International Journal of Molecular Sciences

van der Laan, Liselot;Rooney, Kathleen;Alders, Mariëlle;Relator, Raissa;McConkey, Haley;Kerkhof, Jennifer;Levy, Michael A.;Lauffer, Peter;Aerden, Mio;Theunis, Miel;Legius, Eric;Tedder, Matthew L.;Vissers, Lisenka E. L. M.;Koene, Saskia;Ruivenkamp, Claudia;Hoffer, Mariette J. V.;Wieczorek, Dagmar;Bramswig, Nuria C.;Herget, Theresia;González, Vanesa López;Santos-Simarro, Fernando;Tørring, Pernille M.;Denomme-Pichon, Anne-Sophie;Isidor, Bertrand;Keren, Boris;Julia, Sophie;Schaefer, Elise;Francannet, Christine;Maillard, Pierre-Yves;Misra-Isrie, Mala;Van Esch, Hilde;Mannens, Marcel M. A. M.;Sadikovic, Bekim;van Haelst, Mieke M.;Henneman, Peter

doi: 10.3390/ijms232213664pmid: 36430143

Clark–Baraitser syndrome is a rare autosomal dominant intellectual disability syndrome caused by pathogenic variants in the TRIP12 (Thyroid Hormone Receptor Interactor 12) gene. TRIP12 encodes an E3 ligase in the ubiquitin pathway. The ubiquitin pathway includes activating E1, conjugating E2 and ligating E3 enzymes which regulate the breakdown and sorting of proteins. This enzymatic pathway is crucial for physiological processes. A significant proportion of TRIP12 variants are currently classified as variants of unknown significance (VUS). Episignatures have been shown to represent a powerful diagnostic tool to resolve inconclusive genetic findings for Mendelian disorders and to re-classify VUSs. Here, we show the results of DNA methylation episignature analysis in 32 individuals with pathogenic, likely pathogenic and VUS variants in TRIP12. We identified a specific and sensitive DNA methylation (DNAm) episignature associated with pathogenic TRIP12 variants, establishing its utility as a clinical biomarker for Clark–Baraitser syndrome. In addition, we performed analysis of differentially methylated regions as well as functional correlation of the TRIP12 genome-wide methylation profile with the profiles of 56 additional neurodevelopmental disorders.

Bonnechère, Bruno;Amin, Najaf;Duijn, Cornelia van

doi: 10.3390/ijms232213665pmid: 36430144

There is a growing body of evidence highlighting there are significant changes in the gut microbiota composition and relative abundance in various neurological disorders. We performed a systematic review of the different microbiota altered in a wide range of neurological disorders (Alzheimer’s disease (AD), Parkinson’s disease (PD), multiple sclerosis (MS), amyotrophic lateral sclerosis, and stroke). Fifty-two studies were included representing 5496 patients. At the genus level, the most frequently involved microbiota are Akkermansia, Faecalibacterium, and Prevotella. The overlap between the pathologies was strongest for MS and PD, sharing eight genera (Akkermansia, Butyricicoccus, Bifidobacterium, Coprococcus, Dorea, Faecalibacterium, Parabacteroides, and Prevotella) and PD and stroke, sharing six genera (Enterococcus, Faecalibacterium, Lactobacillus, Parabacteroides, Prevotella, and Roseburia). The identification signatures overlapping for AD, PD, and MS raise the question of whether these reflect a common etiology or rather common consequence of these diseases. The interpretation is hampered by the low number and low power for AD, ALS, and stroke with ample opportunity for false positive and false negative findings.

Zhuravlev, Evgenii;Sergeeva, Mariia;Malanin, Sergey;Amirkhanov, Rinat;Semenov, Dmitriy;Grigoryeva, Tatiana;Komissarov, Andrey;Stepanov, Grigory

doi: 10.3390/ijms232213666pmid: 36430145

Small nucleolar RNAs (snoRNAs) are a highly expressed class of non-coding RNAs known for their role in guiding post-transcriptional modifications of ribosomal RNAs and small nuclear RNAs. Emerging studies suggest that snoRNAs are also implicated in regulating other vital cellular processes, such as pre-mRNA splicing and 3′-processing of mRNAs, and in the development of cancer and viral infections. There is an emerging body of evidence for specific snoRNA’s involvement in the optimal replication of RNA viruses. In order to investigate the expression pattern of snoRNAs during influenza A viral infection, we performed RNA sequencing analysis of the A549 human cell line infected by influenza virus A/Puerto Rico/8/1934 (H1N1). We identified 66 that were upregulated and 55 that were downregulated in response to influenza A virus infection. The increased expression of most C/D-box snoRNAs was associated with elevated levels of 5’- and 3’-short RNAs derived from this snoRNA. Analysis of the poly(A)+ RNA sequencing data indicated that most of the differentially expressed snoRNAs synthesis was not correlated with the corresponding host genes expression. Furthermore, influenza A viral infection led to an imbalance in the expression of genes responsible for C/D small nucleolar ribonucleoprotein particles’ biogenesis. In summary, our results indicate that the expression pattern of snoRNAs in A549 cells is significantly altered during influenza A viral infection.

Eilam, Yahav;Pintel, Noam;Khattib, Hamdan;Shagug, Natalie;Taha, Raged;Avni, Dorit

doi: 10.3390/ijms232213667pmid: 36430146

Cholesterol synthesis occurs in almost all cells, but mainly in hepatocytes in the liver. Cholesterol is garnering increasing attention for its central role in various metabolic diseases. In addition, cholesterol is one of the most essential elements for cells as both a structural source and a player participating in various metabolic pathways. Accurate regulation of cholesterol is necessary for the proper metabolism of fats in the body. Disturbances in cholesterol homeostasis have been linked to various metabolic diseases, such as hyperlipidemia and non-alcoholic fatty liver disease (NAFLD). For many years, the use of synthetic chemical drugs has been effective against many health conditions. Furthermore, from ancient to modern times, various plant-based drugs have been considered local medicines, playing important roles in human health. Phytochemicals are bioactive natural compounds that are derived from medicinal plants, fruit, vegetables, roots, leaves, and flowers and are used to treat a variety of diseases. They include flavonoids, carotenoids, polyphenols, polysaccharides, vitamins, and more. Many of these compounds have been proven to have antioxidant, anti-inflammatory, antiobesity and antihypercholesteremic activity. The multifaceted role of phytochemicals may provide health benefits to humans with regard to the treatment and control of cholesterol metabolism and the diseases associated with this disorder, such as NAFLD. In recent years, global environmental climate change, the COVID-19 pandemic, the current war in Europe, and other conflicts have threatened food security and human nutrition worldwide. This further emphasizes the urgent need for sustainable sources of functional phytochemicals to be included in the food industry and dietary habits. This review summarizes the latest findings on selected phytochemicals from sustainable sources—algae and edible mushrooms—that affect the synthesis and metabolism of cholesterol and improve or prevent NAFLD.

Zang, Yuguang;Yao, Yijia;Xu, Zheshu;Wang, Baoqing;Mao, Yiqi;Wang, Weilu;Zhang, Weiyang;Zhang, Hao;Liu, Lijun;Wang, Zhiqin;Liang, Guohua;Yang, Jianchang;Zhou, Yong;Gu, Junfei

doi: 10.3390/ijms232213668pmid: 36430147

The mobilization and translocation of carbohydrates and mineral nutrients from vegetative plant parts to grains are pivotal for grain filling, often involving a whole plant senescence process. Loss of greenness is a hallmark of leaf senescence. However, the relationship between crop yield and senescence has been controversial for many years. Here, in this study, the overexpression and RNA interference lines of gene of OsNYC3 (Non-Yellow Coloring 3), a chlorophyll catabolism gene, were investigated. Furthermore, exogenous phytohormones were applied, and a treatment of alternate wetting and moderate drying (AWMD) was introduced to regulate the processes of leaf senescence. The results indicated that the delayed senescence of the “STAY-GREEN” trait of rice is undesirable for the process of grain filling, and it would cause a lower ratio of grain filling and lower grain weight of inferior grains, because of unused assimilates in the stems and leaves. Through the overexpression of OsNYC3, application of exogenous chemicals of abscisic acid (ABA), and water management of AWMD, leaf photosynthesis was less influenced, a high ratio of carbohydrate assimilates was partitioned to grains other than leaves and stems as labeled by 13C, grain filling was improved, especially for inferior spikelets, and activities of starch-synthesizing enzymes were enhanced. However, application of ethephon not only accelerated leaf senescence, but also caused seed abortion and grain weight reduction. Thus, plant senescence needs to be finely adjusted in order to make a contribution to crop productivity.

Wierzchowski, Kamil;Nowak, Bartosz;Kawka, Mateusz;Więckowicz, Patryk;Dąbkowska-Susfał, Katarzyna;Pietrosiuk, Agnieszka;Sykłowska-Baranek, Katarzyna;Pilarek, Maciej

doi: 10.3390/ijms232213669pmid: 36430149

In situ extraction is a method for separating plant secondary metabolites from in vitro systems of plant biomass cultures. The study aimed to investigate the MTMS-based xerogels morphology effect on the growth kinetics and deoxyshikonin productivity in xerogel-supported in vitro culture systems of Rindera graeca hairy root. Cultures were supplemented with three types of xerogel, i.e., mesoporous gel, microporous gel, and agglomerated precipitate, in the disintegrated or monolithic form. Structure, oil sorption capacity, and SEM analyses for xerogel-based additives were performed. Application of monolithic macroporous xerogel resulted in the highest biomass proliferation, i.e., 5.11-fold fresh biomass increase after four weeks of the screening culture. The highest deoxyshikonin production (i.e., 105.03 µg) was noted when hairy roots were maintained with particles of disintegrated mesoporous xerogel. The detailed kinetics investigations (6-week culture) revealed the highest growth of hairy root biomass and secondary metabolite production, equaling 9.46-fold fresh weight biomass and 204.08 µg deoxyshikonin, respectively. MTMS-based xerogels have been recognized as selective biocompatible scaffolds for boosting the proliferation of transgenic roots or for productivity enhancement of naphthoquinones without detrimental effects on biomass growth, and their successful applicability in in situ removal of secondary plant metabolites has been experimentally confirmed.

Vaicekauskaitė, Ieva;Sabaliauskaitė, Rasa;Lazutka, Juozas Rimantas;Jarmalaitė, Sonata

doi: 10.3390/ijms232213670pmid: 36430148

Ovarian cancer (OC) is the fifth leading cause of women’s death from cancers. The high mortality rate is attributed to the late presence of the disease and the lack of modern diagnostic tools, including molecular biomarkers. Moreover, OC is a highly heterogeneous disease, which contributes to early treatment failure. Thus, exploring OC molecular mechanisms could significantly enhance our understanding of the disease and provide new treatment options. Chromatin remodeling complexes (CRCs) are ATP-dependent molecular machines responsible for chromatin reorganization and involved in many DNA-related processes, including transcriptional regulation, replication, and reparation. Dysregulation of chromatin remodeling machinery may be related to cancer development and chemoresistance in OC. Some forms of OC and other gynecologic diseases have been associated with mutations in specific CRC genes. Most notably, ARID1A in endometriosis-related OC, SMARCA4, and SMARCB1 in hypercalcemic type small cell ovarian carcinoma (SCCOHT), ACTL6A, CHRAC1, RSF1 amplification in high-grade serous OC. Here we review the available literature on CRCs’ involvement in OC to improve our understanding of its development and investigate CRCs as possible biomarkers and treatment targets for OC.

Alveal-Mellado, Daniel;Castillo-Mariqueo, Lidia;Giménez-Llort, Lydia

doi: 10.3390/ijms232213671pmid: 36430150

Alzheimer’s disease (AD) patients suffer from circadian rhythm alterations affecting their daily physical activity patterns with less willingness to perform a voluntary exercise. In preclinical studies, there is no clarity on whether animal models of AD can replicate these impairments. Here, we provide a proof of concept of the performance and behavioral effects of four weeks of voluntary wheel running (VWR) in a group of 14-month-old male and female 3xTg-AD mice at advanced stages of AD and the daily variance (behavioral circadian rhythmicity) of VWR associated with sex and their neuropsychiatric-like phenotype. Higher levels of horizontal exploration in the open field (OF) test were found in mice submitted to exercise. A linear mixed effect model showed significant sex-dependent differences in the VWR activity performed on the first night of follow-up, with high-NIBI males running less than high-NIBI females. Thus, an influence of NPS-like symptoms on the circadian patterns of VWR may account for such differences. In addition, males remained more active than females during diurnal periods. We hypothesize that this increment in energy expenditure during resting periods may be related to hyperactive behavior, similar to that observed in humans’ exacerbated agitation or sundowning behavior. These findings support the usage of the 3xTg-AD mouse as a reliable model for studying circadian rhythm alterations in AD and, at the translational level, the importance of tailored and individualized physical activity programs in clinical settings.

Li, Wei;Liang, Tiangui;Lin, Yuanchuang;Wu, Weixiong;Li, Song

doi: 10.3390/ijms232213672pmid: 36430151

Capturing formaldehydes (HCHO) from indoor air with porous adsorbents still faces challenges due to their low capacity and poor selectivity. Metal-organic frameworks (MOFs) with tunable pore properties were regarded as promising adsorbents for HCHO removal. However, the water presence in humid air heavily influences the formaldehyde capture performance due to the competition adsorption. To find suitable MOFs for formaldehyde capture and explore the relationship between MOFs structure and performance both in dry air and humid air, we performed grand canonical Monte Carlo (GCMC) molecular simulations to obtain working capacity and selectivity that evaluated the HCHO capture performance of MOFs without humidity. The results reveal that small pore size (~5 Å) and moderate heat of adsorption (40–50 kJ/mol) are favored for HCHO capture without water. It was found that the structure with a 3D cage instead of a 2D channel benefits the HCHO adsorption. Atoms in these high-performing MOFs should possess relatively small charges, and large Lennard-jones parameters were also preferred. Furthermore, it was indicated that Henry’s constant (KH) can reflect the HCHO adsorption performance without humidity, in which the optimal range is 10−2–101. Hence, Henry’s constant selectivity of HCHO over water (SKH HCHO/H2O) and HCHO over mixture components (H2O, N2, and O2) was obtained to screen MOFs at an 80% humidity condition. It was suggested that SKH for the mixture component overestimates the influence of N2 and O2, in which the top structures absorb a quantity of water in GCMC simulation, while SKH HCHO/H2O can efficiently find high-performing MOFs for HCHO capture at humidity in low adsorption pressure. The ECATAT found in this work has 0.64 mol/kg working capacity, and barely adsorbs water during 0–1 bar, which is the promising candidate MOF for HCHO capture.

Jeon, Do Yong;Jeong, So Yeon;Lee, Ju Won;Kim, Jeonghwan;Kim, Jee Hyun;Chu, Hun Su;Jeong, Won Jin;Lee, Byung Ju;Ahn, Byungyong;Kim, Junil;Choi, Seong Hee;Park, Jeong Woo

doi: 10.3390/ijms232213673pmid: 36430156

The mRNA destabilizing factor tristetraprolin (TTP) functions as a tumor suppressor by down-regulating cancer-associated genes. TTP expression is significantly reduced in various cancers, which contributes to cancer processes. Enforced expression of TTP impairs tumorigenesis and abolishes maintenance of the malignant state, emphasizing the need to identify a TTP inducer in cancer cells. To search for novel candidate agents for inducing TTP in cancer cells, we screened a library containing 1019 natural compounds using MCF-7 breast cancer cells transfected with a reporter vector containing the TTP promoter upstream of the luciferase gene. We identified one molecule, of which the enantiomers are betamethasone 21-phosphate (BTM-21-P) and dexamethasone 21-phosphate (BTM-21-P), as a potent inducer of TTP in cancer cells. We confirmed that BTM-21-P, DXM-21-P, and dexamethasone (DXM) induced the expression of TTP in MDA-MB-231 cells in a glucocorticoid receptor (GR)-dependent manner. To identify potential pathways linking BTM-21-P and DXM-21-P to TTP induction, we performed an RNA sequencing-based transcriptome analysis of MDA-MB-231 cells at 3 h after treatment with these compounds. A heat map analysis of FPKM expression showed a similar expression pattern between cells treated with the two compounds. The KEGG pathway analysis results revealed that the upregulated DEGs were strongly associated with several pathways, including the Hippo signaling pathway, PI3K-Akt signaling pathway, FOXO signaling pathway, NF-κB signaling pathway, and p53 signaling pathway. Inhibition of the FOXO pathway using a FOXO1 inhibitor blocked the effects of BTM-21-P and DXM-21-P on the induction of TTP in MDA-MB-231 cells. We found that DXM enhanced the binding of FOXO1 to the TTP promoter in a GR-dependent manner. In conclusion, we identified a natural compound of which the enantiomers are DXM-21-P and BTM-21-P as a potent inducer of TTP in breast cancer cells. We also present new insights into the role of FOXO1 in the DXM-21-P- and BTM-21-P-induced expression of TTP in cancer cells.