1
|
Liu X, Xiao C, Xu X, Zhang J, Mo F, Chen JY, Delihas N, Zhang L, An NA, Li CY. Origin of functional de novo genes in humans from "hopeful monsters". WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1845. [PMID: 38605485 DOI: 10.1002/wrna.1845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
For a long time, it was believed that new genes arise only from modifications of preexisting genes, but the discovery of de novo protein-coding genes that originated from noncoding DNA regions demonstrates the existence of a "motherless" origination process for new genes. However, the features, distributions, expression profiles, and origin modes of these genes in humans seem to support the notion that their origin is not a purely "motherless" process; rather, these genes arise preferentially from genomic regions encoding preexisting precursors with gene-like features. In such a case, the gene loci are typically not brand new. In this short review, we will summarize the definition and features of human de novo genes and clarify their process of origination from ancestral non-coding genomic regions. In addition, we define the favored precursors, or "hopeful monsters," for the origin of de novo genes and present a discussion of the functional significance of these young genes in brain development and tumorigenesis in humans. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
Collapse
Affiliation(s)
- Xiaoge Liu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xinwei Xu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Nicholas Delihas
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Ni A An
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Southwest United Graduate School, Kunming, China
| |
Collapse
|
2
|
Kozlov AP. Carcino-Evo-Devo, A Theory of the Evolutionary Role of Hereditary Tumors. Int J Mol Sci 2023; 24:ijms24108611. [PMID: 37239953 DOI: 10.3390/ijms24108611] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
A theory of the evolutionary role of hereditary tumors, or the carcino-evo-devo theory, is being developed. The main hypothesis of the theory, the hypothesis of evolution by tumor neofunctionalization, posits that hereditary tumors provided additional cell masses during the evolution of multicellular organisms for the expression of evolutionarily novel genes. The carcino-evo-devo theory has formulated several nontrivial predictions that have been confirmed in the laboratory of the author. It also suggests several nontrivial explanations of biological phenomena previously unexplained by the existing theories or incompletely understood. By considering three major types of biological development-individual, evolutionary, and neoplastic development-within one theoretical framework, the carcino-evo-devo theory has the potential to become a unifying biological theory.
Collapse
Affiliation(s)
- Andrei P Kozlov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Street, 117971 Moscow, Russia
- Peter the Great St. Petersburg Polytechnic University, 29 Polytekhnicheskaya Street, 195251 St. Petersburg, Russia
| |
Collapse
|
3
|
Liu J, Yuan R, Shao W, Wang J, Silman I, Sussman JL. Do "Newly Born" orphan proteins resemble "Never Born" proteins? A study using three deep learning algorithms. Proteins 2023. [PMID: 37092778 DOI: 10.1002/prot.26496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/26/2023] [Accepted: 04/01/2023] [Indexed: 04/25/2023]
Abstract
"Newly Born" proteins, devoid of detectable homology to any other proteins, known as orphan proteins, occur in a single species or within a taxonomically restricted gene family. They are generated by the expression of novel open reading frames, and appear throughout evolution. We were curious if three recently developed programs for predicting protein structures, namely, AlphaFold2, RoseTTAFold, and ESMFold, might be of value for comparison of such "Newly Born" proteins to random polypeptides with amino acid content similar to that of native proteins, which have been called "Never Born" proteins. The programs were used to compare the structures of two sets of "Never Born" proteins that had been expressed-Group 1, which had been shown experimentally to possess substantial secondary structure, and Group 3, which had been shown to be intrinsically disordered. Overall, although the models generated were scored as being of low quality, they nevertheless revealed some general principles. Specifically, all four members of Group 1 were predicted to be compact by all three algorithms, in agreement with the experimental data, whereas the members of Group 3 were predicted to be very extended, as would be expected for intrinsically disordered proteins, again consistent with the experimental data. These predicted differences were shown to be statistically significant by comparing their accessible surface areas. The three programs were then used to predict the structures of three orphan proteins whose crystal structures had been solved, two of which display novel folds. Surprisingly, only for the protein which did not have a novel fold, and was taxonomically restricted, rather than being a true orphan, did all three algorithms predict very similar, high-quality structures, closely resembling the crystal structure. Finally, they were used to predict the structures of seven orphan proteins with well-identified biological functions, whose 3D structures are not known. Two proteins, which were predicted to be disordered based on their sequences, are predicted by all three structure algorithms to be extended structures. The other five were predicted to be compact structures with only two exceptions in the case of AlphaFold2. All three prediction algorithms make remarkably similar and high-quality predictions for one large protein, HCO_11565, from a nematode. It is conjectured that this is due to many homologs in the taxonomically restricted family of which it is a member, and to the fact that the Dali server revealed several nonrelated proteins with similar folds. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Proteins:3.
Collapse
Affiliation(s)
- Jing Liu
- Department of Biotechnology and Food Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, China
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Rongqing Yuan
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Wei Shao
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jitong Wang
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Israel Silman
- Department of Brain Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Joel L Sussman
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
4
|
Evolution and implications of de novo genes in humans. Nat Ecol Evol 2023:10.1038/s41559-023-02014-y. [PMID: 36928843 DOI: 10.1038/s41559-023-02014-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
Genes and translated open reading frames (ORFs) that emerged de novo from previously non-coding sequences provide species with opportunities for adaptation. When aberrantly activated, some human-specific de novo genes and ORFs have disease-promoting properties-for instance, driving tumour growth. Thousands of putative de novo coding sequences have been described in humans, but we still do not know what fraction of those ORFs has readily acquired a function. Here, we discuss the challenges and controversies surrounding the detection, mechanisms of origin, annotation, validation and characterization of de novo genes and ORFs. Through manual curation of literature and databases, we provide a thorough table with most de novo genes reported for humans to date. We re-evaluate each locus by tracing the enabling mutations and list proposed disease associations, protein characteristics and supporting evidence for translation and protein detection. This work will support future explorations of de novo genes and ORFs in humans.
Collapse
|
5
|
The Theory of Carcino-Evo-Devo and Its Non-Trivial Predictions. Genes (Basel) 2022; 13:genes13122347. [PMID: 36553613 PMCID: PMC9777766 DOI: 10.3390/genes13122347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
To explain the sources of additional cell masses in the evolution of multicellular organisms, the theory of carcino-evo-devo, or evolution by tumor neofunctionalization, has been developed. The important demand for a new theory in experimental science is the capability to formulate non-trivial predictions which can be experimentally confirmed. Several non-trivial predictions were formulated using carcino-evo-devo theory, four of which are discussed in the present paper: (1) The number of cellular oncogenes should correspond to the number of cell types in the organism. The evolution of oncogenes, tumor suppressor and differentiation gene classes should proceed concurrently. (2) Evolutionarily new and evolving genes should be specifically expressed in tumors (TSEEN genes). (3) Human orthologs of fish TSEEN genes should acquire progressive functions connected with new cell types, tissues and organs. (4) Selection of tumors for new functions in the organism is possible. Evolutionarily novel organs should recapitulate tumor features in their development. As shown in this paper, these predictions have been confirmed by the laboratory of the author. Thus, we have shown that carcino-evo-devo theory has predictive power, fulfilling a fundamental requirement for a new theory.
Collapse
|
6
|
MicroRNA-27a-5p Inhibits Proliferation, Migration, and Invasion and Promotes Apoptosis of Wilms' Tumor Cell by Targeting PBOV1. Mol Cell Biol 2022; 42:e0039721. [PMID: 35862727 PMCID: PMC9387294 DOI: 10.1128/mcb.00397-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Wilms' tumor is the most common type of renal tumor in children. MicroRNAs (miRNAs) are small noncoding RNAs that play crucial regulatory roles in tumorigenesis. We aimed to study the expression profile and function of miR-27a-5p in Wilms' tumor. miR-27a-5p expression was downregulated in human Wilms' tumor tissues. Functionally, overexpression of miR-27a-5p promoted cell apoptosis of Wilms' tumor cells. Furthermore, upregulated miR-27a-5p delayed xenograft Wilms' tumor tumorigenesis in vivo. Bioinformatics analysis predicted that miR-27a-5p directly targeted the 3'-untranslated region (3'-UTR) of PBOV1, and luciferase reporter assay confirmed the interaction between miR-27a-5p and PBOV1. The function of PBOV1 in Wilms' tumor was evaluated in vitro, and knockdown of PBOV1 dampened cell migration. In addition, overexpression of PBOV1 antagonized the tumor-suppressive effect of miR-27a-5p in Wilms' tumor cells. Collectively, our findings reveal the regulatory axis of miR-27a-5p/PBOV1 in Wilms' tumor, and miR-27a-5p might serve as a novel therapeutic target in Wilms' tumor.
Collapse
|
7
|
MALAT1 enhances gemcitabine resistance in non-small cell lung cancer cells by directly affecting miR-27a-5p/PBOV1 axis. Cell Signal 2022; 94:110326. [DOI: 10.1016/j.cellsig.2022.110326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022]
|
8
|
Kozlov AP. Mammalian tumor-like organs. 1. The role of tumor-like normal organs and atypical tumor organs in the evolution of development (carcino-evo-devo). Infect Agent Cancer 2022; 17:2. [PMID: 35012580 PMCID: PMC8751115 DOI: 10.1186/s13027-021-00412-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Earlier I hypothesized that hereditary tumors might participate in the evolution of multicellular organisms. I formulated the hypothesis of evolution by tumor neofunctionalization, which suggested that the evolutionary role of hereditary tumors might consist in supplying evolving multicellular organisms with extra cell masses for the expression of evolutionarily novel genes and the origin of new cell types, tissues, and organs. A new theory—the carcino-evo-devo theory—has been developed based on this hypothesis. Main text My lab has confirmed several non-trivial predictions of this theory. Another non-trivial prediction is that evolutionarily new organs if they originated from hereditary tumors or tumor-like structures, should recapitulate some tumor features in their development. This paper reviews the tumor-like features of evolutionarily novel organs. It turns out that evolutionarily new organs such as the eutherian placenta, mammary gland, prostate, the infantile human brain, and hoods of goldfishes indeed have many features of tumors. I suggested calling normal organs, which have many tumor features, the tumor-like organs. Conclusion Tumor-like organs might originate from hereditary atypical tumor organs and represent the part of carcino-evo-devo relationships, i.e., coevolution of normal and neoplastic development. During subsequent evolution, tumor-like organs may lose the features of tumors and the high incidence of cancer and become normal organs without (or with almost no) tumor features.
Collapse
Affiliation(s)
- A P Kozlov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3, Gubkina Street, Moscow, Russia, 117971. .,Peter the Great St. Petersburg Polytechnic University, 29, Polytekhnicheskaya Street, St. Petersburg, Russia, 195251.
| |
Collapse
|
9
|
Cherezov RO, Vorontsova JE, Simonova OB. The Phenomenon of Evolutionary “De Novo Generation” of Genes. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421060035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
10
|
Dowling D, Schmitz JF, Bornberg-Bauer E. Stochastic Gain and Loss of Novel Transcribed Open Reading Frames in the Human Lineage. Genome Biol Evol 2020; 12:2183-2195. [PMID: 33210146 PMCID: PMC7674706 DOI: 10.1093/gbe/evaa194] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2020] [Indexed: 12/12/2022] Open
Abstract
In addition to known genes, much of the human genome is transcribed into RNA. Chance formation of novel open reading frames (ORFs) can lead to the translation of myriad new proteins. Some of these ORFs may yield advantageous adaptive de novo proteins. However, widespread translation of noncoding DNA can also produce hazardous protein molecules, which can misfold and/or form toxic aggregates. The dynamics of how de novo proteins emerge from potentially toxic raw materials and what influences their long-term survival are unknown. Here, using transcriptomic data from human and five other primates, we generate a set of transcribed human ORFs at six conservation levels to investigate which properties influence the early emergence and long-term retention of these expressed ORFs. As these taxa diverged from each other relatively recently, we present a fine scale view of the evolution of novel sequences over recent evolutionary time. We find that novel human-restricted ORFs are preferentially located on GC-rich gene-dense chromosomes, suggesting their retention is linked to pre-existing genes. Sequence properties such as intrinsic structural disorder and aggregation propensity-which have been proposed to play a role in survival of de novo genes-remain unchanged over time. Even very young sequences code for proteins with low aggregation propensities, suggesting that genomic regions with many novel transcribed ORFs are concomitantly less likely to produce ORFs which code for harmful toxic proteins. Our data indicate that the survival of these novel ORFs is largely stochastic rather than shaped by selection.
Collapse
Affiliation(s)
- Daniel Dowling
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Jonathan F Schmitz
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | | |
Collapse
|
11
|
Matyunina EA, Emelyanov AV, Kurbatova TV, Makashov AA, Mizgirev IV, Kozlov AP. Evolutionarily novel genes are expressed in transgenic fish tumors and their orthologs are involved in development of progressive traits in humans. Infect Agent Cancer 2019; 14:46. [PMID: 31827597 PMCID: PMC6896781 DOI: 10.1186/s13027-019-0262-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/20/2019] [Indexed: 01/01/2023] Open
Abstract
Abstract Earlier we suggested a new hypothesis of the possible evolutionary role of hereditary tumors (Kozlov, Evolution by tumor Neofunctionalization, 2014), and described a new class of genes – tumor specifically expressed, evolutionarily novel (TSEEN) genes - that are predicted by this hypothesis (Kozlov, Infect Agents Cancer 11:34, 2016). In this paper we studied evolutionarily novel genes expressed in fish tumors after regression, as a model of evolving organs. As evolutionarily novel genes may not yet have organismal functions, we studied the acquisition of new gene functions by comparing fish evolutionarily novel genes with their human orthologs. We found that many genes involved in development of progressive traits in humans (lung, mammary gland, placenta, ventricular septum, etc.) originated in fish and are expressed in fish tumors and tumors after regression. These findings support a possible evolutionary role of hereditary tumors, and in particular the hypothesis of evolution by tumor neofunctionalization. Research highlights Earlier we described a new class of genes that are tumor-specifically expressed and evolutionarily novel (TSEEN). As the functions of TSEEN genes are often uncertain, we decided to study TSEEN genes of fishes so that we could trace the appearance of their new functions in higher vertebrates. We found that many human genes which are involved in development of progressive traits (placenta development, mammary gland and lung development etc.,) originated in fishes and are expressed in fish tumors.
Collapse
Affiliation(s)
- E A Matyunina
- 1Research Institute of Ultra-Pure Biologicals, Ministry of Public Health of the Russian Federation, St.-Petersburg, Russia.,2Peter the Great Saint-Petersburg Polytechnic University (SPbPU), St.-Petersburg, Russia
| | - A V Emelyanov
- 3The Biomedical Center (BMC), St.-Petersburg, Russia.,4Institute for Research on Cancer and Aging (IRCAN), Nice, France
| | - T V Kurbatova
- 1Research Institute of Ultra-Pure Biologicals, Ministry of Public Health of the Russian Federation, St.-Petersburg, Russia.,2Peter the Great Saint-Petersburg Polytechnic University (SPbPU), St.-Petersburg, Russia.,3The Biomedical Center (BMC), St.-Petersburg, Russia
| | - A A Makashov
- 1Research Institute of Ultra-Pure Biologicals, Ministry of Public Health of the Russian Federation, St.-Petersburg, Russia.,2Peter the Great Saint-Petersburg Polytechnic University (SPbPU), St.-Petersburg, Russia.,3The Biomedical Center (BMC), St.-Petersburg, Russia
| | - I V Mizgirev
- 5Petrov Research Institute of Oncology, St.-Petersburg, Russia
| | - A P Kozlov
- 1Research Institute of Ultra-Pure Biologicals, Ministry of Public Health of the Russian Federation, St.-Petersburg, Russia.,2Peter the Great Saint-Petersburg Polytechnic University (SPbPU), St.-Petersburg, Russia.,3The Biomedical Center (BMC), St.-Petersburg, Russia.,6Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
12
|
Makashov AA, Malov SV, Kozlov AP. Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently. Sci Rep 2019; 9:16410. [PMID: 31712655 PMCID: PMC6848199 DOI: 10.1038/s41598-019-52835-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 10/24/2019] [Indexed: 01/20/2023] Open
Abstract
Earlier we showed that human genome contains many evolutionarily young or novel genes with tumor-specific or tumor-predominant expression. We suggest calling such genes Tumor Specifically Expressed, Evolutionarily New (TSEEN) genes. In this paper we performed a study of the evolutionary ages of different classes of human genes, using homology searches in genomes of different taxa in human lineage. We discovered that different classes of human genes have different evolutionary ages and confirmed the existence of TSEEN gene classes. On the other hand, we found that oncogenes, tumor-suppressor genes and differentiation genes are among the oldest gene classes in humans and their evolution occurs concurrently. These findings confirm non-trivial predictions made by our hypothesis of the possible evolutionary role of hereditary tumors. The results may be important for better understanding of tumor biology. TSEEN genes may become the best tumor markers.
Collapse
Affiliation(s)
- A A Makashov
- Biomedical Center, Viborgskaya str. 8, Saint-Petersburg, 194044, Russia.,Peter the Great St. Petersburg Polytechnic University, Politekhnicheskaya ul., 29, St. Petersburg, 195251, Russia.,Research Institute of Ultra Pure Biologicals, 7 Pudozhskaya str., St. Petersburg, 197110, Russia
| | - S V Malov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St.-Petersburg State University, 41A, Sredniy av., St. Petersburg, 199004, Russia.,Department of Algorithmic Mathematics, St.-Petersburg Electrotechnical University, 5, Prof. Popova str, St. Petersburg, 197376, Russia
| | - A P Kozlov
- Biomedical Center, Viborgskaya str. 8, Saint-Petersburg, 194044, Russia. .,Peter the Great St. Petersburg Polytechnic University, Politekhnicheskaya ul., 29, St. Petersburg, 195251, Russia. .,Research Institute of Ultra Pure Biologicals, 7 Pudozhskaya str., St. Petersburg, 197110, Russia. .,Vavilov Institute of General Genetics, 3 Gubkina str., Moscow, 119333, Russia.
| |
Collapse
|
13
|
Affiliation(s)
- Stephen Branden Van Oss
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
| |
Collapse
|
14
|
Kong Q, Han J, Deng H, Wu F, Guo S, Ye Z. miR-431-5p alters the epithelial-to-mesenchymal transition markers by targeting UROC28 in hepatoma cells. Onco Targets Ther 2018; 11:6489-6503. [PMID: 30323624 PMCID: PMC6177384 DOI: 10.2147/ott.s173840] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE MicroRNA (miR)-431 plays an essential role in various human cancer types, particularly in the process of invasion. However, the function and mechanism of miR-431-5p in the invasion of hepatocellular carcinoma (HCC) remain undefined. METHODS The expression levels of miR-431-5p and its potential target protein UROC28 in hepatocellular carcinoma cells and tissues were detected, and the levels of EMT markers in vivo and in vitro were also detected. RESULTS MiR-431-5p was downregulated in HCC cell lines and tissues and associated with vascular invasion and tumor encapsulation. Furthermore, miR-431-5p was able to influence the epithelialto-mesenchymal transition (EMT) process in HCCLM3 and HUH7 cells. Mechanistically, it was discovered that miR-431-5p repressed invasion by targeting UROC28. Furthermore, miR-431-5p influenced the EMT markers in HCCLM3 and HUH7 cells by downregulating UROC28 expression. Similarly, in vivo assays confirmed that miR-431-5p upregulation in HCC cells remarkably inhibited tumor proliferation and influenced the EMT markers. CONCLUSION The current study has demonstrated that the miR-431-5p/UROC28 axis acts possible influence on the EMT in HCC. Upregulation of miR-431-5p could be an original approach for inhibiting tumor invasion.
Collapse
Affiliation(s)
- Qinglei Kong
- Department of Emergency, The Third Affiliated Hospital of Sun Yat-San University, Guangzhou 510630, China,
| | - Jianhua Han
- Department of Emergency, The Third Affiliated Hospital of Sun Yat-San University, Guangzhou 510630, China,
| | - Hong Deng
- Department of Infectious Disease and Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-San University, Guangzhou 510630, China
| | - Feilong Wu
- Department of Emergency, The Third Affiliated Hospital of Sun Yat-San University, Guangzhou 510630, China,
| | - Shaozhong Guo
- Department of Infectious Disease and Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-San University, Guangzhou 510630, China
| | - Zhiqiang Ye
- Department of Emergency, The Third Affiliated Hospital of Sun Yat-San University, Guangzhou 510630, China,
| |
Collapse
|
15
|
lncRNA NTT/PBOV1 Axis Promotes Monocyte Differentiation and Is Elevated in Rheumatoid Arthritis. Int J Mol Sci 2018; 19:ijms19092806. [PMID: 30231487 PMCID: PMC6163842 DOI: 10.3390/ijms19092806] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/04/2018] [Accepted: 09/13/2018] [Indexed: 12/29/2022] Open
Abstract
Monocytes/macrophages are important in orchestrating inflammatory responses. However, knowledge of the long noncoding RNA (lncRNA) regulation of monocytic cell differentiation and diseases remains limited. We aimed to elucidate the role of the 17 kb lncRNA noncoding transcript in T cells (NTT) in monocyte functions. Knockdown and chromatin immunoprecipitation (ChIP) assays in THP-1 cells (human monocytic leukemia cell line) revealed that NTT is regulated by the monocyte key transcription factor C/EBPβ and that it binds to the promoter of nearby gene PBOV1 via hnRNP-U. Overexpression of PBOV1 in THP-1 cells resulted in cell cycle G1 arrest, differentiation into macrophages, a marked increase in IL-10 and CXCL10 mRNA levels, and upregulation of the costimulatory molecules. In contrast to the downregulated NTT observed in lipopolysaccharide (LPS)-treated THP-1 cells, the C/EBPβ/NTT/PBOV1 axis was found to be hyperactivated in peripheral blood mononuclear cells (PBMCs) of first-time diagnosed untreated early rheumatoid arthritis (RA) patients, and their gene expression levels decreased markedly after treatment. Higher initial C/EBPβ/NTT/PBOV1 expression levels were associated with a trend of higher disease activity DAS28 scores. In conclusion, our study suggests that the lncRNA NTT is a regulator of inflammation in monocytes, and its activation participates in monocyte/macrophage differentiation and the pathogenesis of RA.
Collapse
|
16
|
Nanomedicines reveal how PBOV1 promotes hepatocellular carcinoma for effective gene therapy. Nat Commun 2018; 9:3430. [PMID: 30143633 PMCID: PMC6109108 DOI: 10.1038/s41467-018-05764-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 07/26/2018] [Indexed: 02/07/2023] Open
Abstract
There exists an urgent medical demand at present to develop therapeutic strategies which can improve the treatment outcome of hepatocellular carcinoma (HCC). Here, we explore the biological functions and clinical significance of PBOV1 in HCC in order to push forward the diagnosis and treatment of HCC. Using theranostical nanomedicines, PBOV1 is verified to be a key oncogene which greatly promotes HCC proliferation, epithelial-to-mesenchymal transition, and stemness by activating the Wnt/β-catenin signaling pathway. Therefore, single-chain antibody for epidermal growth factor receptor (scAb-EGFR)-targeted nanomedicine effectively silencing the PBOV1 gene exhibits potent anticancer effects. In vivo HCC-targeting siRNA delivery mediated by the theranostical nanomedicine remarkably inhibits the tumor growth and metastasis. In addition, the superparamagnetic iron oxide nanocrystals (SPION)-encapsulated nanomedicines possess high MRI detection sensitivity, which endows them with the potential for MRI diagnosis of HCC. This study shows that PBOV1 represents a prognostic biomarker and therapeutic target for HCC.
Collapse
|
17
|
Xue C, Zhong Z, Ye S, Wang Y, Ye Q. Association between the overexpression of PBOV1 and the prognosis of patients with hepatocellular carcinoma. Oncol Lett 2018; 16:3401-3407. [PMID: 30127941 DOI: 10.3892/ol.2018.9013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/11/2018] [Indexed: 12/21/2022] Open
Abstract
Prostate and breast cancer overexpressed 1 (PBOV1) is a known human protein-coding gene with an uncharacterized function; it has been demonstrated to be overexpressed in a variety of human cancer types. The overexpression of PBOV1 has been indicated as significantly associated with the poor prognosis of these types of cancer. However, the function of PBOV1 in hepatocellular carcinoma (HCC) has not yet been elucidated. The present study was designed to evaluate the expression and prognostic significance of PBOV1 in HCC. Reverse transcription-quantitative polymerase chain reaction and western blot analyses were conducted to measure the expression of PBOV1 in HCC cell lines and tissues. The associations between PBOV1 expression and clinicopathological features were statistically analyzed. The association between PBOV1 expression and the prognosis of HCC patients was analyzed by the Kaplan-Meier method. The mRNA and protein expression levels of PBOV1 were significantly increased in the HCC cell lines and HCC tissues (all P<0.05) compared with normal cell lines and tissues. In addition, PBOV1 expression was significantly associated with maximal tumor size (P=0.032), tumor metastasis (P=0.035) and tumor stage (P=0.017). The Kaplan-Meier survival curves indicated that overall survival was significantly poorer in patients with HCC with PBOV1 overexpression (P<0.05) compared with patients with low expression levels. The multivariate analysis indicated that high PBOV1 expression was an independent predictor of poor overall survival. To the best of our knowledge, the data of the present study describes the expression pattern of PBOV1 in HCC for the first time, and also suggests that PBOV1 may serve as a valuable prognostic biomarker for HCC.
Collapse
Affiliation(s)
- Chengbiao Xue
- Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan, Hubei 430071, P.R. China
| | - Zibiao Zhong
- Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan, Hubei 430071, P.R. China
| | - Shaojun Ye
- Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan, Hubei 430071, P.R. China
| | - Yanfeng Wang
- Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan, Hubei 430071, P.R. China
| | - Qifa Ye
- Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan, Hubei 430071, P.R. China
| |
Collapse
|
18
|
Carleton NM, Zhu G, Gorbounov M, Miller MC, Pienta KJ, Resar LM, Veltri RW. PBOV1 as a potential biomarker for more advanced prostate cancer based on protein and digital histomorphometric analysis. Prostate 2018; 78. [PMID: 29520928 PMCID: PMC5882516 DOI: 10.1002/pros.23499] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND There are few tissue-based biomarkers that can accurately predict prostate cancer (PCa) progression and aggressiveness. We sought to evaluate the clinical utility of prostate and breast overexpressed 1 (PBOV1) as a potential PCa biomarker. METHODS Patient tumor samples were designated by Grade Groups using the 2014 Gleason grading system. Primary radical prostatectomy tumors were obtained from 48 patients and evaluated for PBOV1 levels using Western blot analysis in matched cancer and benign cancer-adjacent regions. Immunohistochemical evaluation of PBOV1 was subsequently performed in 80 cancer and 80 benign cancer-adjacent patient samples across two tissue microarrays (TMAs) to verify protein levels in epithelial tissue and to assess correlation between PBOV1 proteins and nuclear architectural changes in PCa cells. Digital histomorphometric analysis was used to track 22 parameters that characterized nuclear changes in PBOV1-stained cells. Using a training and test set for validation, multivariate logistic regression (MLR) models were used to identify significant nuclear parameters that distinguish Grade Group 3 and above PCa from Grade Group 1 and 2 PCa regions. RESULTS PBOV1 protein levels were increased in tumors from Grade Group 3 and above (GS 4 + 3 and ≥ 8) regions versus Grade Groups 1 and 2 (GS 3 + 3 and 3 + 4) regions (P = 0.005) as assessed by densitometry of immunoblots. Additionally, by immunoblotting, PBOV1 protein levels differed significantly between Grade Group 2 (GS 3 + 4) and Grade Group 3 (GS 4 + 3) PCa samples (P = 0.028). In the immunohistochemical analysis, measures of PBOV1 staining intensity strongly correlated with nuclear alterations in cancer cells. An MLR model retaining eight parameters describing PBOV1 staining intensity and nuclear architecture discriminated Grade Group 3 and above PCa from Grade Group 1 and 2 PCa and benign cancer-adjacent regions with a ROC-AUC of 0.90 and 0.80, respectively, in training and test sets. CONCLUSIONS Our study demonstrates that the PBOV1 protein could be used to discriminate Grade Group 3 and above PCa. Additionally, the PBOV1 protein could be involved in modulating changes to the nuclear architecture of PCa cells. Confirmatory studies are warranted in an independent population for further validation.
Collapse
Affiliation(s)
- Neil M. Carleton
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
- Corresponding Authors: Neil M. Carleton, Carnegie Mellon University, Department of Biomedical Engineering, 5000 Forbes Ave., Pittsburgh, PA 15213, Tel: 412-266-1991, , . Robert W. Veltri, PhD, James Buchanan Brady Urological Institute, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD 21287, Tel: 410-952-5411,
| | - Guangjing Zhu
- The James Buchanan Brady Urological Institute, Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Mikhail Gorbounov
- Division of Hematology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | | | - Kenneth J. Pienta
- The James Buchanan Brady Urological Institute, Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Linda M.S. Resar
- Division of Hematology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Robert W. Veltri
- The James Buchanan Brady Urological Institute, Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Corresponding Authors: Neil M. Carleton, Carnegie Mellon University, Department of Biomedical Engineering, 5000 Forbes Ave., Pittsburgh, PA 15213, Tel: 412-266-1991, , . Robert W. Veltri, PhD, James Buchanan Brady Urological Institute, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD 21287, Tel: 410-952-5411,
| |
Collapse
|
19
|
Luis Villanueva-Cañas J, Ruiz-Orera J, Agea MI, Gallo M, Andreu D, Albà MM. New Genes and Functional Innovation in Mammals. Genome Biol Evol 2017; 9:1886-1900. [PMID: 28854603 PMCID: PMC5554394 DOI: 10.1093/gbe/evx136] [Citation(s) in RCA: 35] [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] [Accepted: 07/20/2017] [Indexed: 12/22/2022] Open
Abstract
The birth of genes that encode new protein sequences is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected for. To address these questions, we have obtained a large collection of mammalian-specific gene families that lack homologues in other eukaryotic groups. We have combined gene annotations and de novo transcript assemblies from 30 different mammalian species, obtaining ∼6,000 gene families. In general, the proteins in mammalian-specific gene families tend to be short and depleted in aromatic and negatively charged residues. Proteins which arose early in mammalian evolution include milk and skin polypeptides, immune response components, and proteins involved in reproduction. In contrast, the functions of proteins which have a more recent origin remain largely unknown, despite the fact that these proteins also have extensive proteomics support. We identify several previously described cases of genes originated de novo from noncoding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes.
Collapse
Affiliation(s)
- José Luis Villanueva-Cañas
- Evolutionary Genomics Group, Research Programme in Biomedical Informatics, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Present address: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Jorge Ruiz-Orera
- Evolutionary Genomics Group, Research Programme in Biomedical Informatics, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - M. Isabel Agea
- Evolutionary Genomics Group, Research Programme in Biomedical Informatics, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Maria Gallo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - David Andreu
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - M. Mar Albà
- Evolutionary Genomics Group, Research Programme in Biomedical Informatics, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| |
Collapse
|
20
|
McLysaght A, Hurst LD. Open questions in the study of de novo genes: what, how and why. Nat Rev Genet 2016; 17:567-78. [PMID: 27452112 DOI: 10.1038/nrg.2016.78] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The study of de novo protein-coding genes is maturing from the ad hoc reporting of individual cases to the systematic analysis of extensive genomic data from several species. We identify three key challenges for this emerging field: understanding how best to identify de novo genes, how they arise and why they spread. We highlight the intellectual challenges of understanding how a de novo gene becomes integrated into pre-existing functions and becomes essential. We suggest that, as with protein sequence evolution, antagonistic co-evolution may be key to de novo gene evolution, particularly for new essential genes and new cancer-associated genes.
Collapse
Affiliation(s)
- Aoife McLysaght
- The Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset BA2 7AY, UK
| |
Collapse
|
21
|
Kozlov AP. Expression of evolutionarily novel genes in tumors. Infect Agent Cancer 2016; 11:34. [PMID: 27437030 PMCID: PMC4949931 DOI: 10.1186/s13027-016-0077-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023] Open
Abstract
The evolutionarily novel genes originated through different molecular mechanisms are expressed in tumors. Sometimes the expression of evolutionarily novel genes in tumors is highly specific. Moreover positive selection of many human tumor-related genes in primate lineage suggests their involvement in the origin of new functions beneficial to organisms. It is suggested to consider the expression of evolutionarily young or novel genes in tumors as a new biological phenomenon, a phenomenon of TSEEN (tumor specifically expressed, evolutionarily novel) genes.
Collapse
Affiliation(s)
- A. P. Kozlov
- The Biomedical Center and Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| |
Collapse
|
22
|
McLysaght A, Guerzoni D. New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. Philos Trans R Soc Lond B Biol Sci 2016; 370:20140332. [PMID: 26323763 PMCID: PMC4571571 DOI: 10.1098/rstb.2014.0332] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages. There is now evidence that this mechanism has contributed a significant number of genes to genomes of organisms as diverse as Saccharomyces, Drosophila, Plasmodium, Arabidopisis and human. From simple beginnings, these genes have in some instances acquired complex structure, regulated expression and important functional roles. New genes are often thought of as dispensable late additions; however, some recent de novo genes in human can play a role in disease. Rather than an extremely rare occurrence, it is now evident that there is a relatively constant trickle of proto-genes released into the testing ground of natural selection. It is currently unknown whether de novo genes arise primarily through an ‘RNA-first’ or ‘ORF-first’ pathway. Either way, evolutionary tinkering with this pool of genetic potential may have been a significant player in the origins of lineage-specific traits and adaptations.
Collapse
Affiliation(s)
- Aoife McLysaght
- Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Daniele Guerzoni
- Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Republic of Ireland
| |
Collapse
|
23
|
Guerzoni D, McLysaght A. De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting. Genome Biol Evol 2016; 8:1222-32. [PMID: 27056411 PMCID: PMC4860702 DOI: 10.1093/gbe/evw074] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
De novo protein-coding gene origination is increasingly recognized as an important evolutionary mechanism. However, there remains a large amount of uncertainty regarding the frequency of these events and the mechanisms and speed of gene establishment. Here, we describe a rigorous search for cases of de novo gene origination in the great apes. We analyzed annotated proteomes as well as full genomic DNA and transcriptional and translational evidence. It is notable that results vary between database updates due to the fluctuating annotation of these genes. Nonetheless we identified 35 de novo genes: 16 human-specific; 5 human and chimpanzee specific; and 14 that originated prior to the divergence of human, chimpanzee, and gorilla and are found in all three genomes. The taxonomically restricted distribution of these genes cannot be explained by loss in other lineages. Each gene is supported by an open reading frame-creating mutation that occurred within the primate lineage, and which is not polymorphic in any species. Similarly to previous studies we find that the de novo genes identified are short and frequently located near pre-existing genes. Also, they may be associated with Alu elements and prior transcription and RNA-splicing at the locus. Additionally, we report the first case of apparent independent lineage sorting of a de novo gene. The gene is present in human and gorilla, whereas chimpanzee has the ancestral noncoding sequence. This indicates a long period of polymorphism prior to fixation and thus supports a model where de novo genes may, at least initially, have a neutral effect on fitness.
Collapse
Affiliation(s)
- Daniele Guerzoni
- Smurfit Institute of Genetics, Department of Genetics, Trinity College Dublin, University of Dublin, Ireland
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Department of Genetics, Trinity College Dublin, University of Dublin, Ireland
| |
Collapse
|
24
|
Pan T, Wu R, Liu B, Wen H, Tu Z, Guo J, Yang J, Shen G. PBOV1 promotes prostate cancer proliferation by promoting G1/S transition. Onco Targets Ther 2016; 9:787-95. [PMID: 26937201 PMCID: PMC4762445 DOI: 10.2147/ott.s92682] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Prostate cancer (PC) is one of the leading causes of cancer death in men, and thus, finding new regulators is critical for PC therapy. Prostate and breast cancer overexpressed 1 (PBOV1) is overexpressed in breast, prostate, and bladder cancers, as it is upregulated in the serum of patients with PC, but the role of PBOV1 in PC has not been studied. In this article, we found that PBOV1 was indeed overexpressed in PC cells; PBOV1 overexpression promoted cell proliferation and colony formation ability and arrested cell cycle in the G0/G1 phase and tumorigenicity ability in vitro, whereas knockdown of PBOV1 reduced these effects. Further analysis of PBOV1 overexpression inhibited cell cycle inhibitors, P21 and P27, and increased the phosphorylation level of Rb and cyclin D1 expression, suggesting that PBOV1 promoted cell proliferation through promoting G1/S transition.
Collapse
Affiliation(s)
- Tiejun Pan
- Department of Urology, Wuhan General Hospital of Guangzhou Military Command, Wuhan, Hubei, People's Republic of China
| | - Rongpei Wu
- Department of Urology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Bo Liu
- Department of Urology, Wuhan General Hospital of Guangzhou Military Command, Wuhan, Hubei, People's Republic of China
| | - Handong Wen
- Department of Urology, Wuhan General Hospital of Guangzhou Military Command, Wuhan, Hubei, People's Republic of China
| | - Zhong Tu
- Department of Urology, Wuhan General Hospital of Guangzhou Military Command, Wuhan, Hubei, People's Republic of China
| | - Jun Guo
- Department of Urology, Wuhan General Hospital of Guangzhou Military Command, Wuhan, Hubei, People's Republic of China
| | - Jiarong Yang
- Department of Urology, Wuhan General Hospital of Guangzhou Military Command, Wuhan, Hubei, People's Republic of China
| | - Guoqiu Shen
- Department of Urology, Wuhan General Hospital of Guangzhou Military Command, Wuhan, Hubei, People's Republic of China
| |
Collapse
|
25
|
Wang L, Niu CH, Wu S, Wu HM, Ouyang F, He M, He SY. PBOV1 correlates with progression of ovarian cancer and inhibits proliferation of ovarian cancer cells. Oncol Rep 2015; 35:488-96. [PMID: 26549570 DOI: 10.3892/or.2015.4396] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/05/2015] [Indexed: 11/06/2022] Open
Abstract
Prostate and breast cancer overexpressed 1 (PBOV1) is significantly upregulated in prostate, breast and bladder cancer, while its expression status in ovarian cancer and its clinical significance are unclear. We examined the expression levels of PBOV1 mRNA and protein in ovarian cancer cell lines and primary tissues using real-time PCR and western blotting. Immunohistochemistry was employed to analyze PBOV1 expression in 17 normal ovaries, 13 cystadenoma tissues, 14 borderline tumor tissues, and 165 clinicopathologically characterized ovarian cancers. There was negative PBOV1 expression in the 17 normal ovarian epithelial tissues. Compared to the normal ovarian epithelial cells, PBOV1 mRNA and protein were overexpressed in ovarian cancer cell lines. There was high PBOV1 protein expression in the ovarian cancer tissues from 59 of the 165 (35.8%) patients; PBOV1 expression was weak in 106 (64.2%) patients. Notably, there were significant negative associations between high PBOV1 expression and ascending histological grade, late pT/pN/pM, and International Federation of Gynecology and Obstetrics (FIGO) stage (P<0.05). Patients with high PBOV1 expression had longer overall survival; patients with low PBOV1 expression had shorter survival. Multivariate analysis revealed that PBOV1 upregulation is an independent prognostic indicator for ovarian cancer and might serve as a tumor-suppressor gene. Furthermore, PBOV1 overexpression inhibited ovarian cancer cell proliferation and tumorigenesis in vitro and in a tumor transplantation nude mouse model. In conclusion, our results suggest that PBOV1 may play an important role in suppressing ovarian cancer proliferation and carcinogenesis. PBOV1 may be a novel and useful prognostic marker and potential target for treating human ovarian cancer.
Collapse
Affiliation(s)
- Lan Wang
- Department of Pathogen Biology and Immunology, School of Basic Courses, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Chun-Hao Niu
- Department of Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Shu Wu
- State Key Laboratory of Oncology in South China, Guangzhou, Guangdong 510060, P.R. China
| | - Hong-Mei Wu
- Department of Pathogen Biology and Immunology, School of Basic Courses, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Fei Ouyang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510700, P.R. China
| | - Mian He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510700, P.R. China
| | - Shan-Yang He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510700, P.R. China
| |
Collapse
|
26
|
Sun W, Zhao XW, Zhang Z. Identification and evolution of the orphan genes in the domestic silkworm, Bombyx mori. FEBS Lett 2015; 589:2731-8. [PMID: 26296317 DOI: 10.1016/j.febslet.2015.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 07/24/2015] [Accepted: 08/01/2015] [Indexed: 10/23/2022]
Abstract
Orphan genes (OGs) which have no recognizable homology to any sequences in other species could contribute to the species specific adaptations. In this study, we identified 738 OGs in the silkworm genome. About 31% of the silkworm OGs is derived from transposable elements, and 5.1% of the silkworm OGs emerged from gene duplication followed by divergence of paralogs. Five de novo silkworm OGs originated from non-coding regions. Microarray data suggested that most of the silkworm OGs were expressed in limited tissues. RNA interference experiments suggested that five de novo OGs are not essential to the silkworm, implying that they may contribute to genetic redundancy or species-specific adaptation. Our results provide some new insights into the evolutionary significance of the silkworm OGs.
Collapse
Affiliation(s)
- Wei Sun
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Xin-Wei Zhao
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Ze Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 400044, China.
| |
Collapse
|
27
|
Cao PR, Wang L, Jiang YC, Yi YS, Qu F, Liu TC, Lv Y. De novo origin of VCY2 from autosome to Y-transposed amplicon. PLoS One 2015; 10:e0119651. [PMID: 25799347 PMCID: PMC4370482 DOI: 10.1371/journal.pone.0119651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 02/02/2015] [Indexed: 12/02/2022] Open
Abstract
The formation of new genes is a primary driving force of evolution in all organisms. The de novo evolution of new genes from non-protein-coding genomic regions is emerging as an important additional mechanism for novel gene creation. Y chromosomes underlie sex determination in mammals and contain genes that are required for male-specific functions. In this study, a search was undertaken for Y chromosome de novo genes derived from non-protein-coding sequences. The Y chromosome orphan gene variable charge, Y-linked (VCY)2, is an autosome-derived gene that has sequence similarity to large autosomal fragments but lacks an autosomal protein-coding homolog. VCY2 locates in the amplicon containing long DNA fragments that were transposed from autosomes to the Y chromosome before the ape-monkey split. We confirmed that VCY2cannot be encoded by autosomes due to the presence of multiple disablers that disrupt the open reading frame, such as the absence of start or stop codons and the presence of premature stop codons. Similar observations have been made for homologs in the autosomes of the chimpanzee, gorilla, rhesus macaque, baboon and out-group marmoset, which suggests that there was a non-protein-coding ancestral VCY2 that was common to apes and monkeys that predated the transposition event. Furthermore, while protein-coding orthologs are absent, a putative non-protein-coding VCY2 with conserved disablers was identified in the rhesus macaque Y chromosome male-specific region. This finding implies that VCY2 might have not acquired its protein-coding ability before the ape-monkey split. VCY2 encodes a testis-specific expressed protein and is involved in the pathologic process of male infertility, and the acquisition of this gene might improve male fertility. This is the first evidence that de novo genes can be generated from transposed autosomal non-protein-coding segments, and this evidence provides novel insights into the evolutionary history of the Y chromosome.
Collapse
Affiliation(s)
- Peng-Rong Cao
- Department of Epidemiology, Medical College of Hunan Normal University, Changsha, China
| | - Lei Wang
- Department of Epidemiology, Medical College of Hunan Normal University, Changsha, China
| | - Yu-Chao Jiang
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology School of Life Sciences, Fudan University, Shanghai, China
| | - Yin-Sha Yi
- Department of Epidemiology, Medical College of Hunan Normal University, Changsha, China
| | - Fang Qu
- Department of Epidemiology, Medical College of Hunan Normal University, Changsha, China
| | - Tao-Cheng Liu
- Department of Epidemiology, Medical College of Hunan Normal University, Changsha, China
| | - Yuan Lv
- Department of Epidemiology, Medical College of Hunan Normal University, Changsha, China
- * E-mail:
| |
Collapse
|
28
|
Zhang YE, Long M. New genes contribute to genetic and phenotypic novelties in human evolution. Curr Opin Genet Dev 2014; 29:90-6. [PMID: 25218862 PMCID: PMC4631527 DOI: 10.1016/j.gde.2014.08.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/26/2014] [Accepted: 08/27/2014] [Indexed: 12/31/2022]
Abstract
New genes in human genomes have been found relevant in evolution and biology of humans. It was conservatively estimated that the human genome encodes more than 300 human-specific genes and 1000 primate-specific genes. These new arrivals appear to be implicated in brain function and male reproduction. Surprisingly, increasing evidence indicates that they may also bring negative pleiotropic effects, while assuming various possible biological functions as sources of phenotypic novelties, suggesting a non-progressive route for functional evolution. Similar to these fixed new genes, polymorphic new genes were found to contribute to functional evolution within species, for example, with respect to digestion or disease resistance, revealing that new genes can acquire new or diverged functions in its initial stage as prototypic genes. These progresses have provided new opportunities to explore the genetic basis of human biology and human evolutionary history in a new dimension.
Collapse
Affiliation(s)
- Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, USA.
| |
Collapse
|