Current Issues in Molecular Biology

20 pages, 7378 KiB

Open AccessArticle

Insight into the lncRNA–mRNA Co-Expression Profile and ceRNA Network in Lipopolysaccharide-Induced Acute Lung Injury

by Yue Shen, Linjing Gong, Fan Xu, Sijiao Wang, Hanhan Liu, Yali Wang, Lijuan Hu and Lei Zhu

Curr. Issues Mol. Biol. 2023, 45(7), 6170-6189; https://doi.org/10.3390/cimb45070389 - 24 Jul 2023

Cited by 2 | Viewed by 1680

Abstract

Long non-coding RNAs (lncRNAs) participate in acute lung injury (ALI). However, their latent biological function and molecular mechanism have not been fully understood. In the present study, the global expression profiles of lncRNAs and mRNAs between the control and lipopolysaccharide (LPS)-stimulated groups of [...] Read more.

Long non-coding RNAs (lncRNAs) participate in acute lung injury (ALI). However, their latent biological function and molecular mechanism have not been fully understood. In the present study, the global expression profiles of lncRNAs and mRNAs between the control and lipopolysaccharide (LPS)-stimulated groups of human normal lung epithelial cells (BEAS-2B) were determined using high-throughput sequencing. Overall, a total of 433 lncRNAs and 183 mRNAs were differentially expressed. A lncRNA–mRNA co-expression network was established, and then the top 10 lncRNAs were screened using topological methods. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis results showed that the key lncRNAs targeting mRNAs were mostly enriched in the inflammatory-related biological processes. Gene set variation analysis and Pearson’s correlation coefficients confirmed the close correlation for the top 10 lncRNAs with inflammatory responses. A protein–protein interaction network analysis was conducted based on the key lncRNAs targeting mRNAs, where IL-1β, IL-6, and CXCL8 were regarded as the hub genes. A competing endogenous RNA (ceRNA) modulatory network was created with five lncRNAs, thirteen microRNAs, and twelve mRNAs. Finally, real-time quantitative reverse transcription-polymerase chain reaction was employed to verify the expression levels of several key lncRNAs in BEAS-2B cells and human serum samples. Full article

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

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16 pages, 2669 KiB

Open AccessArticle

Identification of a Novel ERK5 (MAPK7) Inhibitor, MHJ-627, and Verification of Its Potent Anticancer Efficacy in Cervical Cancer HeLa Cells

by Jeonghye Hwang, Hyejin Moon, Hakwon Kim and Ki-Young Kim

Curr. Issues Mol. Biol. 2023, 45(7), 6154-6169; https://doi.org/10.3390/cimb45070388 - 24 Jul 2023

Cited by 3 | Viewed by 2478

Abstract

Extracellular signal-regulated kinase 5 (ERK5), a member of the mitogen-activated protein kinase (MAPK) family, is involved in key cellular processes. However, overexpression and upregulation of ERK5 have been reported in various cancers, and ERK5 is associated with almost every biological characteristic of cancer [...] Read more.

Extracellular signal-regulated kinase 5 (ERK5), a member of the mitogen-activated protein kinase (MAPK) family, is involved in key cellular processes. However, overexpression and upregulation of ERK5 have been reported in various cancers, and ERK5 is associated with almost every biological characteristic of cancer cells. Accordingly, ERK5 has become a novel target for the development of anticancer drugs as inhibition of ERK5 shows suppressive effects of the deleterious properties of cancer cells. Herein, we report the synthesis and identification of a novel ERK5 inhibitor, MHJ-627, and verify its potent anticancer efficacy in a yeast model and the cervical cancer HeLa cell line. MHJ-627 successfully inhibited the kinase activity of ERK5 (IC₅₀: 0.91 μM) and promoted the mRNA expression of tumor suppressors and anti-metastatic genes. Moreover, we observed significant cancer cell death, accompanied by a reduction in mRNA levels of the cell proliferation marker, proliferating cell nuclear antigen (PCNA), following ERK5 inhibition due to MHJ-627 treatment. We expect this finding to serve as a lead compound for further identification of inhibitors for ERK5-directed novel approaches for oncotherapy with increased specificity. Full article

(This article belongs to the Special Issue Advanced Molecular Solutions for Cancer Therapy)

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14 pages, 11567 KiB

Open AccessArticle

Interactions of piRNAs with the mRNA of Candidate Genes in Esophageal Squamous Cell Carcinoma

by Aizhan Rakhmetullina, Aigul Akimniyazova, Togzhan Niyazova, Anna Pyrkova, Makpal Tauassarova, Anatoliy Ivashchenko and Piotr Zielenkiewicz

Curr. Issues Mol. Biol. 2023, 45(7), 6140-6153; https://doi.org/10.3390/cimb45070387 - 23 Jul 2023

Cited by 2 | Viewed by 1728

Abstract

Recently, a database of human piRNAs (piwi-interacting RNAs) was created, which allows the study of the binding of many piRNAs to the mRNAs of genes involved in many diseases, including cancer. In the present work, we identified the piRNAs that can interact with [...] Read more.

Recently, a database of human piRNAs (piwi-interacting RNAs) was created, which allows the study of the binding of many piRNAs to the mRNAs of genes involved in many diseases, including cancer. In the present work, we identified the piRNAs that can interact with candidate esophageal squamous cell carcinoma (ESCC) genes. The binding of 480 thousand piRNAs with the mRNAs of 66 candidate ESCC genes was studied. Bioinformatic studies found that piRNAs bind only to the mRNAs of nine candidate genes: AURKA, BMP7, GCOM1, ERCC1, MTHFR, SASH1, SIX4, SULT1A1, and TP53. It has been shown that piRNAs can bind to mRNA by overlapping nucleotide sequences in limited 3′UTR and 5′UTR regions called clusters of binding sites (BSs). The existence of clusters of piRNA BSs significantly reduces the proportion of the nucleotide sequences of these sites in the mRNA of target genes. Competition between piRNAs occurs for binding to the mRNA of target genes. Individual piRNAs and groups of piRNAs that have separate BSs and clusters of BSs in the mRNAs of two or more candidate genes have been identified in the mRNAs of these genes. This organization of piRNAs BSs indicates the interdependence of the expression of candidate genes through piRNAs. Significant differences in the ability of genes to interact with piRNAs prevent the side effects of piRNAs on genes with a lack of the ability to bind such piRNAs. Individual piRNAs and sets of piRNAs are proposed and recommended for the diagnosis and therapy of ESCC. Full article

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

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24 pages, 34881 KiB

Open AccessArticle

Small Leucine-Rich Proteoglycan PODNL1 Identified as a Potential Tumor Matrix-Mediated Biomarker for Prognosis and Immunotherapy in a Pan-Cancer Setting

by Geyang Dai, Yue Sun, Rui Wei and Ling Xi

Curr. Issues Mol. Biol. 2023, 45(7), 6116-6139; https://doi.org/10.3390/cimb45070386 - 22 Jul 2023

Cited by 2 | Viewed by 2217

Abstract

The podocan-like protein 1 (PODNL1), an important member of the small leucine-rich proteoglycans (SLRP) family, is a crucial component of the tumor microenvironment (TME). But its prognostic values and the role in the TME have not been systematically estimated in a pan-cancer setting. [...] Read more.

The podocan-like protein 1 (PODNL1), an important member of the small leucine-rich proteoglycans (SLRP) family, is a crucial component of the tumor microenvironment (TME). But its prognostic values and the role in the TME have not been systematically estimated in a pan-cancer setting. Targeting PODNL1, a systematic exploration into the TCGA datasets, reconciling with the analyses of single-cell transcriptomes and immunotherapeutic cohorts in cancers, and validation by tissue microarray-based multiplex immunofluorescence staining was performed. PODNL1 was significantly correlated with the poor prognosis and immunotherapeutic responses in various cancers. In-depth demonstration of molecular mechanisms indicated that PODNL1 expressions were notably positively correlated with cancer-associated fibroblast (CAF) infiltration levels in 33 types of cancers. It also positively correlated with the pan-fibroblast TGF-β response signature score, and the hallmarks including TGF-β, TNF-α, inflammatory response, apical junction, epithelial–mesenchymal transition and hedgehog in pan-cancer. Furthermore, high PODNL1 expressions were positively related with the regulation of tumor-promoting TGF-β signaling through downregulating SMAD2/3:4 heterotrimer regulations transcription and up-regulating the pathway restricted SMAD protein phosphorylation. Single-cell transcriptome analyses and immunofluorescence validations indicated that PODNL1 was predominantly expressed in the cancer cells and CAFs in various cancers. Additionally, the heterogeneity of cancer genotype–phenotype cross-talking was also observed associated with PODNL1. Our systematic study indicates that PODNL1 plays an important role in the complex regulation network of tumor progression, and lays a foundation for further exploration to develop PODNL1 as a valuable matrix-mediated biomarker for cancer immunotherapy and prognosis in a pan-cancer setting. Full article

(This article belongs to the Special Issue Targeting Tumor Microenvironment for Cancer Therapy, 2nd Edition)

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19 pages, 3934 KiB

Open AccessArticle

Structural Analysis of Mitochondria in Cardiomyocytes: Insights into Bioenergetics and Membrane Remodeling

by Raquel A. Adams, Zheng Liu, Chongere Hsieh, Michael Marko, W. Jonathan Lederer, M. Saleet Jafri and Carmen Mannella

Curr. Issues Mol. Biol. 2023, 45(7), 6097-6115; https://doi.org/10.3390/cimb45070385 - 21 Jul 2023

Cited by 3 | Viewed by 2521

Abstract

Mitochondria in mammalian cardiomyocytes display considerable structural heterogeneity, the significance of which is not currently understood. We use electron microscopic tomography to analyze a dataset of 68 mitochondrial subvolumes to look for correlations among mitochondrial size and shape, crista morphology and membrane density, [...] Read more.

Mitochondria in mammalian cardiomyocytes display considerable structural heterogeneity, the significance of which is not currently understood. We use electron microscopic tomography to analyze a dataset of 68 mitochondrial subvolumes to look for correlations among mitochondrial size and shape, crista morphology and membrane density, and organelle location within rat cardiac myocytes. A tomographic analysis guided the definition of four classes of crista morphology: lamellar, tubular, mixed and transitional, the last associated with remodeling between lamellar and tubular cristae. Correlations include an apparent bias for mitochondria with lamellar cristae to be located in the regions between myofibrils and a two-fold larger crista membrane density in mitochondria with lamellar cristae relative to mitochondria with tubular cristae. The examination of individual cristae inside mitochondria reveals local variations in crista topology, such as extent of branching, alignment of fenestrations and progressive changes in membrane morphology and packing density. The findings suggest both a rationale for the interfibrillar location of lamellar mitochondria and a pathway for crista remodeling from lamellar to tubular morphology. Full article

(This article belongs to the Special Issue Mitochondrial Function and Dysfunction)

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12 pages, 573 KiB

Open AccessReview

Exosome Analysis in Prostate Cancer: How They Can Improve Biomarkers’ Performance

by Stefano Salciccia, Marco Frisenda, Giulio Bevilacqua, Luca Gobbi, Bruno Bucca, Martina Moriconi, Pietro Viscuso, Alessandro Gentilucci, Gianna Mariotti, Susanna Cattarino, Flavio Forte, Stefano Fais, Mariantonia Logozzi, Beatrice Sciarra and Alessandro Sciarra

Curr. Issues Mol. Biol. 2023, 45(7), 6085-6096; https://doi.org/10.3390/cimb45070384 - 21 Jul 2023

Cited by 5 | Viewed by 2391

Abstract

Exosomes are extracellular nanovesicles (EV), that is, carriers of different biomolecules such as lipids, proteins, nucleic acids. Their composition and the fact that their release dramatically increases in cases of tumorigenesis open up different scenarios on their possible application to research into new [...] Read more.

Exosomes are extracellular nanovesicles (EV), that is, carriers of different biomolecules such as lipids, proteins, nucleic acids. Their composition and the fact that their release dramatically increases in cases of tumorigenesis open up different scenarios on their possible application to research into new biomarkers. The first purpose of the present review was to specifically analyze and compare different methodologies available for the use of exosomes in prostate cancer (PC). The most widely applied methodologies include ultracentrifugation techniques, size-based techniques, immunoaffinity capture-based techniques (mainly ELISA), and precipitation. To optimize the acquisition of exosomes from the reference sample, more techniques can be applied in sequence for a single extraction, thereby determining an increase in labor time and costs. The second purpose was to describe clinical results obtained with the analysis of PSA-expressing exosomes in PC; this provides an incredibly accurate method of discriminating between healthy patients and those with prostate disease. Specifically, the IC-ELISA alone method achieved 98.57% sensitivity and 80.28% specificity in discriminating prostate cancer (PC) from benign prostatic hyperplasia (BPH). An immunocapture-based ELISA assay was performed to quantify and characterize carbonic anhydrase (CA) IX expression in exosomes. The results revealed that CA IX positive exosomes were 25-fold higher in plasma samples from PC patients than in those from healthy controls. The analysis of PC-linked exosomes represents a promising diagnostic model that can effectively distinguish patients with PC from those with non-malignant prostatic disease. However, the use of exosome analysis in clinical practice is currently limited by several issues, including a lack of standardization in the analytical process and high costs, which are still too high for large-scale use. Full article

(This article belongs to the Special Issue Exosomes in Cancers)

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18 pages, 12742 KiB

Open AccessArticle

Whole Transcriptome Analysis of Intervention Effect of Sophora subprostrate Polysaccharide on Inflammation in PCV2 Infected Murine Splenic Lymphocytes

by Yi Zhao, Nina Jia, Xiaodong Xie, Qi Chen and Tingjun Hu

Curr. Issues Mol. Biol. 2023, 45(7), 6067-6084; https://doi.org/10.3390/cimb45070383 - 20 Jul 2023

Cited by 2 | Viewed by 1632

Abstract

(1) Background: Sophora subprostrate, is the dried root and rhizome of Sophora tonkinensis Gagnep. Sophora subprostrate polysaccharide (SSP1) was extracted from Sophora subprostrate, which has shown good anti-inflammatory and antioxidant effects. Previous studies showed SSP1 could modulate inflammatory damage induced by [...] Read more.

(1) Background: Sophora subprostrate, is the dried root and rhizome of Sophora tonkinensis Gagnep. Sophora subprostrate polysaccharide (SSP1) was extracted from Sophora subprostrate, which has shown good anti-inflammatory and antioxidant effects. Previous studies showed SSP1 could modulate inflammatory damage induced by porcine circovirus type 2 (PCV2) in murine splenic lymphocytes, but the specific regulatory mechanism is unclear. (2) Methods: Whole transcriptome analysis was used to characterize the differentially expressed mRNA, lncRNA, and miRNA in PCV2-infected cells and SSP1-treated infected cells. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and other analyses were used to screen for key inflammation-related differentially expressed genes. The sequencing results were verified by RT-qPCR, and western blot was used to verify the key protein in main enriched signal pathways. (3) Results: SSP1 can regulate inflammation-related gene changes induced by PCV2, and its interventional mechanism is mainly involved in the key differential miRNA including miR-7032-y, miR-328-y, and miR-484-z. These inflammation-related genes were mainly enriched in the TNF signal pathway and NF-κB signal pathway, and SSP1 could significantly inhibit the protein expression levels of p-IκB, p-p65, TNF-α, IRF1, GBP2 and p-SAMHD1 to alleviate inflammatory damage. (4) Conclusions: The mechanism of SSP1 regulating PCV2-induced murine splenic lymphocyte inflammation was explored from a whole transcriptome perspective, which provides a theoretical basis for the practical application of SSP1. Full article

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

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12 pages, 1350 KiB

Open AccessArticle

Molecular Characterisation of Mycobacterium bovis Isolates from Cattle Slaughtered in Adamawa and Gombe States, North-Eastern Nigeria

by Sadiq Mohammed Damina, David Atomanyi Barnes, Bitrus Inuwa, Gulak Hussaini Ularamu, Mohammed Bello, Olu Solomon Okaiyeto, Ayuba Caleb Kudi, Jeewan Thapa, Chie Nakajima and Yasuhiko Suzuki

Curr. Issues Mol. Biol. 2023, 45(7), 6055-6066; https://doi.org/10.3390/cimb45070382 - 19 Jul 2023

Cited by 1 | Viewed by 1532

Abstract

Bovine tuberculosis is endemic in Nigeria with control measures as provided by the laws of the country being minimally enforced mostly at the abattoirs only. This study focused on bovine tuberculosis in Adamawa and Gombe States. Tuberculosis lesions were observed in 183 of [...] Read more.

Bovine tuberculosis is endemic in Nigeria with control measures as provided by the laws of the country being minimally enforced mostly at the abattoirs only. This study focused on bovine tuberculosis in Adamawa and Gombe States. Tuberculosis lesions were observed in 183 of 13,688 slaughtered cattle in the regions between June and December 2020. Analysis of tissue samples resulted in 17 Mycobacterium bovis isolates, predominantly from Gombe State. Spoligotyping identified four spoligotypes, including SB0944, SB1025, SB1104, and one novel pattern. MIRU-VNTR analysis further differentiated these spoligotypes into eight profiles. All isolates belonged to the Af1 clonal complex. The study emphasises the need for broader coverage and more isolates to comprehensively understand the molecular epidemiology of bovine tuberculosis in Nigeria. To enhance research and surveillance, a cost-effective approach is proposed, utilising a discriminatory VNTR panel comprising five or nine loci. The five-locus panel consists of ETR-C, QUB26, QUB11b, MIRU04, and QUB323. Alternatively, the nine-locus panel includes ETR-A, ETR-B, QUB11a, and MIRU26. Implementing this approach would provide valuable insights into the genetic diversity of M. bovis strains in Nigeria. These findings are crucial for developing effective control measures and minimising the impact of bovine tuberculosis on both animal and human health. Full article

(This article belongs to the Special Issue Human and Animal Infectious Diseases: Prevention, Diagnosis, and Treatment)

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15 pages, 1644 KiB

Open AccessArticle

EMT Features in Claudin-Low versus Claudin-Non-Suppressed Breast Cancers and the Role of Epigenetic Modifications

by Ioannis A. Voutsadakis

Curr. Issues Mol. Biol. 2023, 45(7), 6040-6054; https://doi.org/10.3390/cimb45070381 - 19 Jul 2023

Cited by 2 | Viewed by 1606

Abstract

Background: Breast cancers are heterogeneous and are classified according to the expression of ER, PR and HER2 receptors to distinct groups with prognostic and therapeutic implications. Within the triple-negative group, with no expression of these three receptors, molecular heterogeneity exists but is currently [...] Read more.

Background: Breast cancers are heterogeneous and are classified according to the expression of ER, PR and HER2 receptors to distinct groups with prognostic and therapeutic implications. Within the triple-negative group, with no expression of these three receptors, molecular heterogeneity exists but is currently not exploited in the clinic. The claudin-low phenotype is present in a subset of triple-negative breast cancers and constitutes together with basal-like cancers the most extensive groups within triple-negative breast cancers. Suppression of epithelial cell adhesion molecules in claudin-low cancers is also a hallmark of Epithelial Mesenchymal Transition (EMT). Methods: The groups of claudin-low and claudin-non-suppressed breast cancers from the extensive publicly available genomic cohorts of the METABRIC study were examined to delineate and compare their molecular landscape. Genetic and epigenetic alterations of key factors involved in EMT and potentially associated with the pathogenesis of the claudin-low phenotype were analyzed in the two groups. Results: Claudin-low cancers displayed up-regulation of several core transcription factors of EMT at the mRNA level, compared with claudin-non-suppressed breast cancers. Global promoter DNA methylation was increased in both groups of triple-negative cancers and in claudin-low ER-positive cancers compared with the rest of ER-positive cancers. Histone modifier enzymes, including methyltransferases, demethylases, acetyltransferases and deacetylases displayed amplifications more frequently in claudin-non-suppressed triple-negative cancers than in claudin-low counterparts and the expression of some of these enzymes differed significantly between the two groups. Conclusion: Claudin-low and claudin-non-suppressed triple-negative breast cancers differ in their landscape of EMT core regulators and epigenetic regulators. These differences may be explored as targets for therapeutic interventions specific to the two groups of triple-negative breast cancers. Full article

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

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16 pages, 2355 KiB

Open AccessArticle

X-rays Stimulate Granular Secretions and Activate Protein Kinase C Signaling in Human Platelets

by Muhammad Shoaib Khan, Chunliang Liu, Fanbi Meng, Mengnan Yang, Kangxi Zhou, Renping Hu, Xuexiang Wang and Kesheng Dai

Curr. Issues Mol. Biol. 2023, 45(7), 6024-6039; https://doi.org/10.3390/cimb45070380 - 19 Jul 2023

Cited by 3 | Viewed by 1849

Abstract

X-rays can induce morphological as well as functional changes in cells. Platelets are anuclear cellular fragments originating from megakaryocytes and are the major regulators in hemostasis and thrombosis. Platelet products are irradiated to avoid medical complications associated with platelet transfusion. So far, gamma, [...] Read more.

X-rays can induce morphological as well as functional changes in cells. Platelets are anuclear cellular fragments originating from megakaryocytes and are the major regulators in hemostasis and thrombosis. Platelet products are irradiated to avoid medical complications associated with platelet transfusion. So far, gamma, UV, and laser radiation have been used for this purpose. However, scientists are divided about the effects of radiation on platelet quality. The present study was designed to explore the possible effects of X-rays in washed human platelets and understand the molecular mechanism behind them. In the present study, we exposed washed human platelets to 10 or 30 Gy X-rays at 0.25 Gy/min. Flow cytometry, aggregometry, and western blot were performed to investigate the effect of X-rays on platelet degranulation, integrin activation, platelet aggregation, and apoptosis. It was found that X-rays immediately induced granular secretions with no effect on GP IIb/IIIa activation. Not surprisingly, due to granule secretions in irradiated platelets, platelet aggregation was significantly reduced. In contrast to granular secretions and platelet aggregation, X-rays induced mitochondrial transmembrane potential depolarization in a time-dependent manner to induce apoptosis and activated protein kinase C (PKC) signaling. This study revealed and explained the molecular mechanism activated by X-rays in washed human platelets. Here we also introduced Gö 6983, a PKC inhibitor, as an agent that counteracts X-ray-induced changes and maintains the integrity of platelets. Full article

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

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21 pages, 1517 KiB

Open AccessArticle

A Clinical Qualification Protocol Highlights Overlapping Genomic Influences and Neuro-Autonomic Mechanisms in Ehlers–Danlos and Long COVID-19 Syndromes

by Golder N. Wilson

Curr. Issues Mol. Biol. 2023, 45(7), 6003-6023; https://doi.org/10.3390/cimb45070379 - 17 Jul 2023

Cited by 3 | Viewed by 3422

Abstract

A substantial fraction of the 15% with double-jointedness or hypermobility have the traditionally ascertained joint-skeletal, cutaneous, and cardiovascular symptoms of connective tissue dysplasia and its particular manifestation as Ehlers–Danlos syndrome (EDS). The holistic ascertainment of 120 findings in 1261 EDS patients added neuro-autonomic [...] Read more.

A substantial fraction of the 15% with double-jointedness or hypermobility have the traditionally ascertained joint-skeletal, cutaneous, and cardiovascular symptoms of connective tissue dysplasia and its particular manifestation as Ehlers–Danlos syndrome (EDS). The holistic ascertainment of 120 findings in 1261 EDS patients added neuro-autonomic symptoms like headaches, muscle weakness, brain fog, chronic fatigue, dyspnea, and bowel irregularity to those of arthralgia and skin laxity, 15 of these symptoms shared with those of post-infectious SARS-CoV-2 (long COVID-19). Underlying articulo-autonomic mechanisms guided a clinical qualification protocol that qualified DNA variants in 317 genes as having diagnostic utility for EDS, six of them identical (F2-LIFR-NLRP3-STAT1-T1CAM1-TNFRSF13B) and eighteen similar to those modifying COVID-19 severity/EDS, including ADAMTS13/ADAMTS2-C3/C1R-IKBKG/IKBKAP-PIK3C3/PIK3R1-POLD4/POLG-TMPRSS2/TMPRSS6-WNT3/WNT10A. Also, contributing to EDS and COVID-19 severity were forty and three genes, respectively, impacting mitochondrial functions as well as parts of an overlapping gene network, or entome, that are hypothesized to mediate the cognitive–behavioral, neuro-autonomic, and immune-inflammatory alterations of connective tissue in these conditions. The further characterization of long COVID-19 natural history and genetic predisposition will be necessary before these parallels to EDS can be carefully delineated and translated into therapies. Full article

(This article belongs to the Special Issue Tailored Molecular and Pathophysiological Approach to COVID-19: Ambition and Need)

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22 pages, 1206 KiB

Open AccessReview

The Role of Genetic Risk Factors in Pathogenesis of Childhood-Onset Systemic Lupus Erythematosus

by Mario Sestan, Nastasia Kifer, Todor Arsov, Matthew Cook, Julia Ellyard, Carola G. Vinuesa and Marija Jelusic

Curr. Issues Mol. Biol. 2023, 45(7), 5981-6002; https://doi.org/10.3390/cimb45070378 - 17 Jul 2023

Cited by 7 | Viewed by 3496

Abstract

The pathogenesis of childhood-onset systemic lupus erythematosus (cSLE) is complex and not fully understood. It involves three key factors: genetic risk factors, epigenetic mechanisms, and environmental triggers. Genetic factors play a significant role in the development of the disease, particularly in younger individuals. [...] Read more.

The pathogenesis of childhood-onset systemic lupus erythematosus (cSLE) is complex and not fully understood. It involves three key factors: genetic risk factors, epigenetic mechanisms, and environmental triggers. Genetic factors play a significant role in the development of the disease, particularly in younger individuals. While cSLE has traditionally been considered a polygenic disease, it is now recognized that in rare cases, a single gene mutation can lead to the disease. Although these cases are uncommon, they provide valuable insights into the disease mechanism, enhance our understanding of pathogenesis and immune tolerance, and facilitate the development of targeted treatment strategies. This review aims to provide a comprehensive overview of both monogenic and polygenic SLE, emphasizing the implications of specific genes in disease pathogenesis. By conducting a thorough analysis of the genetic factors involved in SLE, we can improve our understanding of the underlying mechanisms of the disease. Furthermore, this knowledge may contribute to the identification of effective biomarkers and the selection of appropriate therapies for individuals with SLE. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Regulation in Allergy and Immune Diseases, Immunodeficiencies)

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14 pages, 7124 KiB

Open AccessArticle

Alveolar Bone Preservation Using a Combination of Nanocrystalline Hydroxyapatite and Injectable Platelet-Rich Fibrin: A Study in Rats

by Andries Pascawinata, Gusti Revilla, Roni Eka Sahputra and Syukri Arief

Curr. Issues Mol. Biol. 2023, 45(7), 5967-5980; https://doi.org/10.3390/cimb45070377 - 17 Jul 2023

Cited by 1 | Viewed by 1530

Abstract

Alveolar bone resorption is a post-extraction complication wherein there is a reduction in the dimensions and quality of the alveolar bone. This study aimed to examine the effects of implantation of a combination of nanocrystalline hydroxyapatite (nHA) and injectable platelet-rich fibrin (IPRF) on [...] Read more.

Alveolar bone resorption is a post-extraction complication wherein there is a reduction in the dimensions and quality of the alveolar bone. This study aimed to examine the effects of implantation of a combination of nanocrystalline hydroxyapatite (nHA) and injectable platelet-rich fibrin (IPRF) on the expression of tartrate-resistant acid phosphatase (TRAP), alkaline phosphatase (ALP), osteocalcin (OCN), and new bone formation. A total of 32 male rats had their upper right incisors extracted under general anesthesia and were then divided into a control group, nHA group, IPRF group, and nHA-IPRF group. Decapitation was carried out on day 14 and day 28 in each group and the jaws of each rat were subjected to immunohistochemical and histological analysis. The results showed a decrease in TRAP expression in the nHA-IPRF group compared with the control group on day 14 (p = 0.074) and day 28 (p = 0.017). The study also showed an increase in ALP and OCN in the HA-IPRF group on day 14 and day 28 compared with the control group. New bone formation suggested a significant increase in the nHA-IPRF group compared with the control group on day 14 (p = 0.001) and day 28 (p = 0.001). nHA-IPRF implantation can suppress alveolar bone resorption, which is indicated by decreased TRAP expression, and it can increase bone growth, as indicated by increased expression of ALP, OCN, and new bone formation. Full article

(This article belongs to the Section Molecular Medicine)

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17 pages, 3333 KiB

Open AccessArticle

Protocatechuic Acid and Syringin from Saussurea neoserrata Nakai Attenuate Prostaglandin Production in Human Keratinocytes Exposed to Airborne Particulate Matter

by Myeongguk Jeong, Yeongdon Ju, Hyeokjin Kwon, Yeeun Kim, Kyung-Yae Hyun and Go-Eun Choi

Curr. Issues Mol. Biol. 2023, 45(7), 5950-5966; https://doi.org/10.3390/cimb45070376 - 16 Jul 2023

Cited by 2 | Viewed by 1638

Abstract

Saussurea neoserrata Nakai offers a reliable and efficient source of antioxidants that can help alleviate adverse skin reactions triggered by air pollutants. Air pollutants, such as particulate matter (PM), have the ability to infiltrate the skin and contribute to the higher occurrence of [...] Read more.

Saussurea neoserrata Nakai offers a reliable and efficient source of antioxidants that can help alleviate adverse skin reactions triggered by air pollutants. Air pollutants, such as particulate matter (PM), have the ability to infiltrate the skin and contribute to the higher occurrence of cardiovascular, cerebrovascular, and respiratory ailments. Individuals with compromised skin barriers are particularly susceptible to the impact of PM since it can be absorbed more readily through the skin. This study investigated the impact of protocatechuic acid and syringin, obtained from the n-BuOH extract of S. neoserrata Nakai, on the release of PGE₂ and PGD₂ induced by PM₁₀. Additionally, it examined the gene expression of the synthesis of PGE₂ and PGD₂ in human keratinocytes. The findings of this research highlight the potential of utilizing safe and efficient plant-derived antioxidants in dermatological and cosmetic applications to mitigate the negative skin reactions caused by exposure to air pollution. Full article

(This article belongs to the Section Bioorganic Chemistry and Medicinal Chemistry)

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15 pages, 2257 KiB

Open AccessArticle

The Synergistic Antitumor Effect of Decitabine and Vorinostat Combination on HepG2 Human Hepatocellular Carcinoma Cell Line via Epigenetic Modulation of Autophagy–Apoptosis Molecular Crosstalk

by Basant M. Salama, Maged W. Helmy, Hosny Fouad, Marium M. Shamaa and Maha E. Houssen

Curr. Issues Mol. Biol. 2023, 45(7), 5935-5949; https://doi.org/10.3390/cimb45070375 - 16 Jul 2023

Cited by 4 | Viewed by 1858

Abstract

Hepatocellular carcinoma (HCC) is a worldwide health issue. Epigenetic alterations play a crucial role in HCC tumorigenesis. Using epigenetic modulators for HCC treatment confers a promising therapeutic effect. The aim of this study was to explore the effect of a decitabine (DAC) and [...] Read more.

Hepatocellular carcinoma (HCC) is a worldwide health issue. Epigenetic alterations play a crucial role in HCC tumorigenesis. Using epigenetic modulators for HCC treatment confers a promising therapeutic effect. The aim of this study was to explore the effect of a decitabine (DAC) and vorinostat (VOR) combination on the crosstalk between apoptosis and autophagy in the HCC HepG2 cell line at 24 h and 72 h. Median inhibitory concentrations (IC₅₀s) of VOR and DAC were assessed in the HepG2 cell line. The activity of caspase-3 was evaluated colorimetrically, and Cyclin D1(CCND1), Bcl-2, ATG5, ATG7, and P62 levels were assessed using ELISA at different time intervals (24 h and 72 h), while LC3IIB and Beclin-1gene expression were measured by using qRT-PCR. The synergistic effect of VOR and DAC was confirmed due to the observed combination indices (CIs) and dose reduction indices (DRIs). The combined treatment with both drugs inhibited the proliferation marker (CCND1), and enhanced apoptosis compared with each drug alone at 24 h and 72 h (via active caspase-3 upregulation and Bcl-2 downregulation). Moreover, the combination induced autophagy as an early event via upregulation of Beclin-1, LC3IIB, ATG5, and ATG7 gene expression. The initial induction of autophagy started to decrease after 72 h due to Beclin-1 downregulation, and there was decreased expression of LC3IIB compared with the value at 24 h. Herein, epigenetic modulation via the VOR/DAC combination showed an antitumor effect through the coordination of an autophagy–apoptosis crosstalk and promotion of autophagy-induced apoptosis, which ultimately led to the cellular death of HCC cancer cells. Full article

(This article belongs to the Section Molecular Medicine)

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21 pages, 1989 KiB

Open AccessReview

How Plants Tolerate Salt Stress

by Haiqi Fu and Yongqing Yang

Curr. Issues Mol. Biol. 2023, 45(7), 5914-5934; https://doi.org/10.3390/cimb45070374 - 15 Jul 2023

Cited by 38 | Viewed by 4987

Abstract

Soil salinization inhibits plant growth and seriously restricts food security and agricultural development. Excessive salt can cause ionic stress, osmotic stress, and ultimately oxidative stress in plants. Plants exclude excess salt from their cells to help maintain ionic homeostasis and stimulate phytohormone signaling [...] Read more.

Soil salinization inhibits plant growth and seriously restricts food security and agricultural development. Excessive salt can cause ionic stress, osmotic stress, and ultimately oxidative stress in plants. Plants exclude excess salt from their cells to help maintain ionic homeostasis and stimulate phytohormone signaling pathways, thereby balancing growth and stress tolerance to enhance their survival. Continuous innovations in scientific research techniques have allowed great strides in understanding how plants actively resist salt stress. Here, we briefly summarize recent achievements in elucidating ionic homeostasis, osmotic stress regulation, oxidative stress regulation, and plant hormonal responses under salt stress. Such achievements lay the foundation for a comprehensive understanding of plant salt-tolerance mechanisms. Full article

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

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12 pages, 2932 KiB

Open AccessCommunication

Escin Activates Canonical Wnt/β-Catenin Signaling Pathway by Facilitating the Proteasomal Degradation of Glycogen Synthase Kinase-3β in Cultured Human Dermal Papilla Cells

by Jae Young Shin, Jaeyoon Kim, Yun-Ho Choi, Sanghwa Lee and Nae-Gyu Kang

Curr. Issues Mol. Biol. 2023, 45(7), 5902-5913; https://doi.org/10.3390/cimb45070373 - 14 Jul 2023

Viewed by 1702

Abstract

Abnormal inactivation of the Wnt/β-catenin signaling pathway is involved in skin diseases like androgenetic alopecia, vitiligo and canities, but small-molecule activators are rarely described. In this study, we investigated the stimulatory effects of escin on the canonical Wnt/β-catenin signaling pathway in cultured human [...] Read more.

Abnormal inactivation of the Wnt/β-catenin signaling pathway is involved in skin diseases like androgenetic alopecia, vitiligo and canities, but small-molecule activators are rarely described. In this study, we investigated the stimulatory effects of escin on the canonical Wnt/β-catenin signaling pathway in cultured human dermal papilla cells (hDPCs). Escin stimulated Wnt/β-catenin signaling, resulting in increased β-catenin and lymphoid enhancer-binding factor 1 (LEF1), the accumulation of nuclear β-catenin and the enhanced expression of Wnt target genes in cultured hDPCs. Escin drastically reduced the protein level of glycogen synthase kinase (GSK)-3β, a key regulator of the Wnt/β-catenin signaling pathway, while the presence of the proteasome inhibitor MG-132 fully restored the GSK-3β protein level. The treatment of secreted frizzled-related proteins (sFRPs) 1 and 2 attenuated the activity of escin in Wnt reporter assays. Our data demonstrate that escin is a natural agonist of the canonical Wnt/β-catenin signaling pathway and downregulates GSK-3β protein expression by facilitating the proteasomal degradation of GSK-3β in cultured hDPCs. Our data suggest that escin likely stimulates Wnt signaling through direct interactions with frizzled receptors. This study underscores the therapeutic potential of escin for Wnt-related diseases such as androgenetic alopecia, vitiligo and canities. Full article

(This article belongs to the Special Issue Natural Products in Biomedicine and Pharmacotherapy)

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23 pages, 3576 KiB

Open AccessArticle

Genome-Wide Mining of Selaginella moellendorffii for Hevein-like Lectins and Their Potential Molecular Mimicry with SARS-CoV-2 Spike Glycoprotein

by Ahmed Alsolami, Amina I. Dirar, Emadeldin Hassan E. Konozy, Makarim El-Fadil M. Osman, Mohanad A. Ibrahim, Khalid Farhan Alshammari, Fawwaz Alshammari, Meshari Alazmi and Kamaleldin B. Said

Curr. Issues Mol. Biol. 2023, 45(7), 5879-5901; https://doi.org/10.3390/cimb45070372 - 14 Jul 2023

Cited by 1 | Viewed by 2090

Abstract

Multidisciplinary research efforts on potential COVID-19 vaccine and therapeutic candidates have increased since the pandemic outbreak of SARS-CoV-2 in 2019. This search has become imperative due to the increasing emergences and limited widely available medicines. The presence of bioactive anti-SARS-CoV-2 molecules was examined [...] Read more.

Multidisciplinary research efforts on potential COVID-19 vaccine and therapeutic candidates have increased since the pandemic outbreak of SARS-CoV-2 in 2019. This search has become imperative due to the increasing emergences and limited widely available medicines. The presence of bioactive anti-SARS-CoV-2 molecules was examined from various plant sources. Among them is a group of proteins called lectins that can bind carbohydrate moieties. In this article, we present ten novel, chitin-specific Hevein-like lectins that were derived from Selaginella moellendorffii v1.0’s genome. The capacity of these lectin homologs to bind with the spike protein of SARS-CoV-2 was examined. Using the HDOCK server, 3D-modeled Hevein-domains were docked to the spike protein’s receptor binding domain (RBD). The Smo446851, Smo125663, and Smo99732 interacted with Asn343-located complex N-glycan and RBD residues, respectively, with binding free energies of −17.5, −13.0, and −26.5 Kcal/mol. The molecular dynamics simulation using Desmond and the normal-state analyses via torsional coordinate association for the Smo99732-RBD complex using iMODS is characterized by overall higher stability and minimum deformity than the other lectin complexes. The three lectins interacting with carbohydrates were docked against five individual mutations that frequently occur in major SARS-CoV-2 variants. These were in the spike protein’s receptor-binding motif (RBM), while Smo125663 and Smo99732 only interacted with the spike glycoprotein in a protein–protein manner. The precursors for the Hevein-like homologs underwent additional characterization, and their expressional profile in different tissues was studied. These in silico findings offered potential lectin candidates targeting key N-glycan sites crucial to the virus’s virulence and infection. Full article

(This article belongs to the Special Issue Design, Synthesis and Discovery of Drug Candidates)

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14 pages, 1633 KiB

Open AccessArticle

Targeting RAF Isoforms and Tumor Microenvironments in RAS or BRAF Mutant Colorectal Cancers with SJ-C1044 for Anti-Tumor Activity

by Sungpyo Hong, Myeongjin Jeon, Jeonghee Kwon, Hanbyeol Park, Goeun Lee, Kilwon Kim and Soonkil Ahn

Curr. Issues Mol. Biol. 2023, 45(7), 5865-5878; https://doi.org/10.3390/cimb45070371 - 13 Jul 2023

Cited by 3 | Viewed by 1853

Abstract

Colorectal cancer (CRC) is a significant global health issue characterized by a high prevalence of KRAS gene mutations. The RAS/MAPK pathway, involving KRAS, plays a crucial role in CRC progression. Although some RAS inhibitors have been approved, their efficacy in CRC is limited. [...] Read more.

Colorectal cancer (CRC) is a significant global health issue characterized by a high prevalence of KRAS gene mutations. The RAS/MAPK pathway, involving KRAS, plays a crucial role in CRC progression. Although some RAS inhibitors have been approved, their efficacy in CRC is limited. To overcome these limitations, pan-RAF inhibitors targeting A-Raf, B-Raf, and C-Raf have emerged as promising therapeutic strategies. However, resistance to RAF inhibition and the presence of an immunosuppressive tumor microenvironment (TME) pose additional obstacles to effective therapy. Here, we evaluated the potential of a novel pan-RAF inhibitor, SJ-C1044, for targeting mutant KRAS-mediated signaling and inhibiting CRC cell proliferation. Notably, SJ-C1044 also exhibited inhibitory effects on immunokinases, specifically, CSF1R, VEGFR2, and TIE2, which play crucial roles in immune suppression. SJ-C1044 demonstrated potent antitumor activity in xenograft models of CRC harboring KRAS or BRAF mutations. Importantly, treatment with SJ-C1044 resulted in increased infiltration of T cells and reduced presence of tumor-associated macrophages and regulatory T cells within the TME. Thus, SJ-C1044 shows immunomodulatory potential and the ability to enhance antitumor responses. The study underscores the therapeutic potential of SJ-C1044 as a novel pan-RAF inhibitor capable of targeting oncogenic signaling pathways and overcoming immune suppression in CRC. Full article

(This article belongs to the Special Issue Molecular-Based Approaches in Therapy for Gastrointestinal Cancers, 2nd Edition)

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16 pages, 4026 KiB

Open AccessArticle

A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota

by Roberto Marín-Paredes, Hermes H. Bolívar-Torres, Alberto Coronel-Gaytán, Esperanza Martínez-Romero and Luis E. Servín-Garcidueñas

Curr. Issues Mol. Biol. 2023, 45(7), 5849-5864; https://doi.org/10.3390/cimb45070370 - 13 Jul 2023

Viewed by 1943

Abstract

Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. [...] Read more.

Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied. Full article

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

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19 pages, 2095 KiB

Open AccessReview

The Role of the Piezo1 Mechanosensitive Channel in Heart Failure

by Weihua Yuan, Xicheng Zhang and Xiangming Fan

Curr. Issues Mol. Biol. 2023, 45(7), 5830-5848; https://doi.org/10.3390/cimb45070369 - 13 Jul 2023

Cited by 4 | Viewed by 3969

Abstract

Mechanotransduction (MT) is inseparable from the pathobiology of heart failure (HF). However, the effects of mechanical forces on HF remain unclear. This review briefly describes how Piezo1 functions in HF-affected cells, including endothelial cells (ECs), cardiac fibroblasts (CFs), cardiomyocytes (CMs), and immune cells. [...] Read more.

Mechanotransduction (MT) is inseparable from the pathobiology of heart failure (HF). However, the effects of mechanical forces on HF remain unclear. This review briefly describes how Piezo1 functions in HF-affected cells, including endothelial cells (ECs), cardiac fibroblasts (CFs), cardiomyocytes (CMs), and immune cells. Piezo1 is a mechanosensitive ion channel that has been extensively studied in recent years. Piezo1 responds to different mechanical forces and converts them into intracellular signals. The pathways that modulate the Piezo1 switch have also been briefly described. Experimental drugs that specifically activate Piezo1-like proteins, such as Yoda1, Jedi1, and Jedi2, are available for clinical studies to treat Piezo1-related diseases. The only mechanosensitive ion-channel-specific inhibitor available is GsMTx4, which can turn off Piezo1 by modulating the local membrane tension. Ultrasound waves can modulate Piezo1 switching in vitro with the assistance of microbubbles. This review provides new possible targets for heart failure therapy by exploring the cellular functions of Piezo1 that are involved in the progression of the disease. Modulation of Piezo1 activity may, therefore, effectively delay the progression of heart failure. Full article

(This article belongs to the Special Issue A Focus on Molecular Basis in Cardiac Diseases)

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6 pages, 205 KiB

Open AccessEditorial

Bioactives and Inflammation

by Guan-Ting Liu and Chan-Yen Kuo

Curr. Issues Mol. Biol. 2023, 45(7), 5824-5829; https://doi.org/10.3390/cimb45070368 - 13 Jul 2023

Cited by 1 | Viewed by 1273

Abstract

Inflammation is one of the body’s most complex physiological defense mechanisms against harmful substances [...] Full article

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

13 pages, 3072 KiB

Open AccessArticle

A Comparative Analysis of NOX4 Protein Expression in Malignant and Non-Malignant Thyroid Tumors

by Salma Fenniche, Mohamed Oukabli, Yassire Oubaddou, Hafsa Chahdi, Amal Damiri, Abir Alghuzlan, Abdelilah Laraqui, Nadia Dakka, Youssef Bakri, Corinne Dupuy and Rabii Ameziane El Hassani

Curr. Issues Mol. Biol. 2023, 45(7), 5811-5823; https://doi.org/10.3390/cimb45070367 - 13 Jul 2023

Cited by 3 | Viewed by 1854

Abstract

The comparative analysis of the expression of the reactive oxygen species-generating NADPH oxidase NOX4 from TCGA data shows that the NOX4 transcript is upregulated in papillary thyroid carcinomas (PTC)-BRAF^V600E tumors compared to PTC-BRAF^wt tumors. However, a comparative analysis of NOX4 at [...] Read more.

The comparative analysis of the expression of the reactive oxygen species-generating NADPH oxidase NOX4 from TCGA data shows that the NOX4 transcript is upregulated in papillary thyroid carcinomas (PTC)-BRAF^V600E tumors compared to PTC-BRAF^wt tumors. However, a comparative analysis of NOX4 at the protein level in malignant and non-malignant tumors is missing. We explored NOX4 protein expression by immunohistochemistry staining in malignant tumors (28 classical forms of PTC (C-PTC), 17 follicular variants of PTC (F-PTC), and three anaplastic thyroid carcinomas (ATCs)) and in non-malignant tumors (six lymphocytic thyroiditis, four Graves’ disease, ten goiters, and 20 hyperplasias). We detected the BRAF^V600E mutation by Sanger sequencing and digital droplet PCR. The results show that NOX4 was found to be higher (score ≥ 2) in C-PTC (92.9%) compared to F-PTC (52.9%) and ATC (33.3%) concerning malignant tumors. Interestingly, all C-PTC-BRAF^V600E expressed a high score for NOX4 at the protein level, strengthening the positive correlation between the BRAF^V600E mutation and NOX4 expression. In addition, independent of the mutational status of BRAF, we observed that 90% of C-PTC infiltrating tumors showed high NOX4 expression, suggesting that NOX4 may be considered a complementary biomarker in PTC aggressiveness. Interestingly, NOX4 was highly expressed in non-malignant thyroid diseases with different subcellular localizations. Full article

(This article belongs to the Special Issue Advanced Molecular Solutions for Cancer Therapy)

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13 pages, 600 KiB

Open AccessArticle

HLA-G Alleles Impact the Perinatal Father–Child HPV Transmission

by Nelli T. Suominen, Michel Roger, Marie-Claude Faucher, Kari J. Syrjänen, Seija E. Grénman, Stina M. Syrjänen and Karolina Louvanto

Curr. Issues Mol. Biol. 2023, 45(7), 5798-5810; https://doi.org/10.3390/cimb45070366 - 12 Jul 2023

Viewed by 1328

Abstract

The host factors that influence father-to-child human papillomavirus (HPV) transmission remain unknown. This study evaluated whether human leukocyte antigen (HLA)-G alleles are important in father-to-child HPV transmission during the perinatal period. Altogether, 134 father–newborn pairs from the Finnish Family HPV Study were included. [...] Read more.

The host factors that influence father-to-child human papillomavirus (HPV) transmission remain unknown. This study evaluated whether human leukocyte antigen (HLA)-G alleles are important in father-to-child HPV transmission during the perinatal period. Altogether, 134 father–newborn pairs from the Finnish Family HPV Study were included. Oral, semen and urethral samples from the fathers were collected before the delivery, and oral samples were collected from their offspring at delivery and postpartum on day 3 and during 1-, 2- and 6-month follow-up visits. HLA-G alleles were tested by direct sequencing. Unconditional logistic regression was used to determine the association of the father–child HLA-G allele and genotype concordance with the father–child HPV prevalence and concordance at birth and during follow-up. HLA-G allele G*01:01:03 concordance was associated with the father’s urethral and child’s oral high-risk (HR)-HPV concordance at birth (OR 17.00, 95% CI: 1.24–232.22). HLA-G allele G*01:04:01 concordance increased the father’s oral and child’s postpartum oral any- and HR-HPV concordance with an OR value of 7.50 (95% CI: 1.47–38.16) and OR value of 7.78 (95% CI: 1.38–43.85), respectively. There was no association between different HLA-G genotypes and HPV concordance among the father–child pairs at birth or postpartum. To conclude, the HLA-G allele concordance appears to impact the HPV transmission between the father and his offspring. Full article

(This article belongs to the Special Issue Complex Molecular Mechanism of Monogenic Diseases 2.0)

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22 pages, 2600 KiB

Open AccessArticle

Genome-Wide SNP and Indel Discovery in Abaca (Musa textilis Née) and among Other Musa spp. for Abaca Genetic Resources Management

by Cris Francis C. Barbosa, Jayson C. Asunto, Rhosener Bhea L. Koh, Daisy May C. Santos, Dapeng Zhang, Ernelea P. Cao and Leny C. Galvez

Curr. Issues Mol. Biol. 2023, 45(7), 5776-5797; https://doi.org/10.3390/cimb45070365 - 12 Jul 2023

Cited by 2 | Viewed by 2916

Abstract

Abaca (Musa textilis Née) is an economically important fiber crop in the Philippines. Its economic potential, however, is hampered by biotic and abiotic stresses, which are exacerbated by insufficient genomic resources for varietal identification vital for crop improvement. To address these gaps, [...] Read more.

Abaca (Musa textilis Née) is an economically important fiber crop in the Philippines. Its economic potential, however, is hampered by biotic and abiotic stresses, which are exacerbated by insufficient genomic resources for varietal identification vital for crop improvement. To address these gaps, this study aimed to discover genome-wide polymorphisms among abaca cultivars and other Musa species and analyze their potential as genetic marker resources. This was achieved through whole-genome Illumina resequencing of abaca cultivars and variant calling using BCFtools, followed by genetic diversity and phylogenetic analyses. A total of 20,590,381 high-quality single-nucleotide polymorphisms (SNP) and DNA insertions/deletions (InDels) were mined across 16 abaca cultivars. Filtering based on linkage disequilibrium (LD) yielded 130,768 SNPs and 13,620 InDels, accounting for 0.396 ± 0.106 and 0.431 ± 0.111 of gene diversity across these cultivars. LD-pruned polymorphisms across abaca, M. troglodytarum, M. acuminata and M. balbisiana enabled genetic differentiation within abaca and across the four Musa spp. Phylogenetic analysis revealed the registered varieties Abuab and Inosa to accumulate a significant number of mutations, eliciting further studies linking mutations to their advantageous phenotypes. Overall, this study pioneered in producing marker resources in abaca based on genome-wide polymorphisms vital for varietal authentication and comparative genotyping with the more studied Musa spp. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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11 pages, 2286 KiB

Open AccessBrief Report

Yeast One-Hybrid Screening to Identify Transcription Factors for IbMYB1-4 in the Purple-Fleshed Sweet Potato (Ipomoea batatas [L.] Lam.)

by Danwen Fu, Shaohua Yang, Rui Liu and Feng Gao

Curr. Issues Mol. Biol. 2023, 45(7), 5765-5775; https://doi.org/10.3390/cimb45070364 - 12 Jul 2023

Cited by 1 | Viewed by 1932

Abstract

IbMYB1 is a transcription factor involved in the biosynthesis of anthocyanin in the purple-fleshed sweet potato. So far, few studies have investigated transcription factors that are upstream of the promoter IbMYB1-4. In this study, a yeast one-hybrid screening aimed at identifying transcription [...] Read more.

IbMYB1 is a transcription factor involved in the biosynthesis of anthocyanin in the purple-fleshed sweet potato. So far, few studies have investigated transcription factors that are upstream of the promoter IbMYB1-4. In this study, a yeast one-hybrid screening aimed at identifying transcription factors upstream of the promoter IbMYB1-4 was performed in the storage roots of the purple-fleshed sweet potato, and IbPDC, IbERF1, and IbPGP19 were identified as upstream binding proteins for the promoter IbMYB1-4. A dual luciferase reporter assay, and yeast one-hybrid assays, were employed to confirm the interaction of these binding proteins with promoters. IbERF1 was found to be an upstream transcription factor for the promoter IbMYB1, and is implicated in the biosynthesis of anthocyanin in the purple-fleshed sweet potato. IbERF1 plays a major role in the biosynthesis of anthocyanin in the purple-fleshed sweet potato. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants)

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13 pages, 3322 KiB

Open AccessArticle

Inhibition of Autophagy and the Cytoprotective Role of Smac Mimetic against ROS-Induced Cancer: A Potential Therapeutic Strategy in Relapse and Chemoresistance Cases in Breast Cancer

by Sahar Rafat, Mohammed Ageeli Hakami, Ali Hazazi, Ahad Amer Alsaiari, Summya Rashid, Mohammad Raghibul Hasan, Abdulaziz A. Aloliqi, Alaa Abdulaziz Eisa, Mohammad Irfan Dar, Mohd Faisal Khan and Kapil Dev

Curr. Issues Mol. Biol. 2023, 45(7), 5752-5764; https://doi.org/10.3390/cimb45070363 - 10 Jul 2023

Cited by 2 | Viewed by 1662

Abstract

With more than a million deaths each year, breast cancer is the top cause of death in women. Around 70% of breast cancers are hormonally responsive. Although several therapeutic options exist, cancer resistance and recurrence render them inefficient and insufficient. The major key [...] Read more.

With more than a million deaths each year, breast cancer is the top cause of death in women. Around 70% of breast cancers are hormonally responsive. Although several therapeutic options exist, cancer resistance and recurrence render them inefficient and insufficient. The major key reason behind this is the failure in the regulation of the cell death mechanism. In addition, ROS was also found to play a major role in this problem. The therapeutic benefits of Smac mimetic compound (SMC) BV6 on MCF7 were examined in the current study. Treatment with BV6 reduces viability and induces apoptosis in MCF7 breast cancer cells. BV6 suppresses autophagy and has demonstrated a defensive role in cancer cells against oxidative stress caused by H₂O₂. Overall, the present investigation shows that SMC has therapeutic and cytoprotective potential against oxidative stress in cancer cells. These Smac mimetic compounds may be used as anti-cancer drugs as well as antioxidants alone or in conjunction with other commonly used antioxidants. Full article

(This article belongs to the Section Molecular Medicine)

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11 pages, 667 KiB

Open AccessArticle

Short Tandem Repeat (STR) Profiling of Earwax DNA Obtained from Healthy Volunteers

by Sayed Amin Amer, Maha Nawar Alotaibi, Sajjad Shahid, Mahmoud Alsafrani and Abdul Rauf Chaudhary

Curr. Issues Mol. Biol. 2023, 45(7), 5741-5751; https://doi.org/10.3390/cimb45070362 - 10 Jul 2023

Viewed by 2858

Abstract

The present study aimed to establish human earwax as a potential source of DNA evidence that could be effectively used in human identification. Sixty earwax samples were obtained from 15 healthy male and female Saudi volunteers living in Riyadh, Saudi Arabia. Four consecutive [...] Read more.

The present study aimed to establish human earwax as a potential source of DNA evidence that could be effectively used in human identification. Sixty earwax samples were obtained from 15 healthy male and female Saudi volunteers living in Riyadh, Saudi Arabia. Four consecutive earwax swab samples were obtained from each volunteer and stored for 1, 15, 30 and 60 days. Earwax samples were stored at room temperature (20–22 °C). Reference oral swab was also taken from each volunteer. DNA was extracted by QIAamp DNA Mini kit and quantified by real-time polymerase chain reaction (RT-PCR) on 7500 Thermal Cycler. Autosomal STR loci were amplified using AmpFLSTR™ Identifiler™ Plus PCR Amplification Kit (Thermo Fisher Scientific, Carlsbad, CA, USA). Amplified fragments were size separated and analyzed on a 3500 Genetic Analyzer. Complete autosomal STR profiles were obtained from the earwax swabs of all the volunteers stored up to 30 days after the collection. Some STR profiles were partially obtained 60 days after the earwax collection. Allelic drop-out, allelic drop-in, and stutters were seen in earwax samples analyzed 60 days after the collection. The results have shown that human earwax can be a potential source of DNA evidence for human identification up to 30 days after the earwax collection. It is recommended to quickly analyze earwax samples or store them at room temperature or at −10 °C after their recovery from the crime scene. Full article

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

16 pages, 680 KiB

Open AccessReview

Correlation between Hepatocyte Growth Factor (HGF) with D-Dimer and Interleukin-6 as Prognostic Markers of Coagulation and Inflammation in Long COVID-19 Survivors

by Bena Zaira, Trilis Yulianti and Jutti Levita

Curr. Issues Mol. Biol. 2023, 45(7), 5725-5740; https://doi.org/10.3390/cimb45070361 - 8 Jul 2023

Cited by 4 | Viewed by 2123

Abstract

In general, an individual who experiences the symptoms of Severe Acute Respiratory Syndrome Coronavirus 2 or SARS-CoV-2 infection is declared as recovered after 2 weeks. However, approximately 10–20% of these survivors have been reported to encounter long-term health problems, defined as ‘long COVID-19’, [...] Read more.

In general, an individual who experiences the symptoms of Severe Acute Respiratory Syndrome Coronavirus 2 or SARS-CoV-2 infection is declared as recovered after 2 weeks. However, approximately 10–20% of these survivors have been reported to encounter long-term health problems, defined as ‘long COVID-19’, e.g., blood coagulation which leads to stroke with an estimated incidence of 3%, and pulmonary embolism with 5% incidence. At the time of infection, the immune response produces pro-inflammatory cytokines that stimulate stromal cells to produce pro-hepatocyte growth factor (pro-HGF) and eventually is activated into hepatocyte growth factor (HGF), which helps the coagulation process in endothelial and epithelial cells. HGF is a marker that appears as an inflammatory response that leads to coagulation. Currently, there is no information on the effect of SARS-CoV-2 infection on serum HGF concentrations as a marker of the prognosis of coagulation in long COVID-19 survivors. This review discusses the pathophysiology between COVID-19 and HGF, IL-6, and D-dimer. Full article

(This article belongs to the Special Issue Advances in Understanding Molecular Basis of Inflammatory Diseases)

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17 pages, 9508 KiB

Open AccessArticle

Molecular Markers of Ovarian Germ Cells of Banana Prawn (Fenneropenaeus merguiensis)

by Tatiyavadee Sengseng, Tomoyuki Okutsu, Anida Songnui, Jaruwan Boonchuay, Chanida Sakunrang and Monwadee Wonglapsuwan

Curr. Issues Mol. Biol. 2023, 45(7), 5708-5724; https://doi.org/10.3390/cimb45070360 - 7 Jul 2023

Viewed by 1333

Abstract

The banana prawn (Fenneropenaeus merguiensis) is a valuable prawn in the worldwide market. However, cultivation of this species is limited owing to the difficulty in culture management and limited knowledge of reproduction. Therefore, we studied the gene expression and molecular mechanisms [...] Read more.

The banana prawn (Fenneropenaeus merguiensis) is a valuable prawn in the worldwide market. However, cultivation of this species is limited owing to the difficulty in culture management and limited knowledge of reproduction. Therefore, we studied the gene expression and molecular mechanisms involved in oogenesis for elucidating ovarian germ cell development in banana prawns. The tissue-specific distribution of certain genes identified from previous transcriptome data showed that FmCyclinB, FmNanos, and nuclear autoantigenic sperm protein (FmNASP) were only expressed in gonads. The in situ hybridization (ISH) of these three genes showed different expression patterns throughout oogenesis. FmCyclinB was highly expressed in pre-vitellogenic oocytes. FmNanos was expressed at almost the same level during oogenesis but showed the most expression in late pre-vitellogenic stages. Based on the highest expression of FmCyclinB and FmNanos in mid pre-vitellogenic and late pre-vitellogenic oocytes, respectively, we suggested that FmNanos may suppress FmCyclinB expression before initiation of vitellogenesis. Meanwhile, FmNASP expression was detected only in pre-vitellogenesis. Moreover, quantitative real-time polymerase chain reaction (qRT-PCR) analysis of FmNASP expression was supported by FmNASP ISH analysis based on high expression of FmNASP in sub-adult ovaries, which contain most of pre-vitellogenic oocytes. In this study, we found three reliable ovarian markers for banana prawns and also found a dynamic change of molecular mechanism during the sub-stage of pre-vitellogenesis. We determined the expression levels of these genes involved in oogenesis. Our findings provide information for further studies on banana prawn reproduction which may assist in their cultivation. Full article

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

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