1
|
Wang Y, Huang H, Chen J, Weng H. Crosstalk between histone/DNA modifications and RNA N 6-methyladenosine modification. Curr Opin Genet Dev 2024; 86:102205. [PMID: 38776766 DOI: 10.1016/j.gde.2024.102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal RNA modification in eukaryotic messenger RNAs (mRNAs), regulating gene expression at the transcription and post-transcription levels. Complex interplay between m6A and other well-studied epigenetic modifications, including histone modifications and DNA modification, has been extensively reported in recent years. The crosstalk between RNA m6A modification and histone/DNA modifications plays a critical role in establishing the chromatin state for the precise and specific fine-tuning of gene expression and undoubtedly has profound impacts on both physiological and pathological processes. In this review, we discuss the crosstalk between RNA m6A modification and histone/DNA modifications, emphasizing their sophisticated communications and the mechanisms underlying to gain a comprehensive view of the biological relevance of m6A-based epigenetic network.
Collapse
Affiliation(s)
- Yushuai Wang
- Guangzhou National Laboratory, Guangzhou 510005, China
| | - Huilin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Gehr Family Center for Leukemia Research & City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA 91010, USA.
| | - Hengyou Weng
- Guangzhou National Laboratory, Guangzhou 510005, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China; The First Affiliated Hospital, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou 510005, China.
| |
Collapse
|
2
|
O'Connor LM, O'Connor BA, Lim SB, Zeng J, Lo CH. Integrative multi-omics and systems bioinformatics in translational neuroscience: A data mining perspective. J Pharm Anal 2023; 13:836-850. [PMID: 37719197 PMCID: PMC10499660 DOI: 10.1016/j.jpha.2023.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 09/19/2023] Open
Abstract
Bioinformatic analysis of large and complex omics datasets has become increasingly useful in modern day biology by providing a great depth of information, with its application to neuroscience termed neuroinformatics. Data mining of omics datasets has enabled the generation of new hypotheses based on differentially regulated biological molecules associated with disease mechanisms, which can be tested experimentally for improved diagnostic and therapeutic targeting of neurodegenerative diseases. Importantly, integrating multi-omics data using a systems bioinformatics approach will advance the understanding of the layered and interactive network of biological regulation that exchanges systemic knowledge to facilitate the development of a comprehensive human brain profile. In this review, we first summarize data mining studies utilizing datasets from the individual type of omics analysis, including epigenetics/epigenomics, transcriptomics, proteomics, metabolomics, lipidomics, and spatial omics, pertaining to Alzheimer's disease, Parkinson's disease, and multiple sclerosis. We then discuss multi-omics integration approaches, including independent biological integration and unsupervised integration methods, for more intuitive and informative interpretation of the biological data obtained across different omics layers. We further assess studies that integrate multi-omics in data mining which provide convoluted biological insights and offer proof-of-concept proposition towards systems bioinformatics in the reconstruction of brain networks. Finally, we recommend a combination of high dimensional bioinformatics analysis with experimental validation to achieve translational neuroscience applications including biomarker discovery, therapeutic development, and elucidation of disease mechanisms. We conclude by providing future perspectives and opportunities in applying integrative multi-omics and systems bioinformatics to achieve precision phenotyping of neurodegenerative diseases and towards personalized medicine.
Collapse
Affiliation(s)
- Lance M. O'Connor
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Blake A. O'Connor
- School of Pharmacy, University of Wisconsin, Madison, WI, 53705, USA
| | - Su Bin Lim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Jialiu Zeng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Chih Hung Lo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| |
Collapse
|
3
|
Cai Q, He B, Tu G, Peng W, Shi S, Qian B, Liang Q, Peng S, Tao Y, Wang X. Whole-genome DNA methylation and DNA methylation-based biomarkers in lung squamous cell carcinoma. iScience 2023; 26:107013. [PMID: 37389184 PMCID: PMC10300376 DOI: 10.1016/j.isci.2023.107013] [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: 09/14/2022] [Revised: 03/11/2023] [Accepted: 05/29/2023] [Indexed: 07/01/2023] Open
Abstract
Exploring early detection methods through comprehensive evaluation of DNA methylation for lung squamous cell carcinoma (LUSC) patients is of great significance. By using different machine learning algorithms for feature selection and model construction based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, five methylation biomarkers in LUSC (along with mapped genes) were identified including cg14823851 (TBX4), cg02772121 (TRIM15), cg10424681 (C6orf201), cg12910906 (ARHGEF4), and cg20181079 (OR4D11), achieving extremely high sensitivity and specificity in distinguishing LUSC from normal samples in independent cohorts. Pyrosequencing assay verified DNA methylation levels, meanwhile qRT-PCR and immunohistochemistry results presented their accordant methylation-related gene expression statuses in paired LUSC and normal lung tissues. The five methylation-based biomarkers proposed in this study have great potential for the diagnosis of LUSC and could guide studies in methylation-regulated tumor development and progression.
Collapse
Affiliation(s)
- Qidong Cai
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Boxue He
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Guangxu Tu
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Weilin Peng
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Shuai Shi
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Banglun Qian
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Qingchun Liang
- Department of Pathology, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Shaoliang Peng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, China
- School of Computer Science, National University of Defense Technology, Changsha 410073, China
- Peng Cheng Lab, Shenzhen 518000, China
| | - Yongguang Tao
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan 410078, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
| | - Xiang Wang
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| |
Collapse
|
4
|
Chemistry revolutionizes genetics and epigenetics. Curr Opin Chem Biol 2023; 72:102247. [PMID: 36549086 DOI: 10.1016/j.cbpa.2022.102247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
5
|
Veerabhadrappa B, Sj S, Rao NN, Dyavaiah M. Loss of tRNA methyltransferase 9 and DNA damage response genes in yeast confers sensitivity to aminoglycosides. FEBS Lett 2023; 597:1149-1163. [PMID: 36708127 DOI: 10.1002/1873-3468.14591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/05/2023] [Accepted: 01/15/2023] [Indexed: 01/29/2023]
Abstract
tRNA methyltransferase 9 (Trm9)-catalysed tRNA modifications have been shown to translationally enhance the DNA damage response (DDR). Here, we show that Saccharomyces cerevisiae trm9Δ, distinct DNA repair and spindle assembly checkpoint (SAC) mutants are differentially sensitive to the aminoglycosides tobramycin, gentamicin and amikacin, indicating DDR and SAC activation might rely on translation fidelity, under aminoglycoside stress. Further, we report that the DNA damage induced by aminoglycosides in the base excision repair mutants ogg1Δ and apn1Δ is mediated by reactive oxygen species, which induce the DNA adduct 8-hydroxy deoxyguanosine. Finally, the synergistic effect of tobramycin and the DNA-damaging agent bleomycin to sensitize trm9Δ and the DDR mutants mlh1Δ, rad51Δ, mre11Δ and sgs1Δ at significantly lower concentrations compared with wild-type suggests that cells with tRNA modification dysregulation and DNA repair gene defects can be selectively sensitized using a combination of translation inhibitors and DNA-damaging agents.
Collapse
Affiliation(s)
- Bhavana Veerabhadrappa
- Department of Biotechnology, R V College of Engineering - Visvesvaraya Technological University, Bengaluru, Karnataka, India.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Sudharshan Sj
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Nagashree N Rao
- Department of Biotechnology, R V College of Engineering - Visvesvaraya Technological University, Bengaluru, Karnataka, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India
| |
Collapse
|
6
|
Potential and Metabolic Pathways of Eugenol in the Management of Xanthomonas perforans, a Pathogen of Bacterial Spot of Tomato. Int J Mol Sci 2022; 23:ijms232314648. [PMID: 36498976 PMCID: PMC9739100 DOI: 10.3390/ijms232314648] [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: 09/29/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022] Open
Abstract
Bacterial spot of tomato continues to pose a significant problem to tomato production worldwide. In Florida, bacterial spot of tomato caused by Xanthomonas perforans is one of the most important diseases responsible for tomato yield loss. This disease is difficult to control, and new strategies are continually being investigated to combat the devastating effect of this disease. Recent efforts focusing on essential oils based on small molecules have spurred interests in the utilization of this class of chemicals for disease management. In this study, we evaluated the efficacy of eugenol for the management of bacterial spot of tomato caused by X. perforans. In the greenhouse experiments, eugenol applied as a foliar spray significantly (p < 0.5) reduced bacterial spot disease compared to the untreated control. In the field experiments, the area under the disease progress curve (AUDPC) was significantly (p < 0.5) lower in the plots treated with eugenol or eugenol combined with the surfactant Cohere than in the untreated control plots, and it was comparable to the copper-based treatments. To provide additional insights into the possible pathways of eugenol activities, we applied a liquid chromatography mass spectrometry (LC-MS)-based metabolomic study using a thermo Q-Exactive orbitrap mass spectrometer with Dionex ultra high-performance liquid chromatography (UHPLC) on X. perforans strain 91−118 treated with eugenol. Our results showed that eugenol affected metabolite production in multiple pathways critical to bacterial survival. For example, treatment of cells with eugenol resulted in the downregulation of the glutathione metabolism pathway and associated metabolites, except for 5-oxoproline, which accumulation is known to be toxic to living cells. While the peaks corresponding to the putatively identified sarmentosin showed the most significant impact and reduced in response to eugenol treatment, branched-chain amino acids, such as L-isoleucine, increased in production, suggesting that eugenol may not negatively affect the protein biosynthesis pathways. The results from our study demonstrated the efficacy of eugenol in the management of bacterial spot of tomato under greenhouse and field conditions and identified multiple pathways that are targeted.
Collapse
|
7
|
Zhang C, Zhang R, Liang C, Deng Y, Li Z, Deng Y, Tang BZ. Charge-elimination strategy for constructing RNA-selective fluorescent probe undisturbed by mitochondria. Biomaterials 2022; 291:121915. [DOI: 10.1016/j.biomaterials.2022.121915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/04/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
|
8
|
Cheng L, Lu L, Chen Z, Ma D, Xi Z. Multiple-Gene Regulation for Enhanced Antitumor Efficacy with Branch-PCR-Assembled TP53 and MYC Gene Nanovector. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27206943. [PMID: 36296536 PMCID: PMC9609172 DOI: 10.3390/molecules27206943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
Multiple proteins are involved in network regulation through the crosstalk of different signaling pathways in cancers. Here, we propose a novel strategy of genome therapy with branch-PCR-assembled gene nanovectors to perform network-based gene regulation at multiple levels for cancer therapy. To validate network-based multiplex-gene regulation for genome therapy, we chose to simultaneously target one tumor suppressor gene (TP53) and one oncogene (MYC) in two different signaling pathways. The results showed that, compared to gene nanovectors targeting single genes (NP-TP53 and NP-shMYC), branch-PCR-assembled gene nanovectors simultaneously expressing p53 proteins and MYC shRNA arrays (NP-TP53-shMYC) showed enhanced antitumor efficacy in both MDA-MB-231 cancer cells and an MDA-MB-231-tumor-bearing mouse model. These findings indicate the feasibility and effectiveness of genome therapy in cancer therapy.
Collapse
Affiliation(s)
| | | | | | - Dejun Ma
- Correspondence: (D.M.); (Z.X.); Tel.: +86-022-23504782 (Z.X.)
| | - Zhen Xi
- Correspondence: (D.M.); (Z.X.); Tel.: +86-022-23504782 (Z.X.)
| |
Collapse
|
9
|
Wang H, Gao X, Yu S, Wang W, Liu G, Jiang X, Sun D. Circular RNAs regulate parental gene expression: A new direction for molecular oncology research. Front Oncol 2022; 12:947775. [PMID: 36091137 PMCID: PMC9453195 DOI: 10.3389/fonc.2022.947775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
CircRNAs have been the focus of research in recent years. They are differentially expressed in various human tumors and can regulate oncogenes and tumor suppressor genes expression through various mechanisms. The diversity, stability, evolutionary conservatism and cell- or tissue-specific expression patterns of circRNAs also endow them with important regulatory roles in promoting or inhibiting tumor cells malignant biological behaviors progression. More interestingly, emerging studies also found that circRNAs can regulate not only other genes expression, but also their parental gene expression and thus influence tumors development. Apart from some conventional features, circRNAs have a certain specificity in the regulation of parental gene expression, with a higher proportion affecting parental gene transcription and easier translation into protein to regulate parental gene expression. CircRNAs are generally thought to be unable to produce proteins and therefore the protein-coding ability exhibited by circRNAs in regulating parental gene expression is unique and indicates that the regulatory effects of parental gene expression by circRNAs are not only a competitive binding relationship, but also a more complex molecular relationship between circRNAs and parental gene, which deserves further study. This review summarizes the molecular mechanisms of circRNAs regulating parental gene expression and their biological roles in tumorigenesis and development, aiming to provide new ideas for the clinical application of circRNAs in tumor-targeted therapy.
Collapse
Affiliation(s)
- Haicun Wang
- General Surgery Department, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xin Gao
- General Surgery Department, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shaobo Yu
- General Surgery Department, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Weina Wang
- Department of Anesthesiology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guanglin Liu
- General Surgery Department, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xingming Jiang
- General Surgery Department, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Xingming Jiang, ; Dongsheng Sun,
| | - Dongsheng Sun
- General Surgery Department, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Xingming Jiang, ; Dongsheng Sun,
| |
Collapse
|
10
|
Cortazzo da Silva L, Aoki JI, Floeter-Winter LM. Finding Correlations Between mRNA and Protein Levels in Leishmania Development: Is There a Discrepancy? Front Cell Infect Microbiol 2022; 12:852902. [PMID: 35903202 PMCID: PMC9318571 DOI: 10.3389/fcimb.2022.852902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
Multiple genes and proteins have been identified as differentially expressed in the stages of the Leishmania life cycle. The differentiation processes are implicated in specific transcriptional and proteomic adjustments driven by gene expression regulation mechanisms. Leishmania parasites lack gene-specific transcriptional control, and gene expression regulation mostly depends on posttranscriptional mechanisms. Due to the lack of transcriptional regulation, criticism regarding the relevance of transcript quantification as a possible and efficient prediction of protein levels is recurrent in studies that use transcriptomic information. The advent of high-throughput technologies has improved the analysis of genomes, transcriptomes and proteomes for different organisms under several conditions. Nevertheless, defining the correlation between transcriptional and proteomic profiles requires arduous and expensive work and remains a challenge in Leishmania. In this review, we analyze transcriptomic and proteomic data for several Leishmania species in two different stages of the parasite life cycle: metacyclogenesis and amastigogenesis (amastigote differentiation). We found a correlation between mRNA and protein levels of 60.9% and 69.8% for metacyclogenesis and amastigogenesis, respectively; showing that majority mRNA and protein levels increase or decrease concomitantly. Among the analyzed genes that did not present correlation indicate that transcriptomic data should be carefully interpreted as protein expression. We also discuss possible explanations and mechanisms involved for this lack of correlation.
Collapse
|
11
|
Ma H, Wen H, Qin Y, Wu S, Zhang G, Wu CI, Cai Q. Homo-harringtonine, highly effective against coronaviruses, is safe in treating COVID-19 by nebulization. SCIENCE CHINA LIFE SCIENCES 2022; 65:1263-1266. [PMID: 35362917 PMCID: PMC8972673 DOI: 10.1007/s11427-021-2093-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/15/2022] [Indexed: 12/03/2022]
Affiliation(s)
- Huajuan Ma
- Cancer Center, Clifford Hospital, Jinan University, Guangzhou, 511495, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275, China
| | - Yaoxu Qin
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275, China
| | - Shijie Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275, China
| | - Ge Zhang
- Cancer Center, Clifford Hospital, Jinan University, Guangzhou, 511495, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275, China.
| | - Qichun Cai
- Cancer Center, Clifford Hospital, Jinan University, Guangzhou, 511495, China.
| |
Collapse
|
12
|
Performance Analysis of Deep Learning Models for Binary Classification of Cancer Gene Expression Data. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:1122536. [PMID: 35310177 PMCID: PMC8926523 DOI: 10.1155/2022/1122536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/09/2022] [Indexed: 11/23/2022]
Abstract
The classification of patients as cancer and normal patients by applying the computational methods on their gene expression profiles is an extremely important task. Recently, deep learning models, mainly multilayer perceptron and convolutional neural networks, have gained popularity for being applied on this type of datasets. This paper aims to analyze the performance of deep learning models on different types of cancer gene expression datasets as no such consolidated work is available. For this purpose, three deep learning models along with two feature selection method and four cancer gene expression datasets have been considered. It has resulted in a total of 24 different combinations to be analyzed. Out of four datasets, two are imbalanced and two are balanced in terms of number of normal and cancer samples. Experimental results show that the deep learning models have performed well in terms of true positive rate, precision, F1-score, and accuracy.
Collapse
|
13
|
Nguyen HVT, Jiang Y, Mohapatra S, Wang W, Barnes JC, Oldenhuis NJ, Chen KK, Axelrod S, Huang Z, Chen Q, Golder MR, Young K, Suvlu D, Shen Y, Willard AP, Hore MJA, Gómez-Bombarelli R, Johnson JA. Bottlebrush polymers with flexible enantiomeric side chains display differential biological properties. Nat Chem 2022; 14:85-93. [PMID: 34824461 PMCID: PMC9122101 DOI: 10.1038/s41557-021-00826-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/27/2021] [Indexed: 11/08/2022]
Abstract
Chirality and molecular conformation are central components of life: biological systems rely on stereospecific interactions between discrete (macro)molecular conformers, and the impacts of stereochemistry and rigidity on the properties of small molecules and biomacromolecules have been intensively studied. Nevertheless, how these features affect the properties of synthetic macromolecules has received comparably little attention. Here we leverage iterative exponential growth and ring-opening metathesis polymerization to produce water-soluble, chiral bottlebrush polymers (CBPs) from two enantiomeric pairs of macromonomers of differing rigidity. Remarkably, CBPs with conformationally flexible, mirror image side chains show several-fold differences in cytotoxicity, cell uptake, blood pharmacokinetics and liver clearance; CBPs with comparably rigid, mirror image side chains show no differences. These observations are rationalized with a simple model that correlates greater conformational freedom with enhanced chiral recognition. Altogether, this work provides routes to the synthesis of chiral nanostructured polymers and suggests key roles for stereochemistry and conformational rigidity in the design of future biomaterials.
Collapse
Affiliation(s)
- Hung V-T Nguyen
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yivan Jiang
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Somesh Mohapatra
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wencong Wang
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan C Barnes
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nathan J Oldenhuis
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kathleen K Chen
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Simon Axelrod
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Zhihao Huang
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qixian Chen
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew R Golder
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katherine Young
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dylan Suvlu
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yizhi Shen
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam P Willard
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael J A Hore
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Rafael Gómez-Bombarelli
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jeremiah A Johnson
- Department of Chemistry and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
14
|
Brunet de Courssou JB, Durr A, Adams D, Corvol JC, Mariani LL. Antisense therapies in neurological diseases. Brain 2021; 145:816-831. [PMID: 35286370 DOI: 10.1093/brain/awab423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/16/2021] [Accepted: 11/01/2021] [Indexed: 12/18/2022] Open
Abstract
Advances in targeted regulation of gene expression allowed new therapeutic approaches for monogenic neurological diseases. Molecular diagnosis has paved the way to personalized medicine targeting the pathogenic roots: DNA or its RNA transcript. These antisense therapies rely on modified nucleotides sequences (single-strand DNA or RNA, both belonging to the antisense oligonucleotides family, or double-strand interfering RNA) to act specifically on pathogenic target nucleic acids, thanks to complementary base pairing. Depending on the type of molecule, chemical modifications and target, base pairing will lead alternatively to splicing modifications of primary transcript RNA or transient messenger RNA degradation or non-translation. The key to success for neurodegenerative diseases also depends on the ability to reach target cells. The most advanced antisense therapies under development in neurological disorders are presented here, at the clinical stage of development, either at phase 3 or market authorization stage, such as in spinal amyotrophy, Duchenne muscular dystrophy, transthyretin-related hereditary amyloidosis, porphyria and amyotrophic lateral sclerosis; or in earlier clinical phase 1 B, for Huntington disease, synucleinopathies and tauopathies. We also discuss antisense therapies at the preclinical stage, such as in some tauopathies, spinocerebellar ataxias or other rare neurological disorders. Each subtype of antisense therapy, antisense oligonucleotides or interfering RNA, has proved target engagement or even clinical efficacy in patients; undisputable recent advances for severe and previously untreatable neurological disorders. Antisense therapies show great promise, but many unknowns remain. Expanding the initial successes achieved in orphan or rare diseases to other disorders will be the next challenge, as shown by the recent failure in Huntington disease or due to long-term preclinical toxicity in multiple system atrophy and cystic fibrosis. This will be critical in the perspective of new planned applications to premanifest mutation carriers, or other non-genetic degenerative disorders such as multiple system atrophy or Parkinson disease.
Collapse
Affiliation(s)
- Jean-Baptiste Brunet de Courssou
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Alexandra Durr
- Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - David Adams
- Department of Neurology, Bicêtre hospital, Assistance Publique Hôpitaux de Paris, Centre de Référence National des Neuropathies Périphériques Rares, Paris Saclay University, INSERM U 1195, Le Kremlin Bicêtre, France
| | - Jean-Christophe Corvol
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France.,Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Louise-Laure Mariani
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France.,Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| |
Collapse
|
15
|
He J, He H, Qi Y, Yang J, Zhi L, Jia Y. Application of epigenetics in dermatological research and skin management. J Cosmet Dermatol 2021; 21:1920-1930. [PMID: 34357681 DOI: 10.1111/jocd.14355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Epigenetics has recently evolved from a collection of diverse phenomena to a defined and far-reaching field of study. Epigenetic modifications of the genome, such as DNA methylation and histone modifications, have been reported to play a role in some skin diseases or cancer. AIMS The purpose of this article was to review the development of epigenetic in recent decades and their applications in dermatological research. METHODS An extensive literature search was conducted on epigenetic modifications since the first research on epigenetic. RESULTS This article summarizes the concept and development of epigenetics, as well as the process and principle of epigenetic modifications such as DNA methylation, histone modification, and non-coding RNA. Their application in some skin diseases and cosmetic research and development is also summarized. CONCLUSIONS This information will help to understand the mechanisms of epigenetics and some non-coding RNA, the discovery of the related drugs, and provide new insights for skin health management and cosmetic research and development.
Collapse
Affiliation(s)
- Jianbiao He
- Beijing Key Laboratory of Plant Resources Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,College of Chemistry and Materials Engineering, Key Laboratory of Cosmetic of China National Light Industry, Beijing Technology and Business University, Beijing, China
| | - Huaming He
- Beijing Key Laboratory of Plant Resources Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,College of Chemistry and Materials Engineering, Key Laboratory of Cosmetic of China National Light Industry, Beijing Technology and Business University, Beijing, China
| | - Yufeng Qi
- Shandong Huawutang Biological Technology Co, Ltd, Shandong, China
| | - Jie Yang
- Shandong Huawutang Biological Technology Co, Ltd, Shandong, China
| | - Leilei Zhi
- Shandong Huawutang Biological Technology Co, Ltd, Shandong, China
| | - Yan Jia
- Beijing Key Laboratory of Plant Resources Research and Development, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China.,College of Chemistry and Materials Engineering, Key Laboratory of Cosmetic of China National Light Industry, Beijing Technology and Business University, Beijing, China
| |
Collapse
|
16
|
Kim JH, Kim DH, Lim YH, Shin CH, Lee YA, Kim BN, Kim JI, Hong YC. Childhood Obesity-Related Mechanisms: MicroRNome and Transcriptome Changes in a Nested Case-Control Study. Biomedicines 2021; 9:biomedicines9080878. [PMID: 34440082 PMCID: PMC8389653 DOI: 10.3390/biomedicines9080878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/20/2022] Open
Abstract
Childhood obesity could contribute to adulthood obesity, leading to adverse health outcomes in adults. However, the mechanisms for how obesity is developed are still unclear. To determine the epigenome-wide and genome-wide expression changes related with childhood obesity, we compared microRNome and transcriptome levels as well as leptin protein levels in whole bloods of 12 obese and 24 normal children aged 6 years. miR-328-3p, miR-1301-3p, miR-4685-3p, and miR-6803-3p were negatively associated with all obesity indicators. The four miRNAs were also associated with 3948 mRNAs, and separate 475 mRNAs (185 among 3948 mRNAs) were associated with all obesity indicators. The 2533 mRNAs (64.2%) among the 3948 mRNAs and 286 mRNAs (60.2%) among the 475 mRNAs were confirmed as targets of the four miRNAs in public databases through miRWalk 2.0. Leptin protein was associated with miR-6803-3p negatively and all obesity indicators positively. Using DAVID bioinformatics resources 6.8, top three pathways for obesity-related gene set were metabolic pathways, pathways in cancer, and PI3K-Akt signaling pathway. The top three obesity-related disease classes were metabolic, cardiovascular, and chemdependency. Our results support that childhood obesity could be developed through miRNAs-related epigenetic mechanism and, further, these obesity-related epigenetic changes could control the pathways related with the development of various diseases.
Collapse
Affiliation(s)
- Jin Hee Kim
- Department of Integrative Bioscience & Biotechnology, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea;
- Correspondence: (J.H.K.); (Y.-C.H.)
| | - Da Hae Kim
- Department of Integrative Bioscience & Biotechnology, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea;
| | - Youn-Hee Lim
- Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul 03080, Korea;
- Environmental Health Center, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Korea; (C.H.S.); (Y.A.L.)
| | - Young Ah Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Korea; (C.H.S.); (Y.A.L.)
| | - Bung-Nyun Kim
- Division of Children and Adolescent Psychiatry, Department of Psychiatry, Seoul National University Hospital, Seoul 03080, Korea;
| | - Johanna Inhyang Kim
- Department of Psychiatry, Hanyang University Medical Center, Seoul 04763, Korea;
| | - Yun-Chul Hong
- Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul 03080, Korea;
- Environmental Health Center, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
- Correspondence: (J.H.K.); (Y.-C.H.)
| |
Collapse
|
17
|
Norepinephrine May Oppose Other Neuromodulators to Impact Alzheimer's Disease. Int J Mol Sci 2021; 22:ijms22147364. [PMID: 34298984 PMCID: PMC8304567 DOI: 10.3390/ijms22147364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/04/2023] Open
Abstract
While much of biomedical research since the middle of the twentieth century has focused on molecular pathways inside the cell, there is increasing evidence that extracellular signaling pathways are also critically important in health and disease. The neuromodulators norepinephrine (NE), serotonin (5-hydroxytryptamine, 5HT), dopamine (DA), acetylcholine (ACH), and melatonin (MT) are extracellular signaling molecules that are distributed throughout the brain and modulate many disease processes. The effects of these five neuromodulators on Alzheimer's disease (AD) are briefly examined in this paper, and it is hypothesized that each of the five molecules has a u-shaped (or Janus-faced) dose-response curve, wherein too little or too much signaling is pathological in AD and possibly other diseases. In particular it is suggested that NE is largely functionally opposed to 5HT, ACH, MT, and possibly DA in AD. In this scenario, physiological "balance" between the noradrenergic tone and that of the other three or four modulators is most healthy. If NE is largely functionally opposed to other prominent neuromodulators in AD, this may suggest novel combinations of pharmacological agents to counteract this disease. It is also suggested that the majority of cases of AD and possibly other diseases involve an excess of noradrenergic tone and a collective deficit of the other four modulators.
Collapse
|
18
|
Ni X, Wang Z, Gao D, Yuan H, Sun L, Zhu X, Zhou Q, Yang Z. A description of the relationship in healthy longevity and aging-related disease: from gene to protein. Immun Ageing 2021; 18:30. [PMID: 34172062 PMCID: PMC8229348 DOI: 10.1186/s12979-021-00241-0] [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: 02/01/2021] [Accepted: 06/14/2021] [Indexed: 11/22/2022]
Abstract
Human longevity is a complex phenotype influenced by both genetic and environmental factors. It is also known to be associated with various types of age-related diseases, such as Alzheimer's disease (AD) and cardiovascular disease (CVD). The central dogma of molecular biology demonstrates the conversion of DNA to RNA to the encoded protein. These proteins interact to form complex cell signaling pathways, which perform various biological functions. With prolonged exposure to the environment, the in vivo homeostasis adapts to the changes, and finally, humans adopt the phenotype of longevity or aging-related diseases. In this review, we focus on two different states: longevity and aging-related diseases, including CVD and AD, to discuss the relationship between genetic characteristics, including gene variation, the level of gene expression, regulation of gene expression, the level of protein expression, both genetic and environmental influences and homeostasis based on these phenotypes shown in organisms.
Collapse
Affiliation(s)
- Xiaolin Ni
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
- Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100001, P.R. China
| | - Zhaoping Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Danni Gao
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, P.R. China
| | - Huiping Yuan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Liang Sun
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Xiaoquan Zhu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Qi Zhou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China
| | - Ze Yang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P.R. China.
- Graduate School of Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100001, P.R. China.
| |
Collapse
|
19
|
Robertson AW, Sandoval J, Mohamed OG, Zhuang Y, Gallagher EE, Schmidt J, Caratelli L, Menon A, Schultz PJ, Torrez RM, Hay CL, Bell BA, Price PA, Garner AL, Tripathi A. Discovery of Surfactins as Inhibitors of MicroRNA Processing Using Cat-ELCCA. ACS Med Chem Lett 2021; 12:878-886. [PMID: 34141065 DOI: 10.1021/acsmedchemlett.1c00046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are a family of small noncoding RNAs that regulate gene expression. Due to their important activity in the fine-tuning of protein translation, abnormal expression of miRNAs has been linked to many human diseases, making the targeting of miRNAs attractive as a novel therapeutic strategy. Accordingly, researchers have been heavily engaged in the discovery of small molecule modulators of miRNAs. With an interest in the identification of new chemical space for targeting miRNAs, we developed a high-throughput screening (HTS) technology, catalytic enzyme-linked click chemistry assay (cat-ELCCA), aimed at the discovery of small molecule ligands for pre-miR-21, a miRNA that is frequently overexpressed in human cancers. From our HTS campaign, we found that natural products, a source of many impactful human medicines, may be a promising source of potential pre-miR-21-selective maturation inhibitors. Herein we describe our first efforts in natural product inhibitor discovery leading to the identification of a depsipeptide class of natural products as RNA-binding inhibitors of Dicer-mediated miRNA processing.
Collapse
Affiliation(s)
- Andrew W. Robertson
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Natural Products Discovery Core, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Jorge Sandoval
- Program in Chemical Biology, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Osama G. Mohamed
- Natural Products Discovery Core, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr el-Aini Street, Cairo 11562, Egypt
| | - Yihao Zhuang
- Natural Products Discovery Core, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Erin E. Gallagher
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Jennifer Schmidt
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Lisa Caratelli
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Arya Menon
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Pamela J. Schultz
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Natural Products Discovery Core, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Rachel M. Torrez
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Catherine L. Hay
- Natural Products Discovery Core, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Bailey A. Bell
- Natural Products Discovery Core, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Paul A. Price
- Biology Department, Eastern Michigan University, Ypsilanti, Michigan United States
| | - Amanda L. Garner
- Program in Chemical Biology, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Natural Products Discovery Core, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
20
|
Hagler LD, Krueger SB, Luu LM, Lanzendorf AN, Mitchell NL, Vergara JI, Curet LD, Zimmerman SC. Versatile Target-Guided Screen for Discovering Bidirectional Transcription Inhibitors of a Trinucleotide Repeat Disease. ACS Med Chem Lett 2021; 12:935-940. [PMID: 34141072 DOI: 10.1021/acsmedchemlett.1c00064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/17/2021] [Indexed: 01/29/2023] Open
Abstract
Myotonic dystrophy type 1 originates from d(CTG·CAG) repeats that undergo aberrant expansion during normal processing because the d(CTG) repeat forms stable hairpin structures. Bidirectional transcription of d(CTG·CAG) yields two RNA transcripts that undergo repeat-associated non-ATG (RAN) translation to form homopolymeric proteins. Thus, both the r(CUG) transcript and the r(CAG) transcript are known to be toxic. We report a pairwise fragment-based, target-guided approach to screen for proximity-induced click dimers formed on the nucleic acid template. This screen uses an azide/alkyne clickable fragment library of nucleic acid-binding ligands incubated in parallel, pairwise reactions as an alternative to our previously reported one-pot screening method. MALDI-TOF mass spectroscopy was used to detect template assisted click products. Hit compounds inhibited the in vitro transcription of d(CTG·CAG)90 bidirectionally with IC50 values in the low micromolar range. This approach may be broadly applicable to other trinucleotide repeat diseases and in targeting other disease-associated nucleic acid sequences.
Collapse
Affiliation(s)
- Lauren D. Hagler
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sarah B. Krueger
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Long M. Luu
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Amie N. Lanzendorf
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Niya L. Mitchell
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - J. Ignacio Vergara
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - L. Daniel Curet
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Steven C. Zimmerman
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
21
|
Pramanik D, Shelake RM, Kim MJ, Kim JY. CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement. MOLECULAR PLANT 2021; 14:127-150. [PMID: 33152519 DOI: 10.1016/j.molp.2020.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/14/2020] [Accepted: 11/02/2020] [Indexed: 05/03/2023]
Abstract
The central dogma (CD) of molecular biology is the transfer of genetic information from DNA to RNA to protein. Major CD processes governing genetic flow include the cell cycle, DNA replication, chromosome packaging, epigenetic changes, transcription, posttranscriptional alterations, translation, and posttranslational modifications. The CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next generation. Engineering of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world population. CRISPR technology enables programmable editing of CD processes to alter DNA, RNA, or protein, which would have been impossible in the past. Here, an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is provided. Furthermore, CRISPR applications in major thriving areas of research, such as gene discovery (allele mining and cryptic gene activation), introgression (de novo domestication and haploid induction), and application of desired traits beneficial to farmers or consumers (biotic/abiotic stress-resilient crops, plant cell factories, and delayed senescence), are described. Finally, the global regulatory policies, challenges, and prospects for CRISPR-mediated crop improvement are discussed.
Collapse
Affiliation(s)
- Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
| | - Mi Jung Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
| |
Collapse
|
22
|
Adil MS, Khulood D, Somanath PR. Targeting Akt-associated microRNAs for cancer therapeutics. Biochem Pharmacol 2020; 189:114384. [PMID: 33347867 DOI: 10.1016/j.bcp.2020.114384] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022]
Abstract
The uncontrolled growth and spread of abnormal cells because of activating protooncogenes and/or inactivating tumor suppressor genes are the hallmarks of cancer. The PI3K/Akt signaling is one of the most frequently activated pathways in cancer cells responsible for the regulation of cell survival and proliferation in stress and hypoxic conditions during oncogenesis. Non-coding RNAs are a large family of RNAs that are not involved in protein-coding, and microRNAs (miRNAs) are a sub-set of non-coding RNAs with a single strand of 18-25 nucleotides. miRNAs are extensively involved in the post-transcriptional regulation of gene expression and play an extensive role in the regulatory mechanisms including cell differentiation, proliferation, apoptosis, and tumorigenesis. The impact of cancer on mRNA stability and translation efficiency is extensive and therefore, cancerous tissues exhibit drastic alterations in the expression of miRNAs. miRNAs can be modulated by utilizing techniques such as miRNA mimics, miRNA antagonists, or CRISPR/Cas9. In addition to their capacity as potential targets in cancer therapy, they can be used as reliable biomarkers to diagnose the disease at the earliest stage. Recent evidence indicates that microRNA-mediated gene regulation intersects with the Akt pathway, forming an Akt-microRNA regulatory network. miRNAs and Akt in this network operate together to exert their cellular tasks. In the current review, we discuss the Akt-associated miRNAs in several cancers, their molecular regulation, and how this newly emerging knowledge may contribute greatly to revolutionize cancer therapy.
Collapse
Affiliation(s)
- Mir S Adil
- Clinical and Experimental Therapeutics, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, United States
| | - Daulat Khulood
- Clinical and Experimental Therapeutics, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, United States
| | - Payaningal R Somanath
- Clinical and Experimental Therapeutics, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, United States.
| |
Collapse
|
23
|
Affiliation(s)
- Chung-I Wu
- School of Life Sciences, Sun Yat-Sen University, China
| | - Guo-Dong Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, China
| | - Shuhua Xu
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, China
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China
| |
Collapse
|
24
|
Martin S, Blankenship C, Rausch JW, Sztuba-Solinska J. Using SHAPE-MaP to probe small molecule-RNA interactions. Methods 2019; 167:105-116. [DOI: 10.1016/j.ymeth.2019.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/20/2019] [Accepted: 04/16/2019] [Indexed: 01/14/2023] Open
|
25
|
Li G, Neuert G. Multiplex RNA single molecule FISH of inducible mRNAs in single yeast cells. Sci Data 2019; 6:94. [PMID: 31209217 PMCID: PMC6572782 DOI: 10.1038/s41597-019-0106-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/17/2019] [Indexed: 12/31/2022] Open
Abstract
Transcript levels powerfully influence cell behavior and phenotype and are carefully regulated at several steps. Recently developed single cell approaches such as RNA single molecule fluorescence in-situ hybridization (smFISH) have produced advances in our understanding of how these steps work within the cell. In comparison to single-cell sequencing, smFISH provides more accurate quantification of RNA levels. Additionally, transcript subcellular localization is directly visualized, enabling the analysis of transcription (initiation and elongation), RNA export and degradation. As part of our efforts to investigate how this type of analysis can generate improved models of gene expression, we used smFISH to quantify the kinetic expression of STL1 and CTT1 mRNAs in single Saccharomyces cerevisiae cells upon 0.2 and 0.4 M NaCl osmotic stress. In this Data Descriptor, we outline our procedure along with our data in the form of raw images and processed mRNA counts. We discuss how these data can be used to develop single cell modelling approaches, to study fundamental processes in transcription regulation and develop single cell image processing approaches.
Collapse
Affiliation(s)
- Guoliang Li
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
| |
Collapse
|