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Pang XL, Du HF, Nie F, Yang XG, Xu Y. Tubulin Alpha-1b as a Potential Biomarker for Lung Adenocarcinoma Diagnosis and Prognosis. Technol Cancer Res Treat 2023; 22:15330338231178391. [PMID: 37489256 PMCID: PMC10369087 DOI: 10.1177/15330338231178391] [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: 01/12/2023] [Revised: 04/25/2023] [Accepted: 05/09/2023] [Indexed: 07/26/2023] Open
Abstract
Background: Because lung cancer is the main cause of cancer deaths and lung adenocarcinoma (LUAD) accounts for more than 40% of all lung malignancies, it is essential to develop clinically useful biomarkers for the disease. The aim of this investigation is to assess the potential application of tubulin alpha-1b (TUBA1B) as a biomarker for diagnosing and monitoring the outcome of LUAD. Methods: The clinical data of the LUAD patients was retrospectively analyzed. Immunohistochemistry (IHC) analysis of a tissue microarray containing 90 LUAD cases was implemented to examine the expression of TUBA1B. The protein and mRNA levels of TUBA1B in serum were detected by enzyme-linked immunosorbent assay (ELISA) and quantitative real-time PCR (qRT-PCR) analysis respectively. UALCAN was employed to confirm the expression levels and survival probability of TUBA1B in LUAD patients. Results: Compared to adjacent non-cancerous tissues in the microarray, the expression of TUBA1B in LUAD tissues was much higher. The expression of TUBA1B in LUAD was statistically correlated with lymph node status (P = .031). Moreover, patients with higher TUBA1B expression had shorter overall survival (P < .0001). Furthermore, cox multi-factor analysis also suggested that TUBA1B may be an independent predictor for LUAD prognosis (P = .030). The results of TCGA data analysis by UALCAN were consistent with the microarray results, except for that TUBA1B was also significantly correlated with clinical tumor stages. Protein levels of TUBA1B in serum were obviously elevated in LUAD patients than control (P < .0001), and the area under the ROC curve was 0.99. TUBA1B also showed better sensitivity of 92.9% for LUAD than common clinical biomarkers. Conclusion: TUBA1B may be a non-invasive prognostic and diagnostic biomarker for LUAD patients.
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Affiliation(s)
- Xue-Li Pang
- School of Clinical Medicine, Chengdu Medical College, Chengdu, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Hong-Fei Du
- School of Clinical Medicine, Chengdu Medical College, Chengdu, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Fang Nie
- Department of Clinical Laboratory, Second People's Hospital of Chengdu, Chengdu, China
| | - Xiang-Gui Yang
- School of Clinical Medicine, Chengdu Medical College, Chengdu, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Ying Xu
- School of Clinical Medicine, Chengdu Medical College, Chengdu, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
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Su H, Tang X, Zhang X, Liu L, Jing L, Pan D, Sun W, He H, Yang C, Zhao D, Zhang H, Qi B. Comparative proteomics analysis reveals the difference during antler regeneration stage between red deer and sika deer. PeerJ 2019; 7:e7299. [PMID: 31346498 PMCID: PMC6642628 DOI: 10.7717/peerj.7299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/14/2019] [Indexed: 12/21/2022] Open
Abstract
Deer antler, as the only mammalian regenerative appendage, provides an optimal model to study regenerative medicine. Antler harvested from red deer or sika deer were mainly study objects used to disclose the mechanism underlying antler regeneration over past decades. A previous study used proteomic technology to reveal the signaling pathways of antler stem cell derived from red deer. Moreover, transcriptome of antler tip from sika deer provide us with the essential genes, which regulated antler development and regeneration. However, antler comparison between red deer and sika deer has not been well studied. In our current study, proteomics were employed to analyze the biological difference of antler regeneration between sika deer and red deer. The proteomics profile was completed by searching the UniProt database, and differentially expressed proteins were identified by bioinformatic software. Thirty-six proteins were highly expressed in red deer antler, while 144 proteins were abundant in sika deer. GO and KEGG analysis revealed that differentially expressed proteins participated in the regulation of several pathways including oxidative phosphorylation, ribosome, extracellular matrix interaction, and PI3K-Akt pathway.
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Affiliation(s)
- Hang Su
- Practice Innovations Center, Changchun University of Chinese Medicine, Changchun, China
| | - Xiaolei Tang
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Xiaocui Zhang
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Li Liu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Li Jing
- Practice Innovations Center, Changchun University of Chinese Medicine, Changchun, China
| | - Daian Pan
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Weijie Sun
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Huinan He
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Chonghui Yang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Daqing Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - He Zhang
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Bin Qi
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
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Comprehensive Analysis of lncRNAs and circRNAs Reveals the Metabolic Specialization in Oxidative and Glycolytic Skeletal Muscles. Int J Mol Sci 2019; 20:ijms20122855. [PMID: 31212733 PMCID: PMC6627206 DOI: 10.3390/ijms20122855] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/31/2019] [Accepted: 06/08/2019] [Indexed: 12/18/2022] Open
Abstract
The biochemical and functional differences between oxidative and glycolytic muscles could affect human muscle health and animal meat quality. However, present understanding of the epigenetic regulation with respect to lncRNAs and circRNAs is rudimentary. Here, porcine oxidative and glycolytic skeletal muscles, which were at the growth curve inflection point, were sampled to survey variant global expression of lncRNAs and circRNAs using RNA-seq. A total of 4046 lncRNAs were identified, including 911 differentially expressed lncRNAs (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and pathways (p < 0.05), including the oxidation-reduction process, glycolytic process, and fatty acid metabolic. All these were closely related to different phenotypes between oxidative and glycolytic muscles. Additionally, 810 circRNAs were identified, of which 137 were differentially expressed (p < 0.05). Interestingly, some circRNA-miRNA-mRNA networks were found, which were closely linked to muscle fiber-type switching and mitochondria biogenesis in muscles. Furthermore, 44.69%, 39.19%, and 54.01% of differentially expressed mRNAs, lncRNAs, and circRNAs respectively were significantly enriched in pig quantitative trait loci (QTL) regions for growth and meat quality traits. This study reveals a mass of candidate lncRNAs and circRNAs involved in muscle physiological functions, which may improve understanding of muscle metabolism and development from an epigenetic perspective.
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Identification of lncRNAs and Genes Responsible for Fatness and Fatty Acid Composition Traits between the Tibetan and Yorkshire Pigs. Int J Genomics 2019; 2019:5070975. [PMID: 31281828 PMCID: PMC6589220 DOI: 10.1155/2019/5070975] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 02/10/2019] [Accepted: 03/03/2019] [Indexed: 12/15/2022] Open
Abstract
Tibetan pigs from the Tibetan Plateau are characterized with a significant phenotypic difference relative to lowland pigs. In this study, a significant difference of the fatness and fatty acid composition traits was observed between the Tibetan and Yorkshire pigs. To uncover the involved mechanism, the expression profile of long noncoding RNAs (lncRNAs) and genes was compared between them. After serial filtered steps, 1,964 lncRNAs were obtained through our computational pipeline. In total, 63 and 715 lncRNAs and genes were identified to be differentially expressed. Evidence from cis- and trans-targeting analysis of lncRNAs demonstrated that some lncRNAs, such as MSTRG.14097 and MSTRG.8034, played important roles in the fatness and fatty acid composition traits. Bioinformatics analysis revealed that many candidate genes were responsible for the two traits. Of these, FASN, ACACA, SCD, ME3, PDHB, ACSS1, ACSS2, and ACLY were identified, which functioned in regulating the level of hexadecanoic acid, hexadecenoic acid, octadecenoic acid, and monounsaturated fatty acid. And LPGAT1, PDK4, ACAA1, and ADIPOQ were associated with the content of stearic acid, octadecadienoic acid, and polyunsaturated fatty acid. Candidate genes, which were responsible for fatness trait, consisted of FGF2, PLAG1, ADIPOQ, IRX3, MIF, IL-34, ADAM8, HMOX1, Vav1, and TLR8. In addition, association analysis also revealed that 34 and 57 genes significantly correlated to the fatness and fatty acid composition trait, respectively. Working out the mechanism caused by these lncRNAs and candidate genes is proven to be complicated but is invaluable to our understanding of fatness and fatty acid composition traits.
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Li Y, Zhang J, Huo C, Ding N, Li J, Xiao J, Lin X, Cai B, Zhang Y, Xu J. Dynamic Organization of lncRNA and Circular RNA Regulators Collectively Controlled Cardiac Differentiation in Humans. EBioMedicine 2017; 24:137-146. [PMID: 29037607 PMCID: PMC5652025 DOI: 10.1016/j.ebiom.2017.09.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/13/2017] [Accepted: 09/13/2017] [Indexed: 02/08/2023] Open
Abstract
Advances in developmental cardiology have increased our understanding of the early aspects of heart differentiation. However, understanding noncoding RNA (ncRNA) transcription and regulation during this process remains elusive. Here, we constructed transcriptomes for both long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) in four important developmental stages ranging from early embryonic to cardiomyocyte based on high-throughput sequencing datasets, which indicate the high stage-specific expression patterns of two ncRNA types. Additionally, higher similarities of samples within each stage were found, highlighting the divergence of samples collected from distinct cardiac developmental stages. Next, we developed a method to identify numerous lncRNA and circRNA regulators whose expression was significantly stage-specific and shifted gradually and continuously during heart differentiation. We inferred that these ncRNAs are important for the stages of cardiac differentiation. Moreover, transcriptional regulation analysis revealed that the expression of stage-specific lncRNAs is controlled by known key stage-specific transcription factors (TFs). In addition, circRNAs exhibited dynamic expression patterns independent from their host genes. Functional enrichment analysis revealed that lncRNAs and circRNAs play critical roles in pathways that are activated specifically during heart differentiation. We further identified candidate TF-ncRNA-gene network modules for each differentiation stage, suggesting the dynamic organization of lncRNAs and circRNAs collectively controlled cardiac differentiation, which may cause heart-related diseases when defective. Our study provides a foundation for understanding the dynamic regulation of ncRNA transcriptomes during heart differentiation and identifies the dynamic organization of novel key lncRNAs and circRNAs to collectively control cardiac differentiation.
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Affiliation(s)
- Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Jinwen Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Caiqin Huo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Junyi Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Jun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Xiaoyu Lin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Benzhi Cai
- Department of Clinical Pharmacy, The Second Affiliated Hospital, Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang 150086, China.
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China.
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China.
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