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Yang X, Lin H, Wang M, Huang X, Li K, Xia W, Zhang Y, Wang S, Chen W, Zheng C. Identification of key genes and pathways in duck fatty liver syndrome using gene set enrichment analysis. Poult Sci 2024; 103:104015. [PMID: 39003797 PMCID: PMC11298935 DOI: 10.1016/j.psj.2024.104015] [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] [Received: 04/25/2024] [Revised: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 07/16/2024] Open
Abstract
High-laying ducks are often fed high-energy, nutritious feeds to maintain high productivity, which predisposes them to lipid metabolism disorders and the development of fatty liver syndrome (FLS), which seriously affects production performance and has a substantial economic impact on the poultry industry. Therefore, it is necessary to elucidate the mechanisms underlying the development of fatty liver syndrome. In this study, seven Shan Partridge ducks, each with fatty liver syndrome and normal laying ducks, were selected, and Hematoxylin Eosin staining (HE staining), Masson staining, and transcriptome sequencing were performed on liver tissue. In addition to exploring key genes and pathways using conventional analysis methods, we constructed the first Kyoto Encyclopedia of Genes and Genomes (KEGG) database-based predefined gene set containing 12,764 pathways and 16,836 genes and further performed gene set enrichment analysis (GSEA) on the liver transcriptome data. Finally, key nodes and biological processes were identified via the protein-protein interaction (PPI) network. The results showed that the liver in the FL group exhibited steatosis and fibrosis, and a total of 3,663 genes with upregulated expression versus 2,296 downregulated genes were screened by conventional analysis. GSEA analysis and PPI network analysis revealed that the liver in the FL group exhibited disruption of the mitochondrial electron transport chain, leading to decreased oxidative phosphorylation and the secretion of excessive proinflammatory factors amid the continuous accumulation of lipids. Under continuous chronic inflammation, cell cycle arrest triggers apoptosis, while fibrosis becomes more severe, and procarcinogenic genes are activated, leading to the continuous development and deterioration of the liver. In conclusion, the predefined gene set constructed in this study can be used for GSEA, and the identified hub genes provide useful reference data and a solid foundation for the study of the genetic regulatory mechanism of fatty liver syndrome in ducks.
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Affiliation(s)
- Xue Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Hao Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China; College of Animal Science, Anhui Science and Technology University, Anhui 233100, P.R. China
| | - Mengpan Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China; College of Animal Science & Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300391, P.R. China
| | - Xuebing Huang
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Kaichao Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Weiguang Xia
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Yanan Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Shuang Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Wei Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China
| | - Chuntian Zheng
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, P.R. China.
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Willoughby O, Karrow NA, Marques Freire Cunha S, Asselstine V, Mallard BA, Cánovas Á. Characterization of the Hepatic Transcriptome for Divergent Immune-Responding Sheep Following Natural Exposure to Gastrointestinal Nematodes. Genes (Basel) 2024; 15:713. [PMID: 38927648 PMCID: PMC11202434 DOI: 10.3390/genes15060713] [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: 04/24/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Infections with gastrointestinal nematodes (GINs) reduce the economic efficiency of sheep operations and compromise animal welfare. Understanding the host's response to GIN infection can help producers identify animals that are naturally resistant to infection. The objective of this study was to characterize the hepatic transcriptome of sheep that had been naturally exposed to GIN parasites. The hepatic transcriptome was studied using RNA-Sequencing technology in animals characterized as high (n = 5) or medium (n = 6) based on their innate immune acute-phase (AP) response phenotype compared with uninfected controls (n = 4), and with biased antibody-mediated (AbMR, n = 5) or cell-mediated (CMR, n = 5) adaptive immune responsiveness compared to uninfected controls (n = 3). Following the assessment of sheep selected for innate responses, 0, 136, and 167 genes were differentially expressed (DE) between high- and medium-responding animals, high-responding and uninfected control animals, and medium-responding and uninfected control animals, respectively (false discovery rate (FDR) < 0.05, and fold change |FC| > 2). When adaptive immune responses were assessed, 0, 53, and 57 genes were DE between antibody- and cell-biased animals, antibody-biased and uninfected control animals, and cell-biased and uninfected control animals, respectively (FDR < 0.05, |FC| > 2). Functional analyses identified enriched gene ontology (GO) terms and metabolic pathways related to the innate immune response and energy metabolism. Six functional candidate genes were identified for further functional and validation studies to better understand the underlying biological mechanisms of host responses to GINs. These, in turn, can potentially help improve decision making and management practices to increase the overall host immune response to GIN infection.
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Affiliation(s)
- Olivia Willoughby
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, Ontario Agriculture College, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada; (O.W.); (N.A.K.); (S.M.F.C.); (V.A.)
| | - Niel A. Karrow
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, Ontario Agriculture College, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada; (O.W.); (N.A.K.); (S.M.F.C.); (V.A.)
| | - Samla Marques Freire Cunha
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, Ontario Agriculture College, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada; (O.W.); (N.A.K.); (S.M.F.C.); (V.A.)
| | - Victoria Asselstine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, Ontario Agriculture College, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada; (O.W.); (N.A.K.); (S.M.F.C.); (V.A.)
| | - Bonnie A. Mallard
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada;
| | - Ángela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, Ontario Agriculture College, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada; (O.W.); (N.A.K.); (S.M.F.C.); (V.A.)
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Liang J, Du B, Wan M, Sun L, Qin S, Nian F, Tang D. Effects of L-Leu-L-Leu peptide on growth, proliferation, and apoptosis in broiler intestinal epithelial cells. Poult Sci 2024; 103:103582. [PMID: 38457989 PMCID: PMC11067774 DOI: 10.1016/j.psj.2024.103582] [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] [Received: 11/12/2023] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 03/10/2024] Open
Abstract
Small peptides are nutrients and bioactive molecules that have dual regulatory effects on nutrition and physiology. They are of great significance for maintaining the intestinal health and production performance of broilers. We here cultured the primary small intestinal epithelial cells (IEC) of chicken in a medium containing L-Leu (Leu) and L-Leu-L-Leu (Leu-Leu) for 24 h. The untreated cells were considered as the control group. The growth, proliferation, and apoptosis of IEC were examined. By combining RNA-seq and label-free sequencing technology, candidate genes, proteins, and pathways related to the growth, proliferation, and apoptosis of IEC were screened. Immunofluorescence detection revealed that the purity of the isolated primary IEC was >90%. The Leu-Leu group significantly promoted IEC growth and proliferation and significantly inhibited IEC apoptosis, and the effect was better than those of the Leu and control groups. Using transcriptome sequencing, four candidate genes, CCL20, IL8L1, IL8, and IL6, were screened in the Leu group, and one candidate gene, IL8, was screened in the Leu-Leu group. Two candidate genes, IL6 and RGN, were screened in the Leu-Leu group compared with the Leu group. Nonquantitative proteomic marker sequencing results revealed that through the screening of candidate proteins and pathways, found one growth-related candidate protein PGM3 and three proliferation-related candidate proteins RPS17, RPS11, and RPL23, and two apoptosis-related candidate proteins GPX4 and PDPK1 were found in the Leu-Leu group compared with Leu group. In short, Leu-Leu could promote IEC growth and proliferation and inhibit IEC apoptosis. On combining transcriptome and proteome sequencing technologies, multiple immune- and energy-related regulatory signal pathways were found to be related to IEC growth, proliferation, and apoptosis. Three candidate genes of IL8, IL6, and RGN were identified, and six candidate proteins of PGM3, RPS17, RPS11, RPL23, GPX4, and PDPK1 were involved in IEC growth, proliferation, and apoptosis. The results provide valuable data for preliminarily elucidating small peptide-mediated IEC regulation pathways, improving the small peptide nutrition theoretical system, and establishing small peptide nutrition regulation technology.
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Affiliation(s)
- Jing Liang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Baolong Du
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Minyan Wan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Likun Sun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shizhen Qin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Fang Nian
- College of Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Defu Tang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
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Liu P, Liu J, Liu J, Yu X. Investigating the mechanisms of drug resistance and prognosis in ovarian cancer using single-cell RNA sequencing and bulk RNA sequencing. Aging (Albany NY) 2024; 16:4736-4758. [PMID: 38461424 PMCID: PMC10968697 DOI: 10.18632/aging.205628] [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] [Received: 10/16/2023] [Accepted: 02/02/2024] [Indexed: 03/12/2024]
Abstract
Ovarian cancer stands as a prevalent malignancy within the realm of gynecology, and the emergence of resistance to chemotherapeutic agents remains a pivotal impediment to both prognosis and treatment. Through a single-cell level investigation, we scrutinize the drug resistance and mitotic activity of the core tumor cells in ovarian cancer. Our study revisits the interrelationships and temporal trajectories of distinct epithelial cells (EPCs) subpopulations, while identifying genes associated with ovarian cancer prognosis. Notably, our findings establish a strong association between the drug resistance of EPCs and oxidative phosphorylation pathways. Subsequently, through subpopulation and temporal trajectory analysis, we confirm the intermediate position of EPCs subpopulation C0. Furthermore, we delve into the immunological functions and differentially expressed genes associated with the prognosis of C0, shedding light on the potential for constructing novel ovarian cancer prognosis models and identifying new therapeutic targets.
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Affiliation(s)
- Pengfei Liu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jinbao Liu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jinxing Liu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiao Yu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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5
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Fausset H, Spietz RL, Cox S, Cooper G, Spurzem S, Tokmina-Lukaszewska M, DuBois J, Broderick JB, Shepard EM, Boyd ES, Bothner B. A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri. Microbiol Spectr 2024; 12:e0041823. [PMID: 38179920 PMCID: PMC10846266 DOI: 10.1128/spectrum.00418-23] [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: 02/07/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Iron (Fe) and sulfur (S) are required elements for life, and changes in their availability can limit the ecological distribution and function of microorganisms. In anoxic environments, soluble Fe typically exists as ferrous iron [Fe(II)] and S as sulfide (HS-). These species exhibit a strong affinity that ultimately drives the formation of sedimentary pyrite (FeS2). Recently, paradigm-shifting studies indicate that Fe and S in FeS2 can be made bioavailable by methanogens through a reductive dissolution process. However, the impact of the utilization of FeS2, as opposed to canonical Fe and S sources, on the phenotype of cells is not fully understood. Here, shotgun proteomics was utilized to measure changes in the phenotype of Methanosarcina barkeri MS grown with FeS2, Fe(II)/HS-, or Fe(II)/cysteine. Shotgun proteomics tracked 1,019 proteins overall, with 307 observed to change between growth conditions. Functional characterization and pathway analyses revealed these changes to be systemic and largely tangential to Fe/S metabolism. As a final step, the proteomics data were viewed with respect to previously collected transcriptomics data to deepen the analysis. Presented here is evidence that M. barkeri adopts distinct phenotypes to exploit specific sources of Fe and S in its environment. This is supported by observed protein abundance changes across broad categories of cellular biology. DNA adjacent metabolism, central carbon metabolism methanogenesis, metal trafficking, quorum sensing, and porphyrin biosynthesis pathways are all features in the phenotypic differentiation. Differences in trace metal availability attributed to complexation with HS-, either as a component of the growth medium [Fe(II)/HS-] or generated through reduction of FeS2, were likely a major factor underpinning these phenotypic differences.IMPORTANCEThe methanogenic archaeon Methanosarcina barkeri holds great potential for industrial bio-mining and energy generation technologies. Much of the biochemistry of this microbe is poorly understood, and its characterization will provide a glimpse into biological processes that evolved close to life's origin. The discovery of its ability to extract iron and sulfur from bulk, solid-phase minerals shifted a longstanding paradigm that these elements were inaccessible to biological systems. The full elucidation of this process has the potential to help scientists and engineers extract valuable metals from low-grade ore and mine waste generating energy in the form of methane while doing so.
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Affiliation(s)
- Hunter Fausset
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Rachel L. Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Savannah Cox
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Gwendolyn Cooper
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Scott Spurzem
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | | | - Jennifer DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Eric M. Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Eric S. Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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Miranda MA, Macias-Velasco JF, Schmidt H, Lawson HA. Integrated transcriptomics contrasts fatty acid metabolism with hypoxia response in β-cell subpopulations associated with glycemic control. BMC Genomics 2023; 24:156. [PMID: 36978008 PMCID: PMC10052828 DOI: 10.1186/s12864-023-09232-5] [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: 05/24/2022] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Understanding how heterogeneous β-cell function impacts diabetes is imperative for therapy development. Standard single-cell RNA sequencing analysis illuminates some factors driving heterogeneity, but new strategies are required to enhance information capture. RESULTS We integrate pancreatic islet single-cell and bulk RNA sequencing data to identify β-cell subpopulations based on gene expression and characterize genetic networks associated with β-cell function in obese SM/J mice. We identify β-cell subpopulations associated with basal insulin secretion, hypoxia response, cell polarity, and stress response. Network analysis associates fatty acid metabolism and basal insulin secretion with hyperglycemic-obesity, while expression of Pdyn and hypoxia response is associated with normoglycemic-obesity. CONCLUSIONS By integrating single-cell and bulk islet transcriptomes, our study explores β-cell heterogeneity and identifies novel subpopulations and genetic pathways associated with β-cell function in obesity.
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Affiliation(s)
- Mario A Miranda
- Department of Genetics, Washington University School of Medicine, 660 South Euclid Ave, Campus Box 8232, Saint Louis, MO, 63110, USA
| | - Juan F Macias-Velasco
- Department of Genetics, Washington University School of Medicine, 660 South Euclid Ave, Campus Box 8232, Saint Louis, MO, 63110, USA
| | - Heather Schmidt
- Department of Genetics, Washington University School of Medicine, 660 South Euclid Ave, Campus Box 8232, Saint Louis, MO, 63110, USA
| | - Heather A Lawson
- Department of Genetics, Washington University School of Medicine, 660 South Euclid Ave, Campus Box 8232, Saint Louis, MO, 63110, USA.
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Elhamamsy AR, Metge BJ, Alsheikh HA, Shevde LA, Samant RS. Ribosome Biogenesis: A Central Player in Cancer Metastasis and Therapeutic Resistance. Cancer Res 2022; 82:2344-2353. [PMID: 35303060 PMCID: PMC9256764 DOI: 10.1158/0008-5472.can-21-4087] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 01/07/2023]
Abstract
Ribosomes are a complex ensemble of rRNA and ribosomal proteins that function as mRNA translation machines. Ribosome biogenesis is a multistep process that begins in the nucleolus and concludes in the cytoplasm. The process is tightly controlled by multiple checkpoint and surveillance pathways. Perturbations in these checkpoints and pathways can lead to hyperactivation of ribosome biogenesis. Emerging evidence suggests that cancer cells harbor a specialized class of ribosomes (onco-ribosomes) that facilitates the oncogenic translation program, modulates cellular functions, and promotes metabolic rewiring. Mutations in ribosomal proteins, rRNA processing, and ribosome assembly factors result in ribosomopathies that are associated with an increased risk of developing malignancies. Recent studies have linked mutations in ribosomal proteins and aberrant ribosomes with poor prognosis, highlighting ribosome-targeted therapy as a promising approach for treating patients with cancer. Here, we summarize various aspects of dysregulation of ribosome biogenesis and the impact of resultant onco-ribosomes on malignant tumor behavior, therapeutic resistance, and clinical outcome. Ribosome biogenesis is a promising therapeutic target, and understanding the important determinants of this process will allow for improved and perhaps selective therapeutic strategies to target ribosome biosynthesis.
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Affiliation(s)
- Amr R. Elhamamsy
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Brandon J. Metge
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Heba A. Alsheikh
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lalita A. Shevde
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama.,O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Rajeev S. Samant
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama.,O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama.,Birmingham VA Medical Center, Birmingham, Alabama.,Corresponding Author: Rajeev S. Samant, The University of Alabama at Birmingham, WTI 320E, 1824 6th Avenue South, Birmingham, AL 35233. Phone: 205-975-6262; E-mail:
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Pseudouridine-modified tRNA fragments repress aberrant protein synthesis and predict leukaemic progression in myelodysplastic syndrome. Nat Cell Biol 2022; 24:299-306. [PMID: 35292784 PMCID: PMC8924001 DOI: 10.1038/s41556-022-00852-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/24/2022] [Indexed: 11/09/2022]
Abstract
Transfer RNA-derived fragments (tRFs) are emerging small noncoding RNAs that, although commonly altered in cancer, have poorly defined roles in tumorigenesis1. Here we show that pseudouridylation (Ψ) of a stem cell-enriched tRF subtype2, mini tRFs containing a 5′ terminal oligoguanine (mTOG), selectively inhibits aberrant protein synthesis programmes, thereby promoting engraftment and differentiation of haematopoietic stem and progenitor cells (HSPCs) in patients with myelodysplastic syndrome (MDS). Building on evidence that mTOG-Ψ targets polyadenylate-binding protein cytoplasmic 1 (PABPC1), we employed isotope exchange proteomics to reveal critical interactions between mTOG and functional RNA-recognition motif (RRM) domains of PABPC1. Mechanistically, this hinders the recruitment of translational co-activator PABPC1-interacting protein 1 (PAIP1)3 and strongly represses the translation of transcripts sharing pyrimidine-enriched sequences (PES) at the 5′ untranslated region (UTR), including 5′ terminal oligopyrimidine tracts (TOP) that encode protein machinery components and are frequently altered in cancer4. Significantly, mTOG dysregulation leads to aberrantly increased translation of 5′ PES messenger RNA (mRNA) in malignant MDS-HSPCs and is clinically associated with leukaemic transformation and reduced patient survival. These findings define a critical role for tRFs and Ψ in difficult-to-treat subsets of MDS characterized by high risk of progression to acute myeloid leukaemia (AML). Bellodi, Dimitriou and colleagues report that pseudouridine-modified transfer-RNA fragments modulate the translation of transcripts sharing pyrimidine-enriched sequences at their 5′ untranslated regions and their dysregulation impacts myelodysplastic syndrome pathogenesis.
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Tsoi H, You CP, Leung MH, Man EPS, Khoo US. Targeting Ribosome Biogenesis to Combat Tamoxifen Resistance in ER+ve Breast Cancer. Cancers (Basel) 2022; 14:1251. [PMID: 35267559 PMCID: PMC8909264 DOI: 10.3390/cancers14051251] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is a heterogeneous disease. Around 70% of breast cancers are estrogen receptor-positive (ER+ve), with tamoxifen being most commonly used as an adjuvant treatment to prevent recurrence and metastasis. However, half of the patients will eventually develop tamoxifen resistance. The overexpression of c-MYC can drive the development of ER+ve breast cancer and confer tamoxifen resistance through multiple pathways. One key mechanism is to enhance ribosome biogenesis, synthesising mature ribosomes. The over-production of ribosomes sustains the demand for proteins necessary to maintain a high cell proliferation rate and combat apoptosis induced by therapeutic agents. c-MYC overexpression can induce the expression of eIF4E that favours the translation of structured mRNA to produce oncogenic factors that promote cell proliferation and confer tamoxifen resistance. Either non-phosphorylated or phosphorylated eIF4E can mediate such an effect. Since ribosomes play an essential role in c-MYC-mediated cancer development, suppressing ribosome biogenesis may help reduce aggressiveness and reverse tamoxifen resistance in breast cancer. CX-5461, CX-3543 and haemanthamine have been shown to repress ribosome biogenesis. Using these chemicals might help reverse tamoxifen resistance in ER+ve breast cancer, provided that c-MYC-mediated ribosome biogenesis is the crucial factor for tamoxifen resistance. To employ these ribosome biogenesis inhibitors to combat tamoxifen resistance in the future, identification of predictive markers will be necessary.
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Affiliation(s)
| | | | | | | | - Ui-Soon Khoo
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (H.T.); (C.-P.Y.); (M.-H.L.); (E.P.S.M.)
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Yang M, Zhou Y, Deng H, Zhou H, Cheng S, Zhang D, He X, Mai L, Chen Y, Chen J. Ribosomal Protein L23 Drives the Metastasis of Hepatocellular Carcinoma via Upregulating MMP9. Front Oncol 2021; 11:779748. [PMID: 34926291 PMCID: PMC8677661 DOI: 10.3389/fonc.2021.779748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths globally. Tumor metastasis is one of the major causes of high mortality of HCC. Identifying underlying key factors contributing to invasion and metastasis is critical to understand the molecular mechanisms of HCC metastasis. Here, we identified RNA binding protein L23 (RPL23) as a tumor metastasis driver in HCC. RPL23 was significantly upregulated in HCC tissues compared to adjacent normal tissues, and closely related to poor clinical outcomes in HCC patients. RPL23 depletion inhibited HCC cell proliferation, migration and invasion, and distant metastasis. Mechanistically, RPL23 directly associated with 3'UTR of MMP9, therefore positively regulated MMP9 expression. In conclusion, we identified that RPL23 might play an important role in HCC metastasis in an MMP9-dependent manner and be a potential therapeutic target for HCC tumorigenesis and metastasis.
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Affiliation(s)
- Minli Yang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yujiao Zhou
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Haijun Deng
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hongzhong Zhou
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Shengtao Cheng
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Dapeng Zhang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xin He
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Li Mai
- Department of Clinical Laboratory, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yao Chen
- Medical Examination Center, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Juan Chen
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
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11
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Wu B, Yu J, Liu Y, Dou G, Hou Y, Zhang Z, Pan X, Wang H, Zhou P, Zhu D. Potential Pathogenic Genes and Mechanism of Ankylosing Spondylitis: A Study Based on WGCNA and Bioinformatics Analysis. World Neurosurg 2021; 158:e543-e556. [PMID: 34775094 DOI: 10.1016/j.wneu.2021.11.014] [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: 08/07/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 10/19/2022]
Abstract
OBJECTIVE The purpose of this study is to explore the high-risk pathogenic driver genes for the occurrence and development of ankylosing spondylitis (AS) based on the bioinformatics method at the molecular level, to further elaborate the molecular mechanism of the pathogenesis of AS, and to provide potential biological targets for the diagnosis and treatment of clinical AS. METHODS The gene expression profile data GSE16879 were downloaded from the GEO (Gene Expression Omnibus) database, and weighted gene coexpression network analysis was performed. Highly correlated genes were divided into 14 modules, and 582 genes contained in the yellow (classic module) and 59 genes contained in grey60 (hematologic module) modules had the strongest correlation with AS. After protein-protein interaction (PPI) analysis, the top 20 genes with the highest scores were obtained from classic module and hematologic module, respectively. The DAVID (Database for Annotation, Visualization, and Integrated Discovery) database was used for Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis to analyze the biological functions of high-risk genes related to AS. RESULTS The results showed that the process of signal recognition particle-dependent cotranslational protein targeting to membrane, ribosome, nicotinamide adenine diphosphate hydride dehydrogenase (ubiquinone) activity, platelet activation, integrin complex, and extracellular matrix binding were enriched. CONCLUSIONS In this study, weighted gene coexpression network analysis, an efficient system biology algorithm, was used to analyze the high-risk pathogenic driver gene of AS. We provide new targets for the diagnosis and treatment of clinical AS and new ideas for further study.
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Affiliation(s)
- Bo Wu
- Department of Orthopaedics, the First Bethune Hospital of Jilin University, Changchun, China; Clinical College, Jilin University, Changchun, China
| | - Jing Yu
- Operating Theatre No. 1, the First Bethune Hospital of Jilin University, Changchun, China
| | - Yibing Liu
- Clinical College, Jilin University, Changchun, China
| | - Gaojing Dou
- Clinical College, Jilin University, Changchun, China; Department of Breast Surgery, the First Bethune Hospital of Jilin University, Changchun, China
| | - Yuanyuan Hou
- Clinical College, Jilin University, Changchun, China
| | - Zhiyun Zhang
- Clinical College, Jilin University, Changchun, China
| | - Xuefeng Pan
- Department of Obstetrics, the First Bethune Hospital of Jilin University, Changchun, China
| | - Hongyu Wang
- Clinical College, Jilin University, Changchun, China
| | - Pengcheng Zhou
- Department of Orthopaedics, the First Bethune Hospital of Jilin University, Changchun, China
| | - Dong Zhu
- Department of Orthopaedics, the First Bethune Hospital of Jilin University, Changchun, China.
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12
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Zhou Y, Gao X, Yuan M, Yang B, He Q, Cao J. Targeting Myc Interacting Proteins as a Winding Path in Cancer Therapy. Front Pharmacol 2021; 12:748852. [PMID: 34658888 PMCID: PMC8511624 DOI: 10.3389/fphar.2021.748852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/10/2021] [Indexed: 12/26/2022] Open
Abstract
MYC, as a well-known oncogene, plays essential roles in promoting tumor occurrence, development, invasion and metastasis in many kinds of solid tumors and hematologic neoplasms. In tumors, the low expression and the short half-life of Myc are reversed, cause tumorigenesis. And proteins that directly interact with different Myc domains have exerted a significant impact in the process of Myc-driven carcinogenesis. Apart from affecting the transcription of Myc target genes, Myc interaction proteins also regulate the stability of Myc through acetylation, methylation, phosphorylation and other post-translational modifications, as well as competitive combination with Myc. In this review, we summarize a series of Myc interacting proteins and recent advances in the related inhibitors, hoping that can provide new opportunities for Myc-driven cancer treatment.
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Affiliation(s)
- Yihui Zhou
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaomeng Gao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Meng Yuan
- Cancer Center of Zhejiang University, Hangzhou, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Cancer Center of Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Cancer Center of Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
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13
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Steffensen LB, Iversen XES, Hansen RS, Jensen PS, Thorsen ASF, Lindholt JS, Riber LPS, Beck HC, Rasmussen LM. Basement membrane proteins in various arterial beds from individuals with and without type 2 diabetes mellitus: a proteome study. Cardiovasc Diabetol 2021; 20:182. [PMID: 34496837 PMCID: PMC8428091 DOI: 10.1186/s12933-021-01375-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Basement membrane (BM) accumulation is a hallmark of micro-vessel disease in diabetes mellitus (DM). We previously reported marked upregulation of BM components in internal thoracic arteries (ITAs) from type 2 DM (T2DM) patients by mass spectrometry. Here, we first sought to determine if BM accumulation is a common feature of different arteries in T2DM, and second, to identify other effects of T2DM on the arterial proteome. METHODS Human arterial samples collected during heart and vascular surgery from well-characterized patients and stored in the Odense Artery Biobank were analysed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). We included ascending thoracic aortas (ATA) (n = 10 (type 2 DM, T2DM) and n = 10 (non-DM)); laser capture micro-dissected plaque- and media compartments from carotid plaques (n = 10 (T2DM) and n = 9 (non-DM)); and media- and adventitia compartments from ITAs (n = 9 (T2DM) and n = 7 (non-DM)). RESULTS We first extended our previous finding of BM accumulation in arteries from T2DM patients, as 7 of 12 pre-defined BM proteins were significantly upregulated in bulk ATAs consisting of > 90% media. Although less pronounced, BM components tended to be upregulated in the media of ITAs from T2DM patients, but not in the neighbouring adventitia. Overall, we did not detect effects on BM proteins in carotid plaques or in the plaque-associated media. Instead, complement factors, an RNA-binding protein and fibrinogens appeared to be regulated in these tissues from T2DM patients. CONCLUSION Our results suggest that accumulation of BM proteins is a general phenomenon in the medial layer of non-atherosclerotic arteries in patients with T2DM. Moreover, we identify additional T2DM-associated effects on the arterial proteome, which requires validation in future studies.
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Affiliation(s)
- Lasse Bach Steffensen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark.,Unit of Cardiovascular and Renal Research, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Xenia Emilie Sinding Iversen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark
| | - Rasmus Søgaard Hansen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark
| | - Pia Søndergaard Jensen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark
| | - Anne-Sofie Faarvang Thorsen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark
| | - Jes Sanddal Lindholt
- Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark.,Department of Cardiac, Thoracic, and Vascular Surgery, Odense University Hospital, Odense, Denmark
| | - Lars Peter Schødt Riber
- Department of Cardiac, Thoracic, and Vascular Surgery, Odense University Hospital, Odense, Denmark
| | - Hans Christian Beck
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark
| | - Lars Melholt Rasmussen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark. .,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark.
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14
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Su Y, Li Q, Zheng Z, Wei X, Hou P. Identification of genes, pathways and transcription factor-miRNA-target gene networks and experimental verification in venous thromboembolism. Sci Rep 2021; 11:16352. [PMID: 34381164 PMCID: PMC8357955 DOI: 10.1038/s41598-021-95909-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
Venous thromboembolism (VTE) is a complex, multifactorial life-threatening disease that involves vascular endothelial cell (VEC) dysfunction. However, the exact pathogenesis and underlying mechanisms of VTE are not completely clear. The aim of this study was to identify the core genes and pathways in VECs that are involved in the development and progression of unprovoked VTE (uVTE). The microarray dataset GSE118259 was downloaded from the Gene Expression Omnibus database, and 341 up-regulated and 8 down-regulated genes were identified in the VTE patients relative to the healthy controls, including CREB1, HIF1α, CBL, ILK, ESM1 and the ribosomal protein family genes. The protein-protein interaction (PPI) network and the transcription factor (TF)-miRNA-target gene network were constructed with these differentially expressed genes (DEGs), and visualized using Cytoscape software 3.6.1. Eighty-nine miRNAs were predicted as the targeting miRNAs of the DEGs, and 197 TFs were predicted as regulators of these miRNAs. In addition, 237 node genes and 4 modules were identified in the PPI network. The significantly enriched pathways included metabolic, cell adhesion, cell proliferation and cellular response to growth factor stimulus pathways. CREB1 was a differentially expressed TF in the TF-miRNA-target gene network, which regulated six miRNA-target gene pairs. The up-regulation of ESM1, HIF1α and CREB1 was confirmed at the mRNA and protein level in the plasma of uVTE patients. Taken together, ESM1, HIF1α and the CREB1-miRNA-target genes axis play potential mechanistic roles in uVTE development.
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Affiliation(s)
- Yiming Su
- Department of Vascular Surgery, LiuzhouWorker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005, Guangxi Province, China
| | - Qiyi Li
- Department of Vascular Surgery, LiuzhouWorker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005, Guangxi Province, China
| | - Zhiyong Zheng
- Department of Vascular Surgery, LiuzhouWorker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005, Guangxi Province, China
| | - Xiaomin Wei
- Department of Vascular Surgery, LiuzhouWorker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005, Guangxi Province, China
| | - Peiyong Hou
- Department of Vascular Surgery, LiuzhouWorker's Hospital, Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005, Guangxi Province, China.
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15
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Kang H, Choi MC, Kim S, Jeong JY, Kwon AY, Kim TH, Kim G, Joo WD, Park H, Lee C, Song SH, Jung SG, Hwang S, An HJ. USP19 and RPL23 as Candidate Prognostic Markers for Advanced-Stage High-Grade Serous Ovarian Carcinoma. Cancers (Basel) 2021; 13:cancers13163976. [PMID: 34439131 PMCID: PMC8391231 DOI: 10.3390/cancers13163976] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Ovarian cancer is one of the leading causes of deaths among patients with gynecological malignancies worldwide. In order to identify prognostic markers for ovarian cancer, we performed RNA-sequencing and analyzed the transcriptome data from 51 patients who received conventional therapies for high-grade serous ovarian carcinoma (HGSC). Patients with early-stage (I or II) HGSC exhibited higher immune gene expression than patients with advanced stage (III or IV) HGSC. In order to predict the prognosis of patients with HGSC, we created machine learning-based models and identified USP19 and RPL23 as candidate prognostic markers. Specifically, patients with lower USP19 mRNA levels and those with higher RPL23 mRNA levels had worse prognoses. This model was then used to analyze the data of patients with HGSC hosted on The Cancer Genome Atlas; this analysis validated the prognostic abilities of these two genes with respect to patient survival. Taken together, the transcriptome profiles of USP19 and RPL23 determined using a machine-learning model could serve as prognostic markers for patients with HGSC receiving conventional therapy.
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Affiliation(s)
- Haeyoun Kang
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (H.K.); (S.K.); (A.-Y.K.); (T.-H.K.); (G.K.)
- Center for Cancer Precision Medicine, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea;
| | - Min Chul Choi
- Center for Cancer Precision Medicine, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea;
- Comprehensive Gynecologic Cancer Center, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (W.D.J.); (H.P.); (C.L.); (S.H.S.); (S.G.J.)
| | - Sewha Kim
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (H.K.); (S.K.); (A.-Y.K.); (T.-H.K.); (G.K.)
| | - Ju-Yeon Jeong
- CHA Advanced Research Institute, CHA Bundang Medical Center, Seongnam-si 13496, Gyeonggi-do, Korea;
| | - Ah-Young Kwon
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (H.K.); (S.K.); (A.-Y.K.); (T.-H.K.); (G.K.)
| | - Tae-Hoen Kim
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (H.K.); (S.K.); (A.-Y.K.); (T.-H.K.); (G.K.)
| | - Gwangil Kim
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (H.K.); (S.K.); (A.-Y.K.); (T.-H.K.); (G.K.)
| | - Won Duk Joo
- Comprehensive Gynecologic Cancer Center, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (W.D.J.); (H.P.); (C.L.); (S.H.S.); (S.G.J.)
| | - Hyun Park
- Comprehensive Gynecologic Cancer Center, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (W.D.J.); (H.P.); (C.L.); (S.H.S.); (S.G.J.)
| | - Chan Lee
- Comprehensive Gynecologic Cancer Center, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (W.D.J.); (H.P.); (C.L.); (S.H.S.); (S.G.J.)
| | - Seung Hun Song
- Comprehensive Gynecologic Cancer Center, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (W.D.J.); (H.P.); (C.L.); (S.H.S.); (S.G.J.)
| | - Sang Geun Jung
- Comprehensive Gynecologic Cancer Center, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (W.D.J.); (H.P.); (C.L.); (S.H.S.); (S.G.J.)
| | - Sohyun Hwang
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (H.K.); (S.K.); (A.-Y.K.); (T.-H.K.); (G.K.)
- Center for Cancer Precision Medicine, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea;
- Department of Biomedical Science, CHA University, Pocheon-si 11160, Gyeonggi-do, Korea
- Correspondence: (S.H.); (H.J.A.); Tel.: +82-317804859 (S.H.); +82-317805045 (H.J.A.)
| | - Hee Jung An
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea; (H.K.); (S.K.); (A.-Y.K.); (T.-H.K.); (G.K.)
- Center for Cancer Precision Medicine, CHA Bundang Medical Center, CHA University, Seongnam-si 13496, Gyeonggi-do, Korea;
- Correspondence: (S.H.); (H.J.A.); Tel.: +82-317804859 (S.H.); +82-317805045 (H.J.A.)
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16
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Hagerty JR, Kim HC, Jolly ER. Multiomic analysis of Schistosoma mansoni reveals unique expression profiles in cercarial heads and tails. Commun Biol 2021; 4:860. [PMID: 34253841 PMCID: PMC8275615 DOI: 10.1038/s42003-021-02366-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Schistosomes require both molluscan and mammalian hosts for development. The larval cercaria exits the snail host and swims to identify and invade the mammalian host. The cercaria has two macrostructures, the head and the tail. The head invades the host, where it matures into an adult worm. The tail is lost after host invasion. Translation in the cercaria differs in each macrostructure, with higher levels of translation in the cercarial tail and little to no translational activity in the cercarial head. We compared the transcriptome and proteome of the cercarial head and tail and observed stark differences between the two macrostructures. We identified unique and differentially expressed transcripts and proteins, including ribosomal components expressed in higher levels in tails than in heads, which may explain the differences in translation levels between heads and tails. We also characterized the weak correlation between transcription and translation in infectious cercarial heads and tails.
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Affiliation(s)
- James R Hagerty
- Case Western Reserve University, Department of Biology, Cleveland, OH, USA
| | - Hyung Chul Kim
- Case Western Reserve University, Department of Biology, Cleveland, OH, USA
| | - Emmitt R Jolly
- Case Western Reserve University, Department of Biology, Cleveland, OH, USA.
- Case Western Reserve University, Center for Global Health and Disease, Cleveland, OH, USA.
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17
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Bonatto Paese CL, Brooks EC, Aarnio-Peterson M, Brugmann SA. Ciliopathic micrognathia is caused by aberrant skeletal differentiation and remodeling. Development 2021; 148:148/4/dev194175. [PMID: 33589509 DOI: 10.1242/dev.194175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/13/2021] [Indexed: 12/16/2022]
Abstract
Ciliopathies represent a growing class of diseases caused by defects in microtubule-based organelles called primary cilia. Approximately 30% of ciliopathies are characterized by craniofacial phenotypes such as craniosynostosis, cleft lip/palate and micrognathia. Patients with ciliopathic micrognathia experience a particular set of difficulties, including impaired feeding and breathing, and have extremely limited treatment options. To understand the cellular and molecular basis for ciliopathic micrognathia, we used the talpid2 (ta2 ), a bona fide avian model for the human ciliopathy oral-facial-digital syndrome subtype 14. Histological analyses revealed that the onset of ciliopathic micrognathia in ta2 embryos occurred at the earliest stages of mandibular development. Neural crest-derived skeletal progenitor cells were particularly sensitive to a ciliopathic insult, undergoing unchecked passage through the cell cycle and subsequent increased proliferation. Furthermore, whereas neural crest-derived skeletal differentiation was initiated, osteoblast maturation failed to progress to completion. Additional molecular analyses revealed that an imbalance in the ratio of bone deposition and resorption also contributed to ciliopathic micrognathia in ta2 embryos. Thus, our results suggest that ciliopathic micrognathia is a consequence of multiple aberrant cellular processes necessary for skeletal development, and provide potential avenues for future therapeutic treatments.
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Affiliation(s)
- Christian Louis Bonatto Paese
- Division of Developmental Biology, Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Evan C Brooks
- Division of Developmental Biology, Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Megan Aarnio-Peterson
- Division of Developmental Biology, Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Samantha A Brugmann
- Division of Developmental Biology, Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA .,Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Shriners Children's Hospital, Cincinnati, OH 45229, USA
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18
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Li X, Guo X, Zhu Y, Wei G, Zhang Y, Li X, Xu H, Cui J, Wu W, He J, Ritchie ME, Weiskittel TM, Li H, Yu H, Ding L, Shao M, Luo Q, Xu X, Teng X, Chang AH, Zhang J, Huang H, Hu Y. Single-Cell Transcriptomic Analysis Reveals BCMA CAR-T Cell Dynamics in a Patient with Refractory Primary Plasma Cell Leukemia. Mol Ther 2021; 29:645-657. [PMID: 33278564 PMCID: PMC7854300 DOI: 10.1016/j.ymthe.2020.11.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/18/2020] [Accepted: 11/25/2020] [Indexed: 11/30/2022] Open
Abstract
Chimeric antigen receptor T cell (CAR-T) therapy has revolutionized the clinical treatment of hematological malignancies due to the prominent anti-tumor effects. B cell maturation antigen (BCMA) CAR-T cells have demonstrated promising effects in patients with relapsed/refractory multiple myeloma. However, the dynamics of CAR-T cell proliferation and cytotoxicity in clinical patients remains unexplored. Here, we longitudinally profiled the transcriptomes of 55,488 T cells including CAR-T products, CAR-T cells, and endogenous T cells at the peak and remission phases in a plasma cell leukemia (PCL) patient treated with BCMA CAR-T cells by single-cell transcriptomic analysis. Our results showed distinct CAR-T and endogenous T cell subsets indicating stage-specific expression in proliferation, cytotoxicity, and intercellular signaling pathways. Furthermore, we found that CAR-T cells at peak phase gradually convert to a highly cytotoxic state from a highly proliferative state along a development trajectory. Moreover, re-analysis of a single cell study from CD8+ CD19 CAR-T confirmed our findings. These commonalities suggest conserved mechanisms for CAR-T treatment across hematological malignancies. Taken together, our current study provides insight into CAR-T cell dynamics during CAR-T therapy and proves that both BCMA CAR-T and CD19 CAR-T have similar transcriptional characteristics, especially at the CAR-T peak phase.
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MESH Headings
- Antigens, CD19/immunology
- B-Cell Maturation Antigen/immunology
- Drug Resistance, Neoplasm
- Gene Expression Profiling
- High-Throughput Nucleotide Sequencing
- Humans
- Immunotherapy, Adoptive/methods
- Leukemia, Plasma Cell/diagnosis
- Leukemia, Plasma Cell/genetics
- Leukemia, Plasma Cell/immunology
- Leukemia, Plasma Cell/therapy
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Recurrence
- Single-Cell Analysis/methods
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Transcriptome
- Treatment Outcome
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Affiliation(s)
- Xue Li
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Xin Guo
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Yuqing Zhu
- Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China; The First Hospital & Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Guoqing Wei
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China
| | - Yanlei Zhang
- Shanghai YaKe Biotechnology Ltd., Shanghai 200090, China
| | - Xia Li
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Huijun Xu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Jiazhen Cui
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Wenjun Wu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China
| | - Jingsong He
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China
| | - Matthew E Ritchie
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Taylor M Weiskittel
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Hua Yu
- Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China; The First Hospital & Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Lijuan Ding
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Mi Shao
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Qian Luo
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Xiaoxiao Xu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Xinyi Teng
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Alex H Chang
- Shanghai YaKe Biotechnology Ltd., Shanghai 200090, China
| | - Jin Zhang
- Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China; The First Hospital & Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China.
| | - Yongxian Hu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310058, China; Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 310058, China.
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19
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Trilla-Fuertes L, Ghanem I, Gámez-Pozo A, Maurel J, G-Pastrián L, Mendiola M, Peña C, López-Vacas R, Prado-Vázquez G, López-Camacho E, Zapater-Moros A, Heredia V, Cuatrecasas M, García-Alfonso P, Capdevila J, Conill C, García-Carbonero R, Ramos-Ruiz R, Fortes C, Llorens C, Nanni P, Fresno Vara JÁ, Feliu J. Genetic Profile and Functional Proteomics of Anal Squamous Cell Carcinoma: Proposal for a Molecular Classification. Mol Cell Proteomics 2020; 19:690-700. [PMID: 32107283 PMCID: PMC7124473 DOI: 10.1074/mcp.ra120.001954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Indexed: 12/21/2022] Open
Abstract
Anal squamous cell carcinoma is a rare tumor. Chemo-radiotherapy yields a 50% 3-year relapse-free survival rate in advanced anal cancer, so improved predictive markers and therapeutic options are needed. High-throughput proteomics and whole-exome sequencing were performed in 46 paraffin samples from anal squamous cell carcinoma patients. Hierarchical clustering was used to establish groups de novo Then, probabilistic graphical models were used to study the differences between groups of patients at the biological process level. A molecular classification into two groups of patients was established, one group with increased expression of proteins related to adhesion, T lymphocytes and glycolysis; and the other group with increased expression of proteins related to translation and ribosomes. The functional analysis by the probabilistic graphical model showed that these two groups presented differences in metabolism, mitochondria, translation, splicing and adhesion processes. Additionally, these groups showed different frequencies of genetic variants in some genes, such as ATM, SLFN11 and DST Finally, genetic and proteomic characteristics of these groups suggested the use of some possible targeted therapies, such as PARP inhibitors or immunotherapy.
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Affiliation(s)
| | - Ismael Ghanem
- Medical Oncology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Angelo Gámez-Pozo
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Joan Maurel
- Medical Oncology Department, Hospital Clinic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, University of Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Laura G-Pastrián
- Pathology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain; Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain
| | - Cristina Peña
- Pathology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | | | - Elena López-Camacho
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Andrea Zapater-Moros
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Victoria Heredia
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain; Translational Oncology Lab, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Hospital Clínic Universitari de Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Pilar García-Alfonso
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, /Dr. Esquerdo 46, 28007, Madrid, Spain
| | - Jaume Capdevila
- Medical Oncology Service, Vall Hebron University Hospital. Vall Hebron Institute of Oncology (VHIO), Paseigg de la Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Carles Conill
- Radiotherapy Oncology Department, Hospital Clínic Universitari de Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Rocío García-Carbonero
- Medical Oncology Service, Hospital Universitario 12 de Ocubre, Av. de Córdoba s/n, 28041, Madrid, Spain
| | - Ricardo Ramos-Ruiz
- Genomics Unit Cantoblanco, Parque Científico de Madrid, C/ Faraday 7, 28049, Madrid, Spain
| | - Claudia Fortes
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Carlos Llorens
- Biotechvana SL, Parque Científico de Madrid, C/ Faraday 7, 28049, Madrid, Spain
| | - Paolo Nanni
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain
| | - Jaime Feliu
- Medical Oncology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain; Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain.
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20
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Velásquez E, Martins-de-Souza D, Velásquez I, Carneiro GRA, Schmitt A, Falkai P, Domont GB, Nogueira FCS. Quantitative Subcellular Proteomics of the Orbitofrontal Cortex of Schizophrenia Patients. J Proteome Res 2019; 18:4240-4253. [PMID: 31581776 DOI: 10.1021/acs.jproteome.9b00398] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Schizophrenia is a chronic disease characterized by the impairment of mental functions with a marked social dysfunction. A quantitative proteomic approach using iTRAQ labeling and SRM, applied to the characterization of mitochondria (MIT), crude nuclear fraction (NUC), and cytoplasm (CYT), can allow the observation of dynamic changes in cell compartments providing valuable insights concerning schizophrenia physiopathology. Mass spectrometry analyses of the orbitofrontal cortex from 12 schizophrenia patients and 8 healthy controls identified 655 protein groups in the MIT fraction, 1500 in NUC, and 1591 in CYT. We found 166 groups of proteins dysregulated among all enriched cellular fractions. Through the quantitative proteomic analysis, we detect as the main biological pathways those related to calcium and glutamate imbalance, cell signaling disruption of CREB activation, axon guidance, and proteins involved in the activation of NF-kB signaling along with the increase of complement protein C3. Based on our data analysis, we suggest the activation of NF-kB as a possible pathway that links the deregulation of glutamate, calcium, apoptosis, and the activation of the immune system in schizophrenia patients. All MS data are available in the ProteomeXchange Repository under the identifier PXD015356 and PXD014350.
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Affiliation(s)
- Erika Velásquez
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry , Federal University of Rio de Janeiro , Rio de Janeiro 21941-909 , Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry, Institute of Biology , University of Campinas (UNICAMP) , Campinas 13083-970 , Brazil.,Experimental Medicine Research Cluster (EMRC) University of Campinas , Campinas 13083-887 , SP , Brazil.,Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION) , Conselho Nacional de Desenvolvimento Cientı́fico e Tecnológico (CNPq) , São Paulo , Brazil
| | | | - Gabriel Reis Alves Carneiro
- Laboratory of Proteomics, LADETEC, Institute of Chemistry , Federal University of Rio de Janeiro , Rio de Janeiro 21941-598 , Brazil
| | - Andrea Schmitt
- Department of Psychiatry and Psychotherapy , Ludwig Maximilian University of Munich (LMU) , 80539 Munich , Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy , Ludwig Maximilian University of Munich (LMU) , 80539 Munich , Germany
| | - Gilberto B Domont
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry , Federal University of Rio de Janeiro , Rio de Janeiro 21941-909 , Brazil
| | - Fabio C S Nogueira
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry , Federal University of Rio de Janeiro , Rio de Janeiro 21941-909 , Brazil.,Laboratory of Proteomics, LADETEC, Institute of Chemistry , Federal University of Rio de Janeiro , Rio de Janeiro 21941-598 , Brazil
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21
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van der Meeren LE, Kluiver J, Rutgers B, Alsagoor Y, Kluin PM, van den Berg A, Visser L. A super-SILAC based proteomics analysis of diffuse large B-cell lymphoma-NOS patient samples to identify new proteins that discriminate GCB and non-GCB lymphomas. PLoS One 2019; 14:e0223260. [PMID: 31603917 PMCID: PMC6788715 DOI: 10.1371/journal.pone.0223260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/17/2019] [Indexed: 11/20/2022] Open
Abstract
Diffuse large B-cell lymphoma—not otherwise specified (DLBCL-NOS) is a large and heterogeneous subgroup of non-Hodgkin lymphoma. DLBCL can be subdivided into germinal centre B-cell like (GCB) and activated B-cell like (ABC or non-GCB) using a gene-expression based or an immunohistochemical approach. In this study we aimed to identify additional proteins that are differentially expressed between GCB and non-GCB DLBCL. A reference super-SILAC mix, including proteins of eight B-cell lymphoma cell lines, was mixed with proteins isolated from seven non-GCB DLBCL and five GCB DLBCL patient tissue samples to quantify protein levels. Protein identification and quantification was performed by LC-MS. We identified a total of 4289 proteins, with a four-fold significant difference in expression between non-GCB and GCB DLBCL for 37 proteins. Four proteins were selected for validation in the same cases and replication in an independent cohort of 47 DLBCL patients by immunohistochemistry. In the validation cohort, we observed a non-significant trend towards the same differential expression pattern as observed in the proteomics. The replication study showed significant and consistent differences for two of the proteins: expression of glomulin (GLMN) was higher in GCB DLBCL, while expression of ribosomal protein L23 (RPL23) was higher in non-GCB DLBCL. These proteins are functionally linked to important pathways involving MYC, p53 and angiogenesis. In summary, we showed increased expression of RPL23 and decreased expression of GLMN in non-GCB compared to GCB DLBCL on purified primary DLBCL patient samples and replicated these results in an independent patient cohort.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/immunology
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/immunology
- Cell Line, Tumor
- Child
- Cohort Studies
- Female
- Gene Expression
- Germinal Center/immunology
- Germinal Center/pathology
- Humans
- Isotope Labeling/methods
- Lymphocyte Activation
- Lymphoma, Large B-Cell, Diffuse/classification
- Lymphoma, Large B-Cell, Diffuse/diagnosis
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Neoplasm Staging
- Proteomics/methods
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/immunology
- Ribosomal Proteins/genetics
- Ribosomal Proteins/immunology
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/immunology
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Affiliation(s)
- L. E. van der Meeren
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands
- * E-mail:
| | - J. Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - B. Rutgers
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Y. Alsagoor
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - P. M. Kluin
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - A. van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - L. Visser
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
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22
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Li XM, Li ZY, Wang YD, Wang JQ, Yang PL. Quercetin Inhibits the Proliferation and Aflatoxins Biosynthesis of Aspergillus flavus. Toxins (Basel) 2019; 11:toxins11030154. [PMID: 30857280 PMCID: PMC6468572 DOI: 10.3390/toxins11030154] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/03/2019] [Accepted: 03/05/2019] [Indexed: 01/10/2023] Open
Abstract
In this work of quercetin’s anti-proliferation action on A. flavus, we revealed that quercetin can effectively hamper the proliferation of A. flavus in dose-effect and time-effect relationships. We tested whether quercetin induced apoptosis in A. flavus via various detection methods, such as phosphatidylserine externalization and Hoechst 33342 staining. The results showed that quercetin had no effect on phosphatidylserine externalization and cell nucleus in A. flavus. Simultaneously, quercetin reduced the levels of reactive oxygen species (ROS). For a better understanding of the molecular mechanism of the A. flavus response to quercetin, the RNA-Seq was used to explore the transcriptomic profiles of A. flavus. According to transcriptome sequencing data, quercetin inhibits the proliferation and aflatoxin biosynthesis by regulating the expression of development-related genes and aflatoxin production-related genes. These results will provide some theoretical basis for quercetin as an anti-mildew agent resource.
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Affiliation(s)
- Xiu-Mei Li
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- National Engineering Research Center of Biological Feed, Beijing 100081, China.
| | - Zhong-Yuan Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Ya-Dong Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Jin-Quan Wang
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Pei-Long Yang
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- National Engineering Research Center of Biological Feed, Beijing 100081, China.
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23
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Molavi G, Samadi N, Hosseingholi EZ. The roles of moonlight ribosomal proteins in the development of human cancers. J Cell Physiol 2018; 234:8327-8341. [PMID: 30417503 DOI: 10.1002/jcp.27722] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 09/23/2018] [Indexed: 12/13/2022]
Abstract
"Moonlighting protein" is a term used to define a single protein with multiple functions and different activities that are not derived from gene fusions, multiple RNA splicing, or the proteolytic activity of promiscuous enzymes. Different proteinous constituents of ribosomes have been shown to have important moonlighting extra-ribosomal functions. In this review, we introduce the impact of key moonlight ribosomal proteins and dependent signal transduction in the initiation and progression of various cancers. As a future perspective, the potential role of these moonlight ribosomal proteins in the diagnosis, prognosis, and development of novel strategies to improve the efficacy of therapies for human cancers has been suggested.
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Affiliation(s)
- Ghader Molavi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasser Samadi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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24
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Abstract
The rates of ribosome production by a nucleolus and of protein biosynthesis by ribosomes are tightly correlated with the rate of cell growth and proliferation. All these processes must be matched and appropriately regulated to provide optimal cell functioning. Deregulation of certain factors, including oncogenes, controlling these processes, especially ribosome biosynthesis, can lead to cell transformation. Cancer cells are characterized by intense ribosome biosynthesis which is advantageous for their growth and proliferation. On the other hand, this feature can be engaged as an anticancer strategy. Numerous nucleolar factors such as nucleolar and ribosomal proteins as well as different RNAs, in addition to their role in ribosome biosynthesis, have other functions, including those associated with cancer biology. Some of them can contribute to cell transformation and cancer development. Others, under stress evoked by different factors which often hamper function of nucleoli and thus induce nucleolar/ribosomal stress, can participate in combating cancer cells. In this sense, intentional application of therapeutic agents affecting ribosome biosynthesis can cause either release of these molecules from nucleoli or their de novo biosynthesis to mediate the activation of pathways leading to elimination of harmful cells. This review underlines the role of a nucleolus not only as a ribosome constituting apparatus but also as a hub of both positive and negative control of cancer development. The article is mainly based on original papers concerning mechanisms in which the nucleolus is implicated directly or indirectly in processes associated with neoplasia.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland.
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25
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Liu X, Li Y, Yang H, Zhou B. Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis. Molecules 2018; 23:E857. [PMID: 29642545 PMCID: PMC6017404 DOI: 10.3390/molecules23040857] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/06/2018] [Accepted: 04/06/2018] [Indexed: 01/10/2023] Open
Abstract
The complete chloroplast (cp) genome of Talinum paniculatum (Caryophyllale), a source of pharmaceutical efficacy similar to ginseng, and a widely distributed and planted edible vegetable, were sequenced and analyzed. The cp genome size of T. paniculatum is 156,929 bp, with a pair of inverted repeats (IRs) of 25,751 bp separated by a large single copy (LSC) region of 86,898 bp and a small single copy (SSC) region of 18,529 bp. The genome contains 83 protein-coding genes, 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes and four pseudogenes. Fifty one (51) repeat units and ninety two (92) simple sequence repeats (SSRs) were found in the genome. The pseudogene rpl23 (Ribosomal protein L23) was insert AATT than other Caryophyllale species by sequence alignment, which located in IRs region. The gene of trnK-UUU (tRNA-Lys) and rpl16 (Ribosomal protein L16) have larger introns in T. paniculatum, and the existence of matK (maturase K) genes, which usually located in the introns of trnK-UUU, rich sequence divergence in Caryophyllale. Complete cp genome comparison with other eight Caryophyllales species indicated that the differences between T. paniculatum and P. oleracea were very slight, and the most highly divergent regions occurred in intergenic spacers. Comparisons of IR boundaries among nine Caryophyllales species showed that T. paniculatum have larger IRs region and the contraction is relatively slight. The phylogenetic analysis among 35 Caryophyllales species and two outgroup species revealed that T. paniculatum and P. oleracea do not belong to the same family. All these results give good opportunities for future identification, barcoding of Talinum species, understanding the evolutionary mode of Caryophyllale cp genome and molecular breeding of T. paniculatum with high pharmaceutical efficacy.
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Affiliation(s)
- Xia Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Street, TEDA, Tianjin 300457, China.
| | - Yuan Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Street, TEDA, Tianjin 300457, China.
| | - Hongyuan Yang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Street, TEDA, Tianjin 300457, China.
| | - Boyang Zhou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Street, TEDA, Tianjin 300457, China.
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Konstantakou EG, Velentzas AD, Anagnostopoulos AK, Giannopoulou AF, Anastasiadou E, Papassideri IS, Voutsinas GE, Tsangaris GT, Stravopodis DJ. Unraveling the human protein atlas of metastatic melanoma in the course of ultraviolet radiation-derived photo-therapy. J Proteomics 2017; 188:119-138. [PMID: 29180045 DOI: 10.1016/j.jprot.2017.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/09/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023]
Abstract
To explore the photo-therapeutic capacity of UV radiation in solid tumors, we herein employed an nLC-MS/MS technology to profile the proteomic landscape of irradiated WM-266-4 human metastatic-melanoma cells. Obtained data resulted in proteomic catalogues of 5982 and 7280 proteins for UVB- and UVC-radiation conditions, respectively, and indicated the ability of UVB/C-radiation forms to eliminate metastatic-melanoma cells through induction of synergistically operating programs of apoptosis and necroptosis. However, it seems that one or more WM-266-4 cell sub-populations may escape from UV-radiation's photo-damaging activity, acquiring, besides apoptosis tolerance, an EMT phenotype that likely offers them the advantage of developing resistance to certain chemotherapeutic drugs. Low levels of autophagy may also critically contribute to the selective survival and growth of UV-irradiated melanoma-cell escapers. These are the cells that must be systemically targeted with novel therapeutic schemes, like the one of UV radiation and Irinotecan herein suggested to be holding strong promise for the effective treatment of metastatic-melanoma patients. Given the dual nature of UV radiation to serve as both anti-tumorigenic and tumorigenic agent, all individuals being subjected to risk factors for melanoma development have to be appropriately informed and educated, in order to integrate the innovative PPPM concept in their healthcare-sector management. SIGNIFICANCE This study reports the application of nLC-MS/MS technology to deeply map the proteomic landscape of UV-irradiated human metastatic-melanoma cells. Data bioinformatics processing led to molecular-network reconstructions that unearthed the dual nature of UV radiation to serve as both anti-tumorigenic and tumorigenic factor in metastatic-melanoma cellular environments. Our UV radiation-derived "photo-proteomic" atlas may prove valuable for the identification of new biomarkers and development of novel therapies for the disease. Given that UV radiation represents a major risk factor causing melanoma, a PPPM-based life style and clinical practice must be embraced by all individuals being prone to disease's appearance and expansion.
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Affiliation(s)
- Eumorphia G Konstantakou
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanassios D Velentzas
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios K Anagnostopoulos
- Proteomics Core Facility, Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Aikaterini F Giannopoulou
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Ema Anastasiadou
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Issidora S Papassideri
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Gerassimos E Voutsinas
- Laboratory of Environmental Mutagenesis and Carcinogenesis, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", Athens, Greece
| | - George Th Tsangaris
- Proteomics Core Facility, Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Dimitrios J Stravopodis
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece.
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