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Kuemper S, Cairns AG, Birchall K, Yao Z, Large JM. Targeted protein degradation in CNS disorders: a promising route to novel therapeutics? Front Mol Neurosci 2024; 17:1370509. [PMID: 38685916 PMCID: PMC11057381 DOI: 10.3389/fnmol.2024.1370509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Targeted protein degradation (TPD) is a rapidly expanding field, with various PROTACs (proteolysis-targeting chimeras) in clinical trials and molecular glues such as immunomodulatory imide drugs (IMiDs) already well established in the treatment of certain blood cancers. Many current approaches are focused on oncology targets, leaving numerous potential applications underexplored. Targeting proteins for degradation offers a novel therapeutic route for targets whose inhibition remains challenging, such as protein aggregates in neurodegenerative diseases. This mini review focuses on the prospect of utilizing TPD for neurodegenerative disease targets, particularly PROTAC and molecular glue formats and opportunities for novel CNS E3 ligases. Some key challenges of utilizing such modalities including molecular design of degrader molecules, drug delivery and blood brain barrier penetrance will be discussed.
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Affiliation(s)
- Sandra Kuemper
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, United Kingdom
| | - Andrew G. Cairns
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, United Kingdom
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Jing K, Mipam TD, Zhang P, Peng W, Wang M, Yue B, Chen X, Wang J, Shu S, Fu C, Zhong J, Cai X. Transcriptomic analysis of yak longissimus dorsi muscle identifies genes associated with tenderness. Anim Biotechnol 2023; 34:3978-3987. [PMID: 37593948 DOI: 10.1080/10495398.2023.2248493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Meat tenderness is an important sensory index when consumers choose meat products, which determines the value of meat products and consumers' buying intentions. Yak meat is rich in nutrition and unique in flavor, which is favored by consumers. However, its meat has the deficiencies of low tenderness and poor taste, which has a negative impact on the value of its meat products and customer satisfaction. To identify the genes affecting the yak meat tenderness, we used RNA-seq to analyze the longissimus dorsi muscle of yaks with different tenderness, screened a total of 1120 differentially expressed genes (DEGs). Meanwhile, 23 pathways were significantly enriched. By further analysis, we identified eight genes related to yak meat tenderness (WNT5A, ARID5B, SERPINE1 KLHL40, RUNX1, MAFF, RFX7 and ARID5A). Notably, SERPINE1 was involved in the significant enrichment pathways of 'complement and coagulation cascade pathway', 'HIF-1 signaling pathway' and 'AGE-RAGE signaling pathway in diabetic complications' which can regulate meat tenderness. This implies that SERPINE1 may play an important regulatory role among them. The DEGs associated with yak meat quality screened in this work will be helpful to identify potential biomarkers related to meat tenderness.
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Affiliation(s)
- Kemin Jing
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, People's Republic of China
| | - Tserang Donko Mipam
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, People's Republic of China
| | - Peng Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, People's Republic of China
| | - Wei Peng
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, People's Republic of China
| | - Mingxiu Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, People's Republic of China
| | - Binglin Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, People's Republic of China
| | - Xuemei Chen
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, People's Republic of China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, People's Republic of China
| | - Shi Shu
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, People's Republic of China
| | - Changqi Fu
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, People's Republic of China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, People's Republic of China
| | - Xin Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, People's Republic of China
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Sharma P, Chatrathi HE. Insights into the diverse mechanisms and effects of variant CUL3-induced familial hyperkalemic hypertension. Cell Commun Signal 2023; 21:286. [PMID: 37845702 PMCID: PMC10577937 DOI: 10.1186/s12964-023-01269-z] [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: 05/17/2023] [Accepted: 08/12/2023] [Indexed: 10/18/2023] Open
Abstract
Familial hyperkalemic hypertension (FHHt), also known as Pseudohypoaldosteronism type II (PHAII) or Gordon syndrome is a rare Mendelian disease classically characterized by hyperkalemia, hyperchloremic metabolic acidosis, and high systolic blood pressure. The most severe form of the disease is caused by autosomal dominant variants in CUL3 (Cullin 3), a critical subunit of the multimeric CUL3-RING ubiquitin ligase complex. The recent identification of a novel FHHt disease variant of CUL3 revealed intricacies within the underlying disease mechanism. When combined with studies on canonical CUL3 variant-induced FHHt, these findings further support CUL3's role in regulating renal electrolyte transport and maintaining systemic vascular tone. However, the pathophysiological effects of CUL3 variants are often accompanied by diverse systemic disturbances in addition to classical FHHt symptoms. Recent global proteomic analyses provide a rationale for these systemic disturbances, paving the way for future mechanistic studies to reveal how CUL3 variants dysregulate processes outside of the renovascular axis. Video Abstract.
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Affiliation(s)
- Prashant Sharma
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA.
| | - Harish E Chatrathi
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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Thareja SK, Anfinson M, Cavanaugh M, Kim MS, Lamberton P, Radandt J, Brown R, Liang HL, Stamm K, Afzal MZ, Strande J, Frommelt MA, Lough JW, Fitts RH, Mitchell ME, Tomita-Mitchell A. Altered contractility, Ca 2+ transients, and cell morphology seen in a patient-specific iPSC-CM model of Ebstein's anomaly with left ventricular noncompaction. Am J Physiol Heart Circ Physiol 2023; 325:H149-H162. [PMID: 37204873 PMCID: PMC10312315 DOI: 10.1152/ajpheart.00658.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
Patients with two congenital heart diseases (CHDs), Ebstein's anomaly (EA) and left ventricular noncompaction (LVNC), suffer higher morbidity than either CHD alone. The genetic etiology and pathogenesis of combined EA/LVNC remain largely unknown. We investigated a familial EA/LVNC case associated with a variant (p.R237C) in the gene encoding Kelch-like protein 26 (KLHL26) by differentiating induced pluripotent stem cells (iPSCs) generated from affected and unaffected family members into cardiomyocytes (iPSC-CMs) and assessing iPSC-CM morphology, function, gene expression, and protein abundance. Compared with unaffected iPSC-CMs, CMs containing the KLHL26 (p.R237C) variant exhibited aberrant morphology including distended endo(sarco)plasmic reticulum (ER/SR) and dysmorphic mitochondria and aberrant function that included decreased contractions per minute, altered calcium transients, and increased proliferation. Pathway enrichment analyses based on RNASeq data indicated that the "structural constituent of muscle" pathway was suppressed, whereas the "ER lumen" pathway was activated. Taken together, these findings suggest that iPSC-CMs containing this KLHL26 (p.R237C) variant develop dysregulated ER/SR, calcium signaling, contractility, and proliferation.NEW & NOTEWORTHY We demonstrate here that iPSCs derived from patients with Ebstein's anomaly and left ventricular noncompaction, when differentiated into cardiomyocytes, display significant structural and functional changes that offer insight into disease pathogenesis, including altered ER/SR and mitochondrial morphology, contractility, and calcium signaling.
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Affiliation(s)
- Suma K Thareja
- Division of Congenital Heart Surgery, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Melissa Anfinson
- Division of Congenital Heart Surgery, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Matthew Cavanaugh
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States
| | - Min-Su Kim
- Division of Congenital Heart Surgery, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Peter Lamberton
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States
| | - Jackson Radandt
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States
| | - Ryan Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Huan-Ling Liang
- Division of Congenital Heart Surgery, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Karl Stamm
- Division of Congenital Heart Surgery, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Muhammad Zeeshan Afzal
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Jennifer Strande
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Michele A Frommelt
- Division of Pediatric Cardiology, Department of Pediatrics, Children's Wisconsin, Milwaukee, Wisconsin, United States
- Herma Heart Institute, Children's Wisconsin, Milwaukee, Wisconsin, United States
| | - John W Lough
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Robert H Fitts
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States
| | - Michael E Mitchell
- Division of Congenital Heart Surgery, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Herma Heart Institute, Children's Wisconsin, Milwaukee, Wisconsin, United States
| | - Aoy Tomita-Mitchell
- Division of Congenital Heart Surgery, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Herma Heart Institute, Children's Wisconsin, Milwaukee, Wisconsin, United States
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5
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Vega-Benedetti AF, Loi E, Moi L, Zavattari P. DNA methylation alterations at RE1-silencing transcription factor binding sites and their flanking regions in cancer. Clin Epigenetics 2023; 15:98. [PMID: 37301955 PMCID: PMC10257853 DOI: 10.1186/s13148-023-01514-9] [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: 01/11/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND DNA methylation changes, frequent early events in cancer, can modulate the binding of transcription factors. RE1-silencing transcription factor (REST) plays a fundamental role in regulating the expression of neuronal genes, and in particular their silencing in non-neuronal tissues, by inducing chromatin modifications, including DNA methylation changes, not only in the proximity of its binding sites but also in the flanking regions. REST has been found aberrantly expressed in brain cancer and other cancer types. In this work, we investigated DNA methylation alterations at REST binding sites and their flanking regions in a brain cancer (pilocytic astrocytoma), two gastrointestinal tumours (colorectal cancer and biliary tract cancer) and a blood cancer (chronic lymphocytic leukemia). RESULTS Differential methylation analyses focused on REST binding sites and their flanking regions were conducted between tumour and normal samples from our experimental datasets analysed by Illumina microarrays and the identified alterations were validated using publicly available datasets. We discovered distinct DNA methylation patterns between pilocytic astrocytoma and the other cancer types in agreement with the opposite oncogenic and tumour suppressive role of REST in glioma and non-brain tumours. CONCLUSIONS Our results suggest that these DNA methylation alterations in cancer may be associated with REST dysfunction opening the enthusiastic possibility to develop novel therapeutic interventions based on the modulation of this master regulator in order to restore the aberrant methylation of its target regions into a normal status.
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Affiliation(s)
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Loredana Moi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy.
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Blood Transcriptome Analysis of Beef Cow with Different Parity Revealed Candidate Genes and Gene Networks Regulating the Postpartum Diseases. Genes (Basel) 2022; 13:genes13091671. [PMID: 36140838 PMCID: PMC9498831 DOI: 10.3390/genes13091671] [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: 08/09/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Maternal parity is an important physiological factor influencing beef cow reproductive performance. However, there are few studies on the influence of different calving periods on early growth and postpartum diseases. Here, we conducted blood transcriptomic analysis on cows of different parities for gene discovery. We used Short Time Series Expression Miner (STEM) analysis to determine gene expression levels in cows of various parities and divided multiple parities into three main periods (nulliparous, primiparous, and multiparous) for subsequent analysis. Furthermore, the top 15,000 genes with the lowest median absolute deviation (MAD) were used to build a co-expression network using weighted correlation network analysis (WGCNA), and six independent modules were identified. Combing with Exon Wide Selection Signature (EWSS) and protein-protein interaction (PPI) analysis revealed that TPCN2, KIF22, MICAL3, RUNX2, PDE4A, TESK2, GPM6A, POLR1A, and KLHL6 involved in early growth and postpartum diseases. The GO and KEGG enrichment showed that the Parathyroid hormone synthesis, secretion, and action pathway and stem cell differentiation function-related pathways were enriched. Collectively, our study revealed candidate genes and gene networks regulating the early growth and postpartum diseases and provided new insights into the potential mechanism of reproduction advantages of different parity selection.
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van Gorp PRR, Zhang J, Liu J, Tsonaka R, Mei H, Dekker SO, Bart CI, De Coster T, Post H, Heck AJR, Schalij MJ, Atsma DE, Pijnappels DA, de Vries AAF. Sbk2, a Newly Discovered Atrium-Enriched Regulator of Sarcomere Integrity. Circ Res 2022; 131:24-41. [PMID: 35587025 DOI: 10.1161/circresaha.121.319300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Heart development relies on tight spatiotemporal control of cardiac gene expression. Genes involved in this intricate process have been identified using animals and pluripotent stem cell-based models of cardio(myo)genesis. Recently, the repertoire of cardiomyocyte differentiation models has been expanded with iAM-1, a monoclonal line of conditionally immortalized neonatal rat atrial myocytes (NRAMs), which allows toggling between proliferative and differentiated (ie, excitable and contractile) phenotypes in a synchronized and homogenous manner. METHODS In this study, the unique properties of conditionally immortalized NRAMs (iAMs) were exploited to identify and characterize (lowly expressed) genes with an as-of-yet uncharacterized role in cardiomyocyte differentiation. RESULTS Transcriptome analysis of iAM-1 cells at different stages during one cycle of differentiation and subsequent dedifferentiation identified ≈13 000 transcripts, of which the dynamic changes in expression upon cardiomyogenic differentiation mostly opposed those during dedifferentiation. Among the genes whose expression increased during differentiation and decreased during dedifferentiation were many with known (lineage-specific) functions in cardiac muscle formation. Filtering for cardiac-enriched low-abundance transcripts, identified multiple genes with an uncharacterized role during cardio(myo)genesis including Sbk2 (SH3 domain binding kinase family member 2). Sbk2 encodes an evolutionarily conserved putative serine/threonine protein kinase, whose expression is strongly up- and downregulated during iAM-1 cell differentiation and dedifferentiation, respectively. In neonatal and adult rats, the protein is muscle-specific, highly atrium-enriched, and localized around the A-band of cardiac sarcomeres. Knockdown of Sbk2 expression caused loss of sarcomeric organization in NRAMs, iAMs and their human counterparts, consistent with a decrease in sarcomeric gene expression as evinced by transcriptome and proteome analyses. Interestingly, co-immunoprecipitation using Sbk2 as bait identified possible interaction partners with diverse cellular functions (translation, intracellular trafficking, cytoskeletal organization, chromatin modification, sarcomere formation). CONCLUSIONS iAM-1 cells are a relevant and suitable model to identify (lowly expressed) genes with a hitherto unidentified role in cardiomyocyte differentiation as exemplified by Sbk2: a regulator of atrial sarcomerogenesis.
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Affiliation(s)
- P R R van Gorp
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, the Netherlands. (P.R.R.v.G., J.Z., J.L., S.O.D., C.I.B., T.D.C., M.J.S., D.E.A., D.A.P., A.A.F.d.V.)
| | - J Zhang
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, the Netherlands. (P.R.R.v.G., J.Z., J.L., S.O.D., C.I.B., T.D.C., M.J.S., D.E.A., D.A.P., A.A.F.d.V.)
| | - J Liu
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, the Netherlands. (P.R.R.v.G., J.Z., J.L., S.O.D., C.I.B., T.D.C., M.J.S., D.E.A., D.A.P., A.A.F.d.V.).,Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, the Netherlands. (H.M.)
| | - R Tsonaka
- Department of Biomedical Data Sciences, Medical Statistics Section, Leiden University Medical Center, the Netherlands. (R.T.)
| | - H Mei
- Central Laboratory, Longgang District People's Hospital of Shenzhen & The Third Affiliated Hospital of The Chinese University of Hong Kong, China (J.L.)
| | - S O Dekker
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, the Netherlands. (P.R.R.v.G., J.Z., J.L., S.O.D., C.I.B., T.D.C., M.J.S., D.E.A., D.A.P., A.A.F.d.V.)
| | - C I Bart
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, the Netherlands. (P.R.R.v.G., J.Z., J.L., S.O.D., C.I.B., T.D.C., M.J.S., D.E.A., D.A.P., A.A.F.d.V.)
| | - T De Coster
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, the Netherlands. (P.R.R.v.G., J.Z., J.L., S.O.D., C.I.B., T.D.C., M.J.S., D.E.A., D.A.P., A.A.F.d.V.)
| | - H Post
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, the Netherlands (H.P., A.J.R.H.).,Netherlands Proteomics Centre, the Netherlands (H.P., A.J.R.H.)
| | - A J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, the Netherlands (H.P., A.J.R.H.).,Netherlands Proteomics Centre, the Netherlands (H.P., A.J.R.H.)
| | - M J Schalij
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, the Netherlands. (P.R.R.v.G., J.Z., J.L., S.O.D., C.I.B., T.D.C., M.J.S., D.E.A., D.A.P., A.A.F.d.V.)
| | - D E Atsma
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, the Netherlands. (P.R.R.v.G., J.Z., J.L., S.O.D., C.I.B., T.D.C., M.J.S., D.E.A., D.A.P., A.A.F.d.V.)
| | - D A Pijnappels
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, the Netherlands. (P.R.R.v.G., J.Z., J.L., S.O.D., C.I.B., T.D.C., M.J.S., D.E.A., D.A.P., A.A.F.d.V.)
| | - A A F de Vries
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, the Netherlands. (P.R.R.v.G., J.Z., J.L., S.O.D., C.I.B., T.D.C., M.J.S., D.E.A., D.A.P., A.A.F.d.V.)
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Tamai S, Fujita SI, Komine R, Kanki Y, Aoki K, Watanabe K, Takekoshi K, Sugasawa T. Acute cold stress induces transient MuRF1 upregulation in the skeletal muscle of zebrafish. Biochem Biophys Res Commun 2022; 608:59-65. [PMID: 35390673 DOI: 10.1016/j.bbrc.2022.03.093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 12/26/2022]
Abstract
Cryotherapy is one of the most common treatments for trauma or fatigue in the field of sports medicine. However, the molecular biological effects of acute cold exposure on skeletal muscle remain unclear. Therefore, we used zebrafish, which have recently been utilized as an animal model for skeletal muscle, to comprehensively investigate and selectively clarify the time-course changes induced by cryotherapy. Zebrafish were exposed intermittently to cold stimulation three times for 15 min each. Thereafter, skeletal muscle samples were collected after 15 min and 1, 2, 4, and 6 h. mRNA sequencing revealed the involvement of trim63a, fbxo32, fbxo30a, and klhl38b in "protein ubiquitination" from the top 10 most upregulated genes. Subsequently, we examined the time-course changes of the four genes by quantitative PCR, and their expression peaked 2 h after cryotherapy and returned to baseline after 6 h. Moreover, the proteins encoded by trim63a and fbxo32 (muscle-specific RING finger protein 1 [MuRF1] and muscle atrophy F-box, respectively), which are known to be major genes encoding E3 ubiquitin ligases, were examined by western blotting, and MuRF1 expression displayed similar temporal changes as trim63a expression. These findings suggest that acute cold exposure transiently upregulates E3 ubiquitin ligases, especially MuRF1; thus, cryotherapy may contribute to the treatment of trauma or fatigue by promoting protein processing.
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Affiliation(s)
- Shinsuke Tamai
- Doctoral Program in Sports Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shin-Ichiro Fujita
- Laboratory of Clinical Examination/Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Ritsuko Komine
- Doctoral Program in Sports Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yasuharu Kanki
- Laboratory of Clinical Examination/Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kai Aoki
- Laboratory of Clinical Examination/Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Koichi Watanabe
- Faculty of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kazuhiro Takekoshi
- Laboratory of Clinical Examination/Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takehito Sugasawa
- Laboratory of Clinical Examination/Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Department of Sports Medicine Analysis, Open Facility Network Office, Research Facility Center for Science and Technology, University of Tsukuba, Japan.
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Ehrlich M. Risks and rewards of big-data in epigenomics research: an interview with Melanie Ehrlich. Epigenomics 2022; 14:351-358. [PMID: 35255735 DOI: 10.2217/epi-2022-0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Melanie Ehrlich, PhD, is a professor in the Tulane Cancer Center, the Tulane Center for Medical Bioinformatics and Genomics and the Hayward Human Genetics Program at Tulane Medical School, New Orleans, LA. She obtained her PhD in molecular biology in 1971 from the State University of New York at Stony Brook and completed postdoctoral research at Albert Einstein College of Medicine in 1972. She has been working on various aspects of epigenetics, starting with DNA methylation, since 1973. Her group made many first findings about DNA methylation (see below). For example, in 1982 and 1983, in collaboration with Charles Gehrke at the University of Missouri, she was the first to report tissue-specific and cancer-specific differences in overall DNA methylation in humans. In 1985, Xian-Yang Zhang and Richard Wang in her lab discovered a class of human DNA sequences specifically hypomethylated in sperm. In 1998, her group was the first to describe extensive losses of DNA methylation in pericentromeric and centromeric DNA repeats in human cancer. Her lab's many publications on the prevalence of both DNA hypermethylation and hypomethylation in the same cancers brought needed balance to our understanding of the epigenetics of cancer and to its clinical implications [1]. Besides working on cancer epigenetics, her research group has helped elucidate cytogenetic and gene expression abnormalities in the immunodeficiency, centromeric and facial anomalies (ICF) syndrome, a rare recessive disease often caused by mutations in DNMT3B. Her group also studied the epigenetics and transcriptomics of facioscapulohumeral muscular dystrophy (FSHD), whose disease locus is a tandem 3.3-kb repeat at subtelomeric 4q (that happens to be hypomethylated in ICF DNA [2]). Her study of FSHD has taken her in the direction of muscle (skeletal muscle, heart and aorta) epigenetics [3-6]. Recently, she has led research that applies epigenetics much more rigorously than usual to the evaluation of genetic variants from genome-wide association studies (GWAS) of osteoporosis and obesity. In continued collaboration with Sriharsa Pradhan at New England Biolabs and Michelle Lacey at Tulane University, she has compared 5-hydroxymethylcytosine and 5-methylcytosine clustering in various human tissues [7] and is studying myoblast methylomes that they generated by a new high-resolution enzymatic technique (enzymatic methyl-seq).
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center, Center for Medical Bioinformatics & Genomics, & Hayward Genetics Center, Tulane University, New Orleans, LA 70112, USA
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Abstract
Targeted protein degradation (TPD) is an emerging therapeutic modality with the potential to tackle disease-causing proteins that have historically been highly challenging to target with conventional small molecules. In the 20 years since the concept of a proteolysis-targeting chimera (PROTAC) molecule harnessing the ubiquitin-proteasome system to degrade a target protein was reported, TPD has moved from academia to industry, where numerous companies have disclosed programmes in preclinical and early clinical development. With clinical proof-of-concept for PROTAC molecules against two well-established cancer targets provided in 2020, the field is poised to pursue targets that were previously considered 'undruggable'. In this Review, we summarize the first two decades of PROTAC discovery and assess the current landscape, with a focus on industry activity. We then discuss key areas for the future of TPD, including establishing the target classes for which TPD is most suitable, expanding the use of ubiquitin ligases to enable precision medicine and extending the modality beyond oncology.
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Affiliation(s)
| | | | - Craig M Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA.
- Department of Pharmacology, Yale University, New Haven, CT, USA.
- Department of Chemistry, Yale University, New Haven, CT, USA.
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Ehrlich KC, Deng HW, Ehrlich M. Epigenetics of Mitochondria-Associated Genes in Striated Muscle. EPIGENOMES 2021; 6:1. [PMID: 35076500 PMCID: PMC8788487 DOI: 10.3390/epigenomes6010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/04/2021] [Accepted: 12/16/2021] [Indexed: 11/16/2022] Open
Abstract
Striated muscle has especially large energy demands. We identified 97 genes preferentially expressed in skeletal muscle and heart, but not in aorta, and found significant enrichment for mitochondrial associations among them. We compared the epigenomic and transcriptomic profiles of the 27 genes associated with striated muscle and mitochondria. Many showed strong correlations between their tissue-specific transcription levels, and their tissue-specific promoter, enhancer, or open chromatin as well as their DNA hypomethylation. Their striated muscle-specific enhancer chromatin was inside, upstream, or downstream of the gene, throughout much of the gene as a super-enhancer (CKMT2, SLC25A4, and ACO2), or even overlapping a neighboring gene (COX6A2, COX7A1, and COQ10A). Surprisingly, the 3' end of the 1.38 Mb PRKN (PARK2) gene (involved in mitophagy and linked to juvenile Parkinson's disease) displayed skeletal muscle/myoblast-specific enhancer chromatin, a myoblast-specific antisense RNA, as well as brain-specific enhancer chromatin. We also found novel tissue-specific RNAs in brain and embryonic stem cells within PPARGC1A (PGC-1α), which encodes a master transcriptional coregulator for mitochondrial formation and metabolism. The tissue specificity of this gene's four alternative promoters, including a muscle-associated promoter, correlated with nearby enhancer chromatin and open chromatin. Our in-depth epigenetic examination of these genes revealed previously undescribed tissue-specific enhancer chromatin, intragenic promoters, regions of DNA hypomethylation, and intragenic noncoding RNAs that give new insights into transcription control for this medically important set of genes.
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Affiliation(s)
- Kenneth C. Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA; (K.C.E.); (H.-W.D.)
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA; (K.C.E.); (H.-W.D.)
| | - Melanie Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA; (K.C.E.); (H.-W.D.)
- Tulane Cancer Center and Hayward Genetics Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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Subedi B, Anderson S, Croft TL, Rouchka EC, Zhang M, Hammond-Weinberger DR. Gene alteration in zebrafish exposed to a mixture of substances of abuse. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 278:116777. [PMID: 33689951 PMCID: PMC8053679 DOI: 10.1016/j.envpol.2021.116777] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/23/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
A recent surge in the use and abuse of diverse prescribed psychotic and illicit drugs necessitates the surveillance of drug residues in source water and the associated ecological impacts of chronic exposure to the aquatic organism. Thirty-six psychotic and illicit drug residues were determined in discharged wastewater from two centralized municipal wastewater treatment facilities and two wastewater receiving creeks for seven consecutive days in Kentucky. Zebrafish (Danio rerio) larvae were exposed to the environmental relevant mixtures of all drug residues, all illicit drugs, and all prescribed psychotic drugs. The extracted RNA from fish homogenates was sequenced, and differentially expressed sequences were analyzed for known or predicted nervous system expression, and screened annotated protein-coding genes to the true environmental cocktail mixture. Illicit stimulant (cocaine and one metabolite), opioids (methadone, methadone metabolite, and oxycodone), hallucinogen (MDA), benzodiazepine (oxazepam and temazepam), carbamazepine, and all target selective serotonin reuptake inhibitors including sertraline, fluoxetine, venlafaxine, and citalopram were quantified in 100% of collected samples from both creeks. The high dose cocktail mixture exposure group revealed the largest group of differentially expressed genes: 100 upregulated and 77 downregulated (p ≤ 0.05; q ≤ 0.05). The top 20 differentially expressed sequences in each exposure group comprise 82 unique transcripts corresponding to 74% annotated genes, 7% non-coding sequences, and 19% uncharacterized sequences. Among 61 differentially expressed sequences that corresponded to annotated protein-coding genes, 23 (38%) genes or their homologs are known to be expressed in the nervous system of fish or other organisms. Several of the differentially expressed sequences are associated primarily with the immune system, including several major histocompatibility complex class I and interferon-induced proteins. Interleukin-1 beta (downregulated in this study) abnormalities are considered a risk factor for psychosis. This is the first study to assess the contributions of multiple classes of psychotic and illicit drugs in combination with developmental gene expression.
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Affiliation(s)
- B Subedi
- Department of Chemistry, Murray State University, Murray, KY, United States.
| | - S Anderson
- Department of Biology, Murray State University, Murray, KY, United States
| | - T L Croft
- Department of Chemistry, Murray State University, Murray, KY, United States
| | - E C Rouchka
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY, United States; KBRIN Bioinformatics Core, University of Louisville, Louisville, KY, United States
| | - M Zhang
- Genomics Facility University of Louisville, Louisville, KY, United States
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Chen G, Yin Y, Lin Z, Wen H, Chen J, Luo W. Transcriptome profile analysis reveals KLHL30 as an essential regulator for myoblast differentiation. Biochem Biophys Res Commun 2021; 559:84-91. [PMID: 33933993 DOI: 10.1016/j.bbrc.2021.04.086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 04/20/2021] [Indexed: 11/29/2022]
Abstract
Skeletal muscle development is a sophisticated multistep process orchestrated by diverse myogenic transcription factors. Recent studies have suggested that Kelch-like genes play vital roles in muscle disease and myogenesis. However, it is still unclear how Kelch-like genes impact myoblast physiology. Here, through integrative analysis of the mRNA expression profile during chicken primary myoblast and C2C12 differentiation, many differentially expressed genes were found and suggested to be enriched in myoblast differentiation and muscle development. Interestingly, a little-known Kelch-like gene KLHL30 was screened as skeletal muscle-specific gene with essential roles in myogenic differentiation. Transcriptomic data and quantitative PCR analysis indicated that the expression of KLHL30 is upregulated under myoblast differentiation state. KLHL30 overexpression upregulated the protein expression of myogenic transcription factors (MYOD, MYOG, MEF2C) and induced myoblast differentiation and myotube formation, while knockdown of KLHL30 caused the opposite effect. Furthermore, KLHL30 was found to significantly decrease the numbers of cells in the S stage and thereby depress myoblast proliferation. Collectively, this study highlights that KLHL30 as a muscle-specific regulator plays essential roles in myoblast proliferation and differentiation.
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Affiliation(s)
- Genghua Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China
| | - Yunqian Yin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China
| | - Zetong Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China
| | - Huaqiang Wen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China
| | - Jiahui Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China.
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