Clinical Update on SARS-CoV-2: Pathology and Development of Potential Inhibitors

by Desh Deepak Singh, Ihn Han, Eun-Ha Choi and Dharmendra Kumar Yadav

Curr. Issues Mol. Biol. 2023, 45(1), 400-433; https://doi.org/10.3390/cimb45010028 - 4 Jan 2023

Cited by 5 | Viewed by 3107

Abstract

SARS-CoV-2 (severe acute respiratory syndrome) is highly infectious and causes severe acute respiratory distress syndrome (SARD), immune suppression, and multi-organ failure. For SARS-CoV-2, only supportive treatment options are available, such as oxygen supportive therapy, ventilator support, antibiotics for secondary infections, mineral and fluid [...] Read more.

SARS-CoV-2 (severe acute respiratory syndrome) is highly infectious and causes severe acute respiratory distress syndrome (SARD), immune suppression, and multi-organ failure. For SARS-CoV-2, only supportive treatment options are available, such as oxygen supportive therapy, ventilator support, antibiotics for secondary infections, mineral and fluid treatment, and a significant subset of repurposed effective drugs. Viral targeted inhibitors are the most suitable molecules, such as ACE2 (angiotensin-converting enzyme-2) and RBD (receptor-binding domain) protein-based inhibitors, inhibitors of host proteases, inhibitors of viral proteases 3CLpro (3C-like proteinase) and PLpro (papain-like protease), inhibitors of replicative enzymes, inhibitors of viral attachment of SARS-CoV-2 to the ACE2 receptor and TMPRSS2 (transmembrane serine proteinase 2), inhibitors of HR1 (Heptad Repeat 1)–HR2 (Heptad Repeat 2) interaction at the S2 protein of the coronavirus, etc. Targeting the cathepsin L proteinase, peptide analogues, monoclonal antibodies, and protein chimaeras as RBD inhibitors interferes with the spike protein’s ability to fuse to the membrane. Targeting the cathepsin L proteinase, peptide analogues, monoclonal antibodies, and protein chimaeras as RBD inhibitors interferes with the spike protein’s ability to fuse to the membrane. Even with the tremendous progress made, creating effective drugs remains difficult. To develop COVID-19 treatment alternatives, clinical studies are examining a variety of therapy categories, including antibodies, antivirals, cell-based therapy, repurposed diagnostic medicines, and more. In this article, we discuss recent clinical updates on SARS-CoV-2 infection, clinical characteristics, diagnosis, immunopathology, the new emergence of variant, SARS-CoV-2, various approaches to drug development and treatment options. The development of therapies has been complicated by the global occurrence of many SARS-CoV-2 mutations. Discussion of this manuscript will provide new insight into drug pathophysiology and drug development. Full article

(This article belongs to the Special Issue Drug Development and Repositioning Methodology on COVID-19)

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21 pages, 5868 KiB

Open AccessArticle

Characterization of Highbush Blueberry (Vaccinium corymbosum L.) Anthocyanin Biosynthesis Related MYBs and Functional Analysis of VcMYB Gene

by Yongyan Zhang, Dingquan Huang, Bin Wang, Xuelian Yang, Huan Wu, Pengyan Qu, Li Yan, Tao Li, Chunzhen Cheng and Dongliang Qiu

Curr. Issues Mol. Biol. 2023, 45(1), 379-399; https://doi.org/10.3390/cimb45010027 - 3 Jan 2023

Cited by 6 | Viewed by 2191

Abstract

As one of the most important transcription factors regulating plant anthocyanin biosynthesis, MYB has attracted great attentions. In this study, we identified fifteen candidate anthocyanin biosynthesis related MYB (ABRM) proteins, including twelve R2R3-MYBs and three 1R-MYBs, from highbush blueberry. The subcellular localization prediction [...] Read more.

As one of the most important transcription factors regulating plant anthocyanin biosynthesis, MYB has attracted great attentions. In this study, we identified fifteen candidate anthocyanin biosynthesis related MYB (ABRM) proteins, including twelve R2R3-MYBs and three 1R-MYBs, from highbush blueberry. The subcellular localization prediction results showed that, with the exception of VcRVE8 (localized in chloroplast and nucleus), all of the blueberry ABRMs were nucleus-localized. The gene structure analysis revealed that the exon numbers of the blueberry ABRM genes varied greatly, ranging between one and eight. There are many light-responsive, phytohormone-responsive, abiotic stress-responsive and plant growth and development related cis-acting elements in the promoters of the blueberry ABRM genes. It is noteworthy that almost all of their promoters contain light-, ABA- and MeJA-responsive elements, which is consistent with the well-established results that anthocyanin accumulation and the expression of MYBs are influenced significantly by many factors, such as light, ABA and JA. The gene expression analysis revealed that VcMYB, VcMYB6, VcMYB23, VcMYBL2 and VcPH4 are expressed abundantly in blueberry fruits, and VcMYB is expressed the highest in the red, purple and blue fruits among all blueberry ABRMs. VcMYB shared high similarity with functionally proven ABRMs from many other plant species. The gene cloning results showed that VcMYB had three variable transcripts, but only the transient overexpression of VcMYB-1 promoted anthocyanin accumulation in the green fruits. Our study can provide a basis for future research on the anthocyanin biosynthesis related MYBs in blueberry. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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15 pages, 3458 KiB

Open AccessArticle

Lavender Essential Oil Modulates Hepatic Cholesterol Metabolism in HepG2 Cells

by Noemi Martella, Mayra Colardo, William Sergio, Michele Petraroia, Michela Varone, Daniele Pensabene, Miriam Russo, Sabrina Di Bartolomeo, Giancarlo Ranalli, Gabriella Saviano and Marco Segatto

Curr. Issues Mol. Biol. 2023, 45(1), 364-378; https://doi.org/10.3390/cimb45010026 - 3 Jan 2023

Cited by 2 | Viewed by 3934

Abstract

Cholesterol is an essential lipid that guarantees several biological processes in eukaryotic cells. Its metabolism is regulated by a complex protein network that could be significantly influenced by numerous exogenous sources, such as essential oils (EOs). For instance, it has been speculated that [...] Read more.

Cholesterol is an essential lipid that guarantees several biological processes in eukaryotic cells. Its metabolism is regulated by a complex protein network that could be significantly influenced by numerous exogenous sources, such as essential oils (EOs). For instance, it has been speculated that monoterpenoid and sesquiterpenoid compounds contained in lavender essential oil (LEO) may exert important hypocholesterolemic activities. However, the molecular mechanisms by which LEO influences cholesterol homeostasis are not characterized. In this work, we evaluated the ability of LEO to regulate the protein network that controls cholesterol metabolism in the HepG2 cell line. The main findings indicate that LEO administration increases intracellular cholesterol content. Concurrently, LEO affects the expression of proteins involved in cholesterol uptake, biosynthesis, and trafficking. These effects are partially mediated by terpinene-4-ol, one of the most abundant compounds in LEO. These results demonstrate that LEO modulates cholesterol metabolism in hepatic cells. Full article

(This article belongs to the Collection Application of Natural and Pseudo Natural Products in Drug Discovery and Development)

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11 pages, 2204 KiB

Open AccessArticle

Iris Pallida Extract Alleviates Cortisol-Induced Decrease in Type 1 Collagen and Hyaluronic Acid Syntheses in Human Skin Cells

by Jung Ha Choo, Hong Gu Lee, So Young Lee and Nae Gyu Kang

Curr. Issues Mol. Biol. 2023, 45(1), 353-363; https://doi.org/10.3390/cimb45010025 - 1 Jan 2023

Cited by 3 | Viewed by 2919

Abstract

Excessive endogenous or exogenous levels of the stress hormone cortisol have negative effects on various tissues, including the skin. Iris pallida (IP), used in traditional medicine and perfumes, exhibits biological activities, such as antioxidant and anti-inflammatory activities. In this study, we aimed to [...] Read more.

Excessive endogenous or exogenous levels of the stress hormone cortisol have negative effects on various tissues, including the skin. Iris pallida (IP), used in traditional medicine and perfumes, exhibits biological activities, such as antioxidant and anti-inflammatory activities. In this study, we aimed to investigate the inhibitory effect of IP extract (IPE) on cortisol activity in human skin cells. We found that IPE alleviated the cortisol-induced decrease in the levels of procollagen type 1 and hyaluronic acid (HA), which were significantly recovered by 106% and 31%, respectively, compared with cortisol-induced reductions. IPE also rescued the suppression of the gene expression of COL1A1 and the HA synthases HAS2 and HAS3 in cortisol-exposed cells. Moreover, IPE blocked the cortisol-induced translocation of the glucocorticoid receptor (GR) from the cytoplasm to the nucleus as effectively as the GR inhibitor mifepristone. Analysis using a high-performance liquid chromatography–diode-array detector system revealed that irigenin, an isoflavone, is the main component of IPE, which restored the cortisol-induced reduction in collagen type 1 levels by 82% relative to the cortisol-induced decrease. Our results suggest that IPE can act as an inhibitor of cortisol in human skin cells, preventing cortisol-induced collagen and HA degradation by blocking the nuclear translocation of the GR. Therefore, IPE may be used as a cosmetic material or herbal medicine to treat stress-related skin changes. Full article

(This article belongs to the Special Issue Molecular Research in Chronic Dermatoses)

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16 pages, 28986 KiB

Open AccessArticle

Antioxidant, Anti-Apoptotic, and Anti-Inflammatory Effects of Farrerol in a Mouse Model of Obstructive Uropathy

by Jung-Yeon Kim, Jaechan Leem and Kwan-Kyu Park

Curr. Issues Mol. Biol. 2023, 45(1), 337-352; https://doi.org/10.3390/cimb45010024 - 1 Jan 2023

Cited by 1 | Viewed by 2258

Abstract

Obstructive uropathy is a clinical condition that can lead to chronic kidney disease. However, treatments that can prevent the progression of renal injury and fibrosis are limited. Farrerol (FA) is a natural flavone with potent antioxidant and anti-inflammatory properties. Here, we investigated the [...] Read more.

Obstructive uropathy is a clinical condition that can lead to chronic kidney disease. However, treatments that can prevent the progression of renal injury and fibrosis are limited. Farrerol (FA) is a natural flavone with potent antioxidant and anti-inflammatory properties. Here, we investigated the effect of FA on renal injury and fibrosis in a mouse model of unilateral ureteral obstruction (UUO). Mice underwent a sham or UUO operation and received intraperitoneal injections of FA (20 mg/kg) daily for 8 consecutive days. Histochemistry, immunohistochemistry and immunofluorescence staining, TdT-mediated dUTP nick end labeling assay, Western blotting, gene expression analysis, and biochemical tests were performed. FA attenuated renal dysfunction (p < 0.05) and ameliorated renal tubular injury (p < 0.01) and interstitial fibrosis (p < 0.001) in UUO mice. FA alleviated 4-hydroxynonenal expression (p < 0.001) and malondialdehyde levels (p < 0.01) by regulating pro-oxidant and antioxidant enzymes. Apoptosis in the kidneys of UUO mice was inhibited by FA (p < 0.001), and this action was accompanied by decreased expression of cleaved caspase-3 (p < 0.01). Moreover, FA alleviated pro-inflammatory cytokine production (p < 0.001) and macrophage infiltration (p < 0.01) in the kidneys of UUO mice. These results suggest that FA ameliorates renal injury and fibrosis in the UUO model by inhibiting oxidative stress, apoptosis, and inflammation. Full article

(This article belongs to the Special Issue Food-Derived Bioactive Compounds in Health and Disease)

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10 pages, 13835 KiB

Open AccessCommunication

Increased mTOR Signaling and Impaired Autophagic Flux Are Hallmarks of SARS-CoV-2 Infection

by Érika Pereira Zambalde, Thomaz Luscher Dias, Grazielle Celeste Maktura, Mariene R. Amorim, Bianca Brenha, Luana Nunes Santos, Lucas Buscaratti, João Gabriel de Angeli Elston, Mariana Camargo Silva Mancini, Isadora Carolina Betim Pavan, Daniel A. Toledo-Teixeira, Karina Bispo-dos-Santos, Pierina L. Parise, Ana Paula Morelli, Luiz Guilherme Salvino da Silva, Ícaro Maia Santos de Castro, Tatiana D. Saccon, Marcelo A. Mori, Fabiana Granja, Helder I. Nakaya, Jose Luiz Proenca-Modena, Henrique Marques-Souza and Fernando Moreira Simabuco Show full author list Hide full author list

Curr. Issues Mol. Biol. 2023, 45(1), 327-336; https://doi.org/10.3390/cimb45010023 - 31 Dec 2022

Cited by 4 | Viewed by 3290

Abstract

The COVID-19 (Coronavirus Disease 2019), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), severely affects mainly individuals with pre-existing comorbidities. Here our aim was to correlate the mTOR (mammalian/mechanistic Target of Rapamycin) and autophagy pathways with the disease severity. Through western [...] Read more.

The COVID-19 (Coronavirus Disease 2019), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), severely affects mainly individuals with pre-existing comorbidities. Here our aim was to correlate the mTOR (mammalian/mechanistic Target of Rapamycin) and autophagy pathways with the disease severity. Through western blotting and RNA analysis, we found increased mTOR signaling and suppression of genes related to autophagy, lysosome, and vesicle fusion in Vero E6 cells infected with SARS-CoV-2 as well as in transcriptomic data mining of bronchoalveolar epithelial cells from severe COVID-19 patients. Immunofluorescence co-localization assays also indicated that SARS-CoV-2 colocalizes within autophagosomes but not with a lysosomal marker. Our findings indicate that SARS-CoV-2 can benefit from compromised autophagic flux and inhibited exocytosis in individuals with chronic hyperactivation of mTOR signaling. Full article

(This article belongs to the Collection Feature Papers in Current Issues in Molecular Biology)

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Open AccessArticle

BSR and Full-Length Transcriptome Approaches Identified Candidate Genes for High Seed Ratio in Camellia vietnamensis

by Bing-Qing Hao, Hong-Ze Liao, Ying-Ying Xia, Dong-Xue Wang and Hang Ye

Curr. Issues Mol. Biol. 2023, 45(1), 311-326; https://doi.org/10.3390/cimb45010022 - 31 Dec 2022

Cited by 2 | Viewed by 1646

Abstract

(1) Background: C. vietnamensis is very suitable for growth in the low hilly areas of southern subtropical regions. Under appropriate conditions, the oil yield of C. vietnamensis can reach 1125 kg/ha (the existing varieties can reach 750 kg/ha). Moreover, the fruit of C. [...] Read more.

(1) Background: C. vietnamensis is very suitable for growth in the low hilly areas of southern subtropical regions. Under appropriate conditions, the oil yield of C. vietnamensis can reach 1125 kg/ha (the existing varieties can reach 750 kg/ha). Moreover, the fruit of C. vietnamensis is large and the pericarp is thick (>5 cm). Therefore, a high seed ratio has become the main target economic trait for the breeding of C. vietnamensis. (2) Methods: A half-sibling population of C. vietnamensis plants with a combination of high and low seed ratios was constructed by crossing a C. vietnamensis female parent. Bulked segregant RNA analysis and full-length transcriptome sequencing were performed to determine the molecular mechanisms underlying a high seed ratio. (3) Results: Seed ratio is a complex quantitative trait with a normal distribution, which is significantly associated with four other traits of fruit (seed weight, seed number, fruit diameter, and pericarp thickness). Two candidate regions related to high seed ratio (HSR) were predicted. One spanned 140.8–148.4 Mb of chromosome 2 and was associated with 97 seed-yield-related candidate genes ranging in length from 278 to 16,628 bp. The other spanned 35.3–37.3 Mb on chromosome 15 and was associated with 38 genes ranging in length from 221 to 16,928 bp. Using the full-length transcript as a template, a total of 115 candidate transcripts were obtained, and 78 transcripts were predicted to be functionally annotated. The DEGs from two set pairs of cDNA sequencing bulks were enriched to cytochrome p450 CYP76F14 (KOG0156; GO:0055114, HSR4, HSR7), the gibberellin phytohormone pathway (GO:0016787, HSR5), the calcium signaling pathway (GO:0005509, HSR6), the polyubiquitin-PPAR signaling pathway (GO:0005515, HSR2, HSR3), and several main transcription factors (bZIP transcription factor, HSR1) in C. vietnamensis. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants)

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Curr. Issues Mol. Biol., Volume 45, Issue 1 (January 2023) – 51 articles

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