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Cheon YP, Ryou C, Svedružić ŽM. Roles of prion proteins in mammalian development. Anim Cells Syst (Seoul) 2024; 28:551-566. [PMID: 39664939 PMCID: PMC11633422 DOI: 10.1080/19768354.2024.2436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 11/02/2024] [Accepted: 11/25/2024] [Indexed: 12/13/2024] Open
Abstract
Prion protein (PrP) is highly conserved and is expressed in most tissues in a developmental stage-specific manner. Glycosylated cellular prion protein (PrPC) is found in most cells and subcellular areas as a physiological regulating molecule. On the other hand, the amyloid form of PrPC, scrapie PrP (PrPSC), causes transmissible pathogenesis in the central nervous system and induces degeneration of the nervous system. Although many amyloids are reversible and critical in determining the fate, differentiation, and physiological functions of cells, thus far, PrPSC originating from PrPC is not. Although many studies have focused on disorders involving PrPC and the deletion mammalian models for PrPC have no severe phenotype, it has been suggested that PrPC has a role in normal development. It is conserved and expressed from gametes to adult somatic cells. In addition, severe developmental phenotypes appear in PrP null zebrafish embryos and in various mammalian cell model systems. In addition, it has been well established that PrPC is strongly involved in the stemness and differentiation of embryonic stem cells and progenitors. Thus far, many studies on PrPC have focused mostly on disease-associated conditions with physiological roles as a complex platform but not on development. The known roles of PrPC depend on the interacting molecules through its flexible tail and domains. PrPC interacts with membrane, and various intracellular and extracellular molecules. In addition, PrPC and amyloid can stimulate signaling pathways differentially. In this review, we summarize the function of prion protein and discuss its role in development.
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Affiliation(s)
- Yong-Pil Cheon
- Division of Developmental Biology and Physiology, Department of Biotechnology, Institute for Basic Sciences, Sungshin University, Seoul, Korea
| | - Chongsuk Ryou
- Department of Pharmacy, College of Pharmacy, Hanyang University, ekcho Ansan, Korea
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Yang S, Kim SH, Yang E, Kang M, Joo JY. Molecular insights into regulatory RNAs in the cellular machinery. Exp Mol Med 2024; 56:1235-1249. [PMID: 38871819 PMCID: PMC11263585 DOI: 10.1038/s12276-024-01239-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 06/15/2024] Open
Abstract
It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.
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Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Eunjeong Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea.
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Darbinian N, Hampe M, Martirosyan D, Bajwa A, Darbinyan A, Merabova N, Tatevosian G, Goetzl L, Amini S, Selzer ME. Fetal Brain-Derived Exosomal miRNAs from Maternal Blood: Potential Diagnostic Biomarkers for Fetal Alcohol Spectrum Disorders (FASDs). Int J Mol Sci 2024; 25:5826. [PMID: 38892014 PMCID: PMC11172088 DOI: 10.3390/ijms25115826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Fetal alcohol spectrum disorders (FASDs) are leading causes of neurodevelopmental disability but cannot be diagnosed early in utero. Because several microRNAs (miRNAs) are implicated in other neurological and neurodevelopmental disorders, the effects of EtOH exposure on the expression of these miRNAs and their target genes and pathways were assessed. In women who drank alcohol (EtOH) during pregnancy and non-drinking controls, matched individually for fetal sex and gestational age, the levels of miRNAs in fetal brain-derived exosomes (FB-Es) isolated from the mothers' serum correlated well with the contents of the corresponding fetal brain tissues obtained after voluntary pregnancy termination. In six EtOH-exposed cases and six matched controls, the levels of fetal brain and maternal serum miRNAs were quantified on the array by qRT-PCR. In FB-Es from 10 EtOH-exposed cases and 10 controls, selected miRNAs were quantified by ddPCR. Protein levels were quantified by ELISA. There were significant EtOH-associated reductions in the expression of several miRNAs, including miR-9 and its downstream neuronal targets BDNF, REST, Synapsin, and Sonic hedgehog. In 20 paired cases, reductions in FB-E miR-9 levels correlated strongly with reductions in fetal eye diameter, a prominent feature of FASDs. Thus, FB-E miR-9 levels might serve as a biomarker to predict FASDs in at-risk fetuses.
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Affiliation(s)
- Nune Darbinian
- Center for Neural Repair and Rehabilitation (Shriners Hospitals Pediatric Research Center), Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.H.); (D.M.); (A.B.); (N.M.); (G.T.)
| | - Monica Hampe
- Center for Neural Repair and Rehabilitation (Shriners Hospitals Pediatric Research Center), Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.H.); (D.M.); (A.B.); (N.M.); (G.T.)
| | - Diana Martirosyan
- Center for Neural Repair and Rehabilitation (Shriners Hospitals Pediatric Research Center), Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.H.); (D.M.); (A.B.); (N.M.); (G.T.)
| | - Ahsun Bajwa
- Center for Neural Repair and Rehabilitation (Shriners Hospitals Pediatric Research Center), Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.H.); (D.M.); (A.B.); (N.M.); (G.T.)
| | - Armine Darbinyan
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - Nana Merabova
- Center for Neural Repair and Rehabilitation (Shriners Hospitals Pediatric Research Center), Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.H.); (D.M.); (A.B.); (N.M.); (G.T.)
- Medical College of Wisconsin-Prevea Health, Green Bay, WI 54304, USA
| | - Gabriel Tatevosian
- Center for Neural Repair and Rehabilitation (Shriners Hospitals Pediatric Research Center), Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.H.); (D.M.); (A.B.); (N.M.); (G.T.)
| | - Laura Goetzl
- Department of Obstetrics & Gynecology, University of Texas, Houston, TX 77030, USA;
| | - Shohreh Amini
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
| | - Michael E. Selzer
- Center for Neural Repair and Rehabilitation (Shriners Hospitals Pediatric Research Center), Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (M.H.); (D.M.); (A.B.); (N.M.); (G.T.)
- Department of Neurology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
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Yaman M, Pirim D. Investigation of Common Pathways and Putative Biomarker Candidates of Colorectal Cancer and Insomnia by Using Integrative In-Silico Approaches. IRANIAN JOURNAL OF BIOTECHNOLOGY 2024; 22:e3827. [PMID: 39220338 PMCID: PMC11364928 DOI: 10.30498/ijb.2024.422185.3827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 03/09/2024] [Indexed: 09/04/2024]
Abstract
Background Colorectal cancer (CRC) is one of the leading causes of cancer-related mortalities across the globe. Accumulating evidence shows that individuals having sleep disorders such as insomnia are at high risk of developing CRC, yet the association of sleep disorders with CRC risk is still unclear. Here, we investigated the potential molecular connections between CRC and insomnia using integrative in silico approaches. Objective This study aims to explore the potential molecular connections between CRC and insomnia utilizing integrative in-silico methodologies. Methods and Methods Gene expression microarray datasets for CRC and insomnia samples were retrieved from the NCBI-GEO database and analyzed using R. Functional enrichment analysis of common differentially expressed genes (DEGs) was performed by the g: Profiler tool. Cytoscape software was used to construct a protein-protein interaction network and hub gene identification. Expression profiles of hub genes in TCGA datasets were also determined, and predicted miRNAs targeting hub genes were analyzed by miRNA target prediction tools. Results Our results revealed a total of 113 shared DEGs between the CRC and insomnia datasets. Six genes (HSP8A, GAPDH, HSP90AA1, EEF1G, RPS6, and RPLP0), which were also differently expressed in TCGA datasets, were prioritized as hub genes and were found to be enriched in pathways related to protein synthesis. hsa-miR-324-3p, hsa-miR-769-3p, and hsa-miR-16-5p were identified as promising miRNA biomarkers for two diseases. Conclusions Our in-silico analysis provides promising evidence of the molecular link between CRC and insomnia and highlights multiple potential molecular biomarkers and pathways. Validation of the results by wet lab work can be utilized for novel translational and precision medicine applications to alleviate the public health burden of CRC.
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Affiliation(s)
- Metehan Yaman
- Institute of Natural and Applied Sciences, Department of Molecular Biology and Genetics, Bursa Uludag University, Bursa, Türkiye
| | - Dilek Pirim
- Institute of Natural and Applied Sciences, Department of Molecular Biology and Genetics, Bursa Uludag University, Bursa, Türkiye
- Institute of Health Sciences, Department of Translational Medicine, Bursa Uludag University, Bursa, Türkiye
- Department of Molecular Biology and Genetics, Bursa Uludag University, Bursa, Türkiye
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Lee SK, Kim SH, Ahnn J. "A broken heart" becomes sleepless, literally. Mol Cells 2024; 47:100009. [PMID: 38211721 PMCID: PMC11004403 DOI: 10.1016/j.mocell.2024.100009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Affiliation(s)
- Sun-Kyung Lee
- Department of Life Sciences, Research Institute for Natural Sciences, Research Institute for Convergence of Basic Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea.
| | - Seung Hyun Kim
- Department of Life Sciences, Research Institute for Natural Sciences, Research Institute for Convergence of Basic Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Joohong Ahnn
- Department of Life Sciences, Research Institute for Natural Sciences, Research Institute for Convergence of Basic Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea.
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Kim YK, Choe HK. Core clock gene, Bmal1, is required for optimal second-level interval production. Anim Cells Syst (Seoul) 2023; 27:425-435. [PMID: 38125761 PMCID: PMC10732218 DOI: 10.1080/19768354.2023.2290827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 11/26/2023] [Indexed: 12/23/2023] Open
Abstract
Perception and production of second-level temporal intervals are critical in several behavioral and cognitive processes, including adaptive anticipation, motor control, and social communication. These processes are impaired in several neurological and psychological disorders, such as Parkinson's disease and attention-deficit hyperactivity disorder. Although evidence indicates that second-level interval timing exhibit circadian patterns, it remains unclear whether the core clock machinery controls the circadian pattern of interval timing. To investigate the role of core clock molecules in interval timing capacity, we devised a behavioral assay called the interval timing task to examine prospective motor interval timing ability. In this task, the mouse produces two separate nose pokes in a pretrained second-level interval to obtain a sucrose solution as a reward. We discovered that interval perception in wild-type mice displayed a circadian pattern, with the best performance observed during the late active phase. To investigate whether the core molecular clock is involved in the circadian control of interval timing, we employed Bmal1 knockout mice (BKO) in the interval timing task. The interval production of BKO did not display any difference between early and late active phase, without reaching the optimal interval production level observed in wild-type. In summary, we report that the core clock gene Bmal1 is required for the optimal performance of prospective motor timing typically observed during the late part of the active period.
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Affiliation(s)
- Yoon Kyoung Kim
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Han Kyoung Choe
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
- Convergence Research Advanced Centre for Olfaction, DGIST, Daegu, Republic of Korea
- Korea Brain Research Institute (KBRI), Daegu, Republic of Korea
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Earnhardt-San AL, Baker EC, Riley DG, Ghaffari N, Long CR, Cardoso RC, Randel RD, Welsh TH. Differential Expression of Circadian Clock Genes in the Bovine Neuroendocrine Adrenal System. Genes (Basel) 2023; 14:2082. [PMID: 38003025 PMCID: PMC10670998 DOI: 10.3390/genes14112082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Knowledge of circadian rhythm clock gene expression outside the suprachiasmatic nucleus is increasing. The purpose of this study was to determine whether expression of circadian clock genes differed within or among the bovine stress axis tissues (e.g., amygdala, hypothalamus, pituitary, adrenal cortex, and adrenal medulla). Tissues were obtained at an abattoir from eight mature nonpregnant Brahman cows that had been maintained in the same pasture and nutritional conditions. Sample tissues were stored in RNase-free sterile cryovials at -80 °C until the total RNA was extracted, quantified, assessed, and sequenced (NovaSeq 6000 system; paired-end 150 bp cycles). The trimmed reads were then mapped to a Bos taurus (B. taurus) reference genome (Umd3.1). Further analysis used the edgeR package. Raw gene count tables were read into RStudio, and low-expression genes were filtered out using the criteria of three minimum reads per gene in at least five samples. Normalization factors were then calculated using the trimmed mean of M values method to produce normalized gene counts within each sample tissue. The normalized gene counts important for a circadian rhythm were analyzed within and between each tissue of the stress axis using the GLM and CORR procedures of the Statistical Analysis System (SAS). The relative expression profiles of circadian clock genes differed (p < 0.01) within each tissue, with neuronal PAS domain protein 2 (NPAS2) having greater expression in the amygdala (p < 0.01) and period circadian regulator (PER1) having greater expression in all other tissues (p < 0.01). The expression among tissues also differed (p < 0.01) for individual circadian clock genes, with circadian locomotor output cycles protein kaput (CLOCK) expression being greater within the adrenal tissues and nuclear receptor subfamily 1 group D member 1 (NR1D1) expression being greater within the other tissues (p < 0.01). Overall, the results indicate that within each tissue, the various circadian clock genes were differentially expressed, in addition to being differentially expressed among the stress tissues of mature Brahman cows. Future use of these findings may assist in improving livestock husbandry and welfare by understanding interactions of the environment, stress responsiveness, and peripheral circadian rhythms.
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Affiliation(s)
- Audrey L. Earnhardt-San
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA; (A.L.E.-S.); (E.C.B.); (D.G.R.); (R.C.C.)
- Texas A&M AgriLife Research Center, Overton, TX 75684, USA; (C.R.L.); (R.D.R.)
| | - Emilie C. Baker
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA; (A.L.E.-S.); (E.C.B.); (D.G.R.); (R.C.C.)
| | - David G. Riley
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA; (A.L.E.-S.); (E.C.B.); (D.G.R.); (R.C.C.)
| | - Noushin Ghaffari
- Department of Computer Science, Prairie View A&M University, Prairie View, TX 77070, USA;
| | - Charles R. Long
- Texas A&M AgriLife Research Center, Overton, TX 75684, USA; (C.R.L.); (R.D.R.)
| | - Rodolfo C. Cardoso
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA; (A.L.E.-S.); (E.C.B.); (D.G.R.); (R.C.C.)
| | - Ronald D. Randel
- Texas A&M AgriLife Research Center, Overton, TX 75684, USA; (C.R.L.); (R.D.R.)
| | - Thomas H. Welsh
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA; (A.L.E.-S.); (E.C.B.); (D.G.R.); (R.C.C.)
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