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Song Q, Zhang W, Shi D, Zhang Z, Zhao Q, Wang M, Huang M, Meng J, Cui W, Luo X. Overexpression of cannabinoid receptor 2 is associated with human breast cancer proliferation, apoptosis, chemosensitivity and prognosis via the PI3K/Akt/mTOR signaling pathway. Cancer Med 2023; 12:13538-13550. [PMID: 37220224 PMCID: PMC10315729 DOI: 10.1002/cam4.6037] [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: 07/20/2022] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 05/25/2023] Open
Abstract
INTRODUCTION The cannabinoid receptor 2 (CB2) is mainly involved in the immune system. However, although CB2 has been reported to play an anti-tumor function in breast cancer (BC), its specific mechanism in BC remains unclear. METHODS We examined the expression and prognostic significance of CB2 in BC tissues by qPCR, second-generation sequencing, western blot, and immunohistochemistry. We assessed the impacts of overexpression and a specific agonist of CB2 on the growth, proliferation, apoptosis, and drug resistance of BC cells in vitro and in vivo using CCK-8, flow cytometry, TUNEL staining, immunofluorescence, tumor xenografts, western blot, and colony formation assays. RESULTS CB2 expression was significantly lower in BC compared with paracancerous tissues. It was also highly expressed in benign tumors and ductal carcinoma in situ, and its expression was correlated with prognosis in BC patients. CB2 overexpression and treatment of BC cells with a CB2 agonist inhibited proliferation and promoted apoptosis, and these actions were achieved by suppressing the PI3K/Akt/mTOR signaling pathway. Moreover, CB2 expression was increased in MDA-MB-231 cell treated with cisplatin, doxorubicin, and docetaxel, and sensitivity to these anti-tumor drugs was increased in BC cells overexpressing CB2. CONCLUSIONS These findings reveal that CB2 mediates BC via the PI3K/Akt/mTOR signaling pathway. CB2 could be a novel target for the diagnosis and treatment of BC.
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Affiliation(s)
- Qiang Song
- Department of Central LaboratoryChongqing University Three Gorges HospitalChongqing UniversityWanzhou, ChongqingChina
| | - Wenjin Zhang
- Department of Central LaboratoryChongqing University Three Gorges HospitalChongqing UniversityWanzhou, ChongqingChina
| | - Dan Shi
- Department of Pathology, Chongqing University Three Gorges HospitalChongqing UniversityWanzhou, ChongqingChina
| | - Zhiliang Zhang
- Department of Breast SurgeryChongqing University Three Gorges Hospital, Chongqing UniversityWanzhou, ChongqingChina
| | - Qiurong Zhao
- Department of Central LaboratoryChongqing University Three Gorges HospitalChongqing UniversityWanzhou, ChongqingChina
| | - Mengyuan Wang
- Department of Breast SurgeryChongqing University Three Gorges Hospital, Chongqing UniversityWanzhou, ChongqingChina
| | - Man Huang
- Department of Breast SurgeryChongqing University Three Gorges Hospital, Chongqing UniversityWanzhou, ChongqingChina
| | - Juanjuan Meng
- Department of Central LaboratoryChongqing University Three Gorges HospitalChongqing UniversityWanzhou, ChongqingChina
| | - Wei Cui
- Department of Central LaboratoryChongqing University Three Gorges HospitalChongqing UniversityWanzhou, ChongqingChina
| | - Xiaohe Luo
- Department of Central LaboratoryChongqing University Three Gorges HospitalChongqing UniversityWanzhou, ChongqingChina
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Song Q, Dou L, Zhang W, Peng Y, Huang M, Wang M. Public transcriptome database-based selection and validation of reliable reference genes for breast cancer research. Biomed Eng Online 2021; 20:124. [PMID: 34895237 PMCID: PMC8665499 DOI: 10.1186/s12938-021-00963-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/21/2021] [Indexed: 11/21/2022] Open
Abstract
Background Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the most sensitive technique for evaluating gene expression levels. Choosing appropriate reference genes (RGs) is critical for normalizing and evaluating changes in the expression of target genes. However, uniform and reliable RGs for breast cancer research have not been identified, limiting the value of target gene expression studies. Here, we aimed to identify reliable and accurate RGs for breast cancer tissues and cell lines using the RNA-seq dataset. Methods First, we compiled the transcriptome profiling data from the TCGA database involving 1217 samples to identify novel RGs. Next, ten genes with relatively stable expression levels were chosen as novel candidate RGs, together with six conventional RGs. To determine and validate the optimal RGs we performed qRT-PCR experiments on 87 samples from 11 types of surgically excised breast tumor specimens (n = 66) and seven breast cancer cell lines (n = 21). Five publicly available algorithms (geNorm, NormFinder, ΔCt method, BestKeeper, and ComprFinder) were used to assess the expression stability of each RG across all breast cancer tissues and cell lines. Results Our results show that RG combinations SF1 + TRA2B + THRAP3 and THRAP3 + RHOA + QRICH1 showed stable expression in breast cancer tissues and cell lines, respectively, and that they displayed good interchangeability. We propose that these combinations are optimal triplet RGs for breast cancer research. Conclusions In summary, we identified novel and reliable RG combinations for breast cancer research based on a public RNA-seq dataset. Our results lay a solid foundation for the accurate normalization of qRT-PCR results across different breast cancer tissues and cells. Supplementary Information The online version contains supplementary material available at 10.1186/s12938-021-00963-8.
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Affiliation(s)
- Qiang Song
- Department of Central Laboratory, Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Chongqing, 404000, China
| | - Lu Dou
- Department of Central Laboratory, Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Chongqing, 404000, China
| | - Wenjin Zhang
- Department of Central Laboratory, Chongqing University Three Gorges Hospital, School of Medicine, Chongqing University, Chongqing, 404000, China
| | - Yang Peng
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Man Huang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, No.165, Xin Cheng Lu, Wanzhou, Chongqing, 404000, China.
| | - Mengyuan Wang
- Department of Breast Surgery, Chongqing University Three Gorges Hospital, No.165, Xin Cheng Lu, Wanzhou, Chongqing, 404000, China.
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Dunham I, Beare DM, Collins JE. The characteristics of human genes: analysis of human chromosome 22. Comp Funct Genomics 2010; 4:635-46. [PMID: 18629020 PMCID: PMC2447302 DOI: 10.1002/cfg.335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Revised: 09/04/2003] [Accepted: 09/08/2003] [Indexed: 11/11/2022] Open
Affiliation(s)
- Ian Dunham
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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Sakai T, Larsen M, Yamada KM. Microanalysis of gene expression in tissues using T7-SAGE: serial analysis of gene expression after high-fidelity T7-based RNA amplification. ACTA ACUST UNITED AC 2008; Chapter 19:Unit 19.3. [PMID: 18228400 DOI: 10.1002/0471143030.cb1903s16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this unit, the authors describe a new technique, T7-SAGE, in which a high-fidelity T7 amplification step is combined with SAGE analysis. In order to avoid extra PCR or other forms of amplification, the authors incorporate only two cycles of T7-based RNA amplification as the initial step. This T7-based amplification step has high accuracy. In addition, T7 RNA polymerase has high processivity and functions effectively even when broad stretches of nucleotides are being amplified. Although no protocol that includes an amplification step can claim to permit determination of absolute transcript number, since slight changes in estimated transcript frequency are always possible, T7 procedures appear to be the safest to date. This new T7-SAGE procedure should facilitate application of SAGE for gene-expression profiling using minimal quantities of starting material, such as from embryonic tissues and microdissected cells from histological sections of tissues.
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Affiliation(s)
- Takayoshi Sakai
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
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Reed J, Mishra B, Pittenger B, Magonov S, Troke J, Teitell MA, Gimzewski JK. Single molecule transcription profiling with AFM. NANOTECHNOLOGY 2007; 18:44032. [PMID: 20721301 PMCID: PMC2922717 DOI: 10.1088/0957-4484/18/4/044032] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.
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Affiliation(s)
- Jason Reed
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Bud Mishra
- Department of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | | | | | - Joshua Troke
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
| | - Michael A Teitell
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
| | - James K Gimzewski
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
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Abstract
The generation of complete and full-length cDNA libraries for potential functional assays of specific gene sequences is essential for most molecules in biotechnology and biomedical research. The field of cDNA library generation has changed rapidly in the past 10 yr. This review presents an overview of the method available for the basic information of generating cDNA libraries, including the definition of the cDNA library, different kinds of cDNA libraries, difference between methods for cDNA library generation using conventional approaches and a novel strategy, and the quality of cDNA libraries. It is anticipated that the high-quality cDNA libraries so generated would facilitate studies involving genechips and the microarray, differential display, subtractive hybridization, gene cloning, and peptide library generation.
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Affiliation(s)
- Shao-Yao Ying
- Department of Cell and neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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Abu SM, Li G, Asiegbu FO. Identification ofHeterobasidion annosum(S-type) genes expressed during initial stages of conidiospore germination and under varying culture conditions. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09484.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Carninci P, Waki K, Shiraki T, Konno H, Shibata K, Itoh M, Aizawa K, Arakawa T, Ishii Y, Sasaki D, Bono H, Kondo S, Sugahara Y, Saito R, Osato N, Fukuda S, Sato K, Watahiki A, Hirozane-Kishikawa T, Nakamura M, Shibata Y, Yasunishi A, Kikuchi N, Yoshiki A, Kusakabe M, Gustincich S, Beisel K, Pavan W, Aidinis V, Nakagawara A, Held WA, Iwata H, Kono T, Nakauchi H, Lyons P, Wells C, Hume DA, Fagiolini M, Hensch TK, Brinkmeier M, Camper S, Hirota J, Mombaerts P, Muramatsu M, Okazaki Y, Kawai J, Hayashizaki Y. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res 2003; 13:1273-89. [PMID: 12819125 PMCID: PMC403712 DOI: 10.1101/gr.1119703] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report the construction of the mouse full-length cDNA encyclopedia,the most extensive view of a complex transcriptome,on the basis of preparing and sequencing 246 libraries. Before cloning,cDNAs were enriched in full-length by Cap-Trapper,and in most cases,aggressively subtracted/normalized. We have produced 1,442,236 successful 3'-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs annotated in the FANTOM-2 annotation. We have also produced 547,149 5' end reads,which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU),which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC),which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large numbers of clusters (and TUs) of this project,which also include non-protein-coding RNAs,and the lower gene number estimation of genome annotations. Altogether,5'-end clusters identify regions that are potential promoters for 8637 known genes and 5'-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.
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Affiliation(s)
- Piero Carninci
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Rabinowicz PD, McCombie WR, Martienssen RA. Gene enrichment in plant genomic shotgun libraries. CURRENT OPINION IN PLANT BIOLOGY 2003; 6:150-156. [PMID: 12667872 DOI: 10.1016/s1369-5266(03)00008-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The Arabidopsis genome (about 130 Mbp) has been completely sequenced; whereas a draft sequence of the rice genome (about 430 Mbp) is now available and the sequencing of this genome will be completed in the near future. The much larger genomes of several important crop species, such as wheat (about 16,000 Mbp) or maize (about 2500 Mbp), may not be fully sequenced with current technology. Instead, sequencing-analysis strategies are being developed to obtain sequencing and mapping information selectively for the genic fraction (gene space) of complex plant genomes.
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Affiliation(s)
- Pablo D Rabinowicz
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
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Gera JF, Hazbun TR, Fields S. Array-based methods for identifying protein-protein and protein-nucleic acid interactions. Methods Enzymol 2002; 350:499-512. [PMID: 12073332 DOI: 10.1016/s0076-6879(02)50981-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Joseph F Gera
- Departments of Hematology and Oncology, University of California/Veterans Administration Medical Center, Los Angeles, California 90073, USA
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Rauyaree P, Choi W, Fang E, Blackmon B, Dean RA. Genes expressed during early stages of rice infection with the rice blast fungus Magnaporthe grisea. MOLECULAR PLANT PATHOLOGY 2001; 2:347-54. [PMID: 20573024 DOI: 10.1046/j.1464-6722.2001.00085.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
summary A system-wide approach was adopted to further elucidate mechanisms regulating disease outcome between rice and the fungal pathogen Magnaporthe grisea. First, a cDNA library was constructed from M. grisea infected rice at 48 h post-inoculation. The 5' end-sequencing of 619 randomly selected clones revealed 359 expressed sequence tags (ESTs) that had not previously been described. A total of 124 from 260 ESTs with high and moderate similarity scores, based on BlastX, were organized into categories according to their putative function. The largest category of sequences (21%) contained stress or defence response genes. Eleven per cent of identified ESTs were redundant. In a second approach, differential hybridization analysis of the cDNA library using high-density filters resulted in the identification of novel genes and previously characterized M. grisea genes, including several that had previously been implicated in the infection process. A survey of up-regulated cDNA clones revealed clone 29003, which corresponded to the rice peroxidase POX22.3. This gene is known to be expressed in rice upon infection with Xanthomonas oryzae pv. oryzae, the bacterial blight pathogen. Importantly, this approach demonstrates the utility of gene discovery, through ESTs, for revealing novel genes in addition to those previously characterized as being potentially implicated in host-pathogen interactions.
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Affiliation(s)
- P Rauyaree
- Department of Plant Pathology and Physiology, Clemson University, Clemson, SC 29634, USA
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2001. [PMCID: PMC2448396 DOI: 10.1002/cfg.59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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