1
|
Gatenby RA, Luddy KA, Teer JK, Berglund A, Freischel AR, Carr RM, Lam AE, Pienta KJ, Amend SR, Austin RH, Hammarlund EU, Cleveland JL, Tsai KY, Brown JS. Lung adenocarcinomas without driver genes converge to common adaptive strategies through diverse genetic, epigenetic, and niche construction evolutionary pathways. Med Oncol 2024; 41:135. [PMID: 38704802 PMCID: PMC11070398 DOI: 10.1007/s12032-024-02344-2] [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: 07/18/2023] [Accepted: 02/21/2024] [Indexed: 05/07/2024]
Abstract
Somatic evolution selects cancer cell phenotypes that maximize survival and proliferation in dynamic environments. Although cancer cells are molecularly heterogeneous, we hypothesized convergent adaptive strategies to common host selection forces can be inferred from patterns of epigenetic and genetic evolutionary selection in similar tumors. We systematically investigated gene mutations and expression changes in lung adenocarcinomas with no common driver genes (n = 313). Although 13,461 genes were mutated in at least one sample, only 376 non-synonymous mutations evidenced positive evolutionary selection with conservation of 224 genes, while 1736 and 2430 genes exhibited ≥ two-fold increased and ≥ 50% decreased expression, respectively. Mutations under positive selection are more frequent in genes with significantly altered expression suggesting they often "hardwire" pre-existing epigenetically driven adaptations. Conserved genes averaged 16-fold higher expression in normal lung tissue compared to those with selected mutations demonstrating pathways necessary for both normal cell function and optimal cancer cell fitness. The convergent LUAD phenotype exhibits loss of differentiated functions and cell-cell interactions governing tissue organization. Conservation with increased expression is found in genes associated with cell cycle, DNA repair, p53 pathway, epigenetic modifiers, and glucose metabolism. No canonical driver gene pathways exhibit strong positive selection, but extensive down-regulation of membrane ion channels suggests decreased transmembrane potential may generate persistent proliferative signals. NCD LUADs perform niche construction generating a stiff, immunosuppressive microenvironment through selection of specific collagens and proteases. NCD LUADs evolve to a convergent phenotype through a network of interconnected genetic, epigenetic, and ecological pathways.
Collapse
Affiliation(s)
- Robert A Gatenby
- Department of Cancer Biology and Evolution, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
| | - Kimberly A Luddy
- Department of Cancer Biology and Evolution, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Jamie K Teer
- Department of Cancer Biology and Evolution, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
- Department of Bioinformatics, Moffitt Cancer Center, Tampa, USA
| | - Anders Berglund
- Department of Cancer Biology and Evolution, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
- Department of Bioinformatics, Moffitt Cancer Center, Tampa, USA
| | | | - Ryan M Carr
- Department of Oncology, Mayo Clinic, Rochester, USA
| | | | - Kenneth J Pienta
- Cancer Ecology Program, Johns Hopkins University, Baltimore, USA
| | - Sarah R Amend
- Cancer Ecology Program, Johns Hopkins University, Baltimore, USA
| | | | - Emma U Hammarlund
- Division of Translational Cancer Research, Lund University, Lund, Sweden
| | - John L Cleveland
- Department of Cancer Biology and Evolution, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Kenneth Y Tsai
- Departments of Pathology and Tumor Biology, Moffitt Cancer Center, Tampa, USA
| | - Joel S Brown
- Department of Cancer Biology and Evolution, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| |
Collapse
|
2
|
WNT3 hypomethylation counteracts low activity of the Wnt signaling pathway in the placenta of preeclampsia. Cell Mol Life Sci 2021; 78:6995-7008. [PMID: 34608506 PMCID: PMC8558176 DOI: 10.1007/s00018-021-03941-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/17/2021] [Accepted: 09/13/2021] [Indexed: 01/12/2023]
Abstract
Preeclampsia is a hypertensive disorder of pregnancy. Many studies have shown that epigenetic mechanisms may play a role in preeclampsia. Moreover, our previous study indicated that the differentially methylated genes in preeclampsia were enriched in the Wnt/β-catenin signaling pathway. This study aimed to identify differentially methylated Wnt/β-catenin signaling pathway genes in the preeclamptic placenta and to study the roles of these genes in trophoblast cells in vitro. Using an Illumina Infinium HumanMethylation 850 K BeadChip, we found that the Wnt signaling pathway was globally hypermethylated in the preeclamptic group compared with the term birth group, but hypomethylated in the preeclamptic group compared with the preterm birth group. Among all Wnt/β-catenin signaling pathway factors, WNT3 was the most significantly differentially expressed gene and was hypomethylated in the preeclamptic group compared to the nonhypertensive groups, namely, the preterm birth group and term birth group. This result was confirmed by pyrosequencing. Through quantitative real-time PCR and western blot analysis, the WNT3 gene was found to be highly expressed in preeclamptic placental tissues, in contrast to other WNT factors, which were previously reported to be expressed at low levels in placental tissues. Additionally, in the HTR8/SVneo cell line, knockdown of WNT3 suppressed the Wnt/β-catenin signaling pathway, consistent with the findings for other WNT factors. These results prompted us to speculate that the WNT3 gene counteracts the low activation state of the Wnt signaling pathway in the preeclamptic placenta through methylation modification.
Collapse
|
3
|
Chen B, Dong X, Dong X, Wang Q, Wu M, Wu J, Lou X, Xia F, Wang W, Dai J, Wang S. Integration of Dual Targeting and Dual Therapeutic Modules Endows Self-Assembled Nanoparticles with Anti-Tumor Growth and Metastasis Functions. Int J Nanomedicine 2021; 16:1361-1376. [PMID: 33658777 PMCID: PMC7917335 DOI: 10.2147/ijn.s291285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/12/2021] [Indexed: 01/10/2023] Open
Abstract
OBJECT High targeting and efficient cytotoxicity toward tumor cells endow NPs excellent anti-tumor activity. Herein, a peptide polymer possessing dual-targeting ability and double therapeutic activity was developed and named TGMF, which can form NPs through self-assembly. It is composed of four functional modules: 1) Active targeting peptide TMTP1 (T) deliver NPs to tumors specifically; 2) Therapeutic peptide GO-203 (G), which can significantly inhibit tumor growth by disrupting the redox balance in cells; 3) A passively targeted enzyme-responsive peptide PLGLGA (M), which can be cleaved specifically by metalloproteinase-2 (MMP-2) highly expressed in the tumor microenvironment (TME); and 4) Hexadecyl (F), which has strong hydrophobicity, can promote the self-assembly of TGMF NPs. METHODS Five modular peptide probes, namely, TGF, TMF, TGM, GMF, and TGMF were synthesized and self-assembled into NPs in solution. The characterization, enzyme reactivity, and cytotoxicity of NPs were evaluated in vitro, and the pharmacokinetics, bio-distribution, anti-tumor activity of NPs were investigated in vivo. In addition, transcriptome sequencing identified the intracellular signaling pathway-related genes involved in the anti-tumor effect of TGMF. RESULTS Upon enzyme cleavage, two types of nanostructure, NPs and nanofibers (NFs), were detected under TEM. Moreover, the cytotoxicity and anti-invasion activity of TGMF against tumor cells used were strongest among the five modular probes examined in vitro. TGMF increased reactive oxygen species (ROS) levels in cytoplasm and produced numerous NFs in extracellular interval and intracellular space. Transcriptome sequencing revealed that TGMF caused 446 genes' down-regulation and 270 genes' up-regulation in HeLa cells. In vivo, TGMF has a good anti-tumor effect, effectively prolonging the survival time of HeLa-tumor-bearing mice without systemic side effects. CONCLUSION Integration of multiple functional modules into NPs could be a promising strategy for the future of nanomedicine design towards tumor treatment.
Collapse
Affiliation(s)
- Biao Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Xiaoqi Dong
- Engineering Research Center of Nano-Geomaterials of the Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, People’s Republic of China
| | - Xiyuan Dong
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Quan Wang
- Engineering Research Center of Nano-Geomaterials of the Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, People’s Republic of China
| | - Meng Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Jun Wu
- Engineering Research Center of Nano-Geomaterials of the Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, People’s Republic of China
| | - Xiaoding Lou
- Engineering Research Center of Nano-Geomaterials of the Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, People’s Republic of China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of the Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, People’s Republic of China
| | - Wenwen Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| |
Collapse
|
4
|
Cao Y, Ao T, Wang X, Wei W, Fan J, Tian X. CD300a and CD300f molecules regulate the function of leukocytes. Int Immunopharmacol 2021; 93:107373. [PMID: 33548578 DOI: 10.1016/j.intimp.2021.107373] [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: 11/19/2020] [Revised: 01/02/2021] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
The CD300 molecule family is a type I transmembrane glycoprotein expressed on cell membrane of human and other mammals, and of its eight members, only CD300a and CD300f are classified as inhibitory receptors. CD300a and CD300f play an important role in regulating the function of leukocytes, such as activation, proliferation, differentiation, migration and immunity function. They are considered as potential targets for studying the development and progression of inflammation, infection and other diseases. Here, we review the expression and regulatory mechanisms of CD300a and CD300f on leukocytes, as well as their effects on relevant diseases.
Collapse
Affiliation(s)
- Yue Cao
- Department of Tissue Engineering, School of Fundamental Science, China Medical University, Shenyang, Liaoning 110122, China
| | - Tianrang Ao
- Department of Cardiology, Peking Union Medical College Hospital, Tsinghua University, Beijing 100730, China
| | - Xiaohong Wang
- Department of Tissue Engineering, School of Fundamental Science, China Medical University, Shenyang, Liaoning 110122, China
| | - Wumei Wei
- Department of Tissue Engineering, School of Fundamental Science, China Medical University, Shenyang, Liaoning 110122, China
| | - Jun Fan
- Department of Tissue Engineering, School of Fundamental Science, China Medical University, Shenyang, Liaoning 110122, China
| | - Xiaohong Tian
- Department of Tissue Engineering, School of Fundamental Science, China Medical University, Shenyang, Liaoning 110122, China.
| |
Collapse
|
5
|
Zhang L, Peng R, Sun Y, Wang J, Chong X, Zhang Z. Identification of key genes in non-small cell lung cancer by bioinformatics analysis. PeerJ 2019; 7:e8215. [PMID: 31844590 PMCID: PMC6911687 DOI: 10.7717/peerj.8215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 11/14/2019] [Indexed: 12/17/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) is one of the most common malignant tumors in the world, and it has become the leading cause of death of malignant tumors. However, its mechanisms are not fully clear. The aim of this study is to investigate the key genes and explore their potential mechanisms involving in NSCLC. Methods We downloaded gene expression profiles GSE33532, GSE30219 and GSE19804 from the Gene Expression Omnibus (GEO) database and analyzed them by using GEO2R. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for the functional and pathway enrichment analysis. We constructed the protein-protein interaction (PPI) network by STRING and visualized it by Cytoscape. Further, we performed module analysis and centrality analysis to find the potential key genes. Finally, we carried on survival analysis of key genes by GEPIA. Results In total, we obtained 685 DEGs. Moreover, GO analysis showed that they were mainly enriched in cell adhesion, proteinaceous extracellular region, heparin binding. KEGG pathway analysis revealed that transcriptional misregulation in cancer, ECM-receptor interaction, cell cycle and p53 signaling pathway were involved in. Furthermore, PPI network was constructed including 249 nodes and 1,027 edges. Additionally, a significant module was found, which included eight candidate genes with high centrality features. Further, among the eight candidate genes, the survival of NSCLC patients with the seven high expression genes were significantly worse, including CDK1, CCNB1, CCNA2, BIRC5, CCNB2, KIAA0101 and MELK. In summary, these identified genes should play an important role in NSCLC, which can provide new insight for NSCLC research.
Collapse
Affiliation(s)
- Li Zhang
- Department of Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Rui Peng
- Department of Bioinformatics, Chongqing Medical University, Chongqing, China
| | - Yan Sun
- Department of Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Jia Wang
- Department of Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Xinyu Chong
- Department of Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Zheng Zhang
- Department of Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| |
Collapse
|
6
|
Tong L, Wu W. Effects of long non-coding RNA (lncRNA) cancer susceptibility candidate 2c (CASC2c) on proliferation, metastasis and drug resistance of non-small cell lung cancer (NSCLC) cells through ERK1/2 and β-catenin signaling pathways. Pathol Res Pract 2019; 215:152522. [PMID: 31300295 DOI: 10.1016/j.prp.2019.152522] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/03/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVES This study was aimed to investigate the effects of long non-coding RNA (lncRNA) cancer susceptibility candidate 2c (CASC2c) on the proliferation, metastasis and drug resistance of non-small cell lung cancer (NSCLC) cells. METHODS The expression of CASC2c in NSCLC tissues and cell lines was detected by real-time fluorescence quantitative PCR (RT-qPCR). MTT and Transwell assay were used to determine the proliferation and migration of NSCLC cells in the experimental group and the control group respectively. The drug sensitivity test was used to confirm whether increasing the CASC2c expression level could reverse the resistance of NSCLC cells to the chemotherapy drug cisplatin. The effects of CASC2c on the expression levels of p-ERK1/2 and β-catenin were detected by western blot. RESULTS The results of RT-qPCR showed that CASC2c was under-expressed in NSCLC tissues and cells compared with normal adjacent lung tissues cells (p < 0.05). In addition, the CASC2c expression was remarkably correlated with TNM staging, tumor cell differentiation, lymph node metastasis, smoking and other pathological indicators of patients with NSCLC (p < 0.05). MTT and Transwell assay showed that the high-expression of CASC2c significantly reduced the proliferation and migration of NSCLC cells compared to that of the control group (p < 0.05). Western blot assay showed that the high-expressed CASC2c can decrease the expression of phosphorylated-ERK1/2 (p-ERK1/2) and β-catenin. CONCLUSIONS CASC2c was low expressed in NSCLC tissues and cells. What's more, it inhibited the proliferation and migration of NSCLC cells by inhibiting the expression of p-ERK1/2 and β-catenin and reversed NSCLC cells' resistance to the chemotherapy drug cisplatin. Therefore, CASC2c may serve as a new biomarker and therapeutic target in the diagnosis and treatment of NSCLC.
Collapse
Affiliation(s)
- Lingfei Tong
- Department of Pharmacy, Jiangxi Provincial People's Hospital, Aiguo Road 152, Donghu, Nanchang, Jiangxi, People's Republic of China.
| | - Wenming Wu
- Department of Pharmacy, Jiangxi Provincial People's Hospital, Aiguo Road 152, Donghu, Nanchang, Jiangxi, People's Republic of China.
| |
Collapse
|
7
|
Yang Y, Li H, Liu Y, Chi C, Ni J, Lin X. MiR-4319 hinders YAP expression to restrain non-small cell lung cancer growth through regulation of LIN28-mediated RFX5 stability. Biomed Pharmacother 2019; 115:108956. [PMID: 31096145 DOI: 10.1016/j.biopha.2019.108956] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/28/2019] [Accepted: 05/03/2019] [Indexed: 11/19/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is demonstrated as one of the most common malignant tumors and accounts for about 25% of cancer-related deaths each year. Extensive bodies of studies have manifested that microRNAs (miRNAs) play pivotal roles in the development of numerous malignant tumors by involving in modulation of cell biological processes. Although miR-4319 has been validated to execute tumor suppressor properties in triple-negative breast cancer, explorations on the function and latent mechanism of miR-4319 participating in NSCLC are still unclear. In this study, we proved that miR-4319 acted as a tumor suppressor in NSCLC progression via restraining cell proliferation and migration as well as boosting apoptosis. Further, miR-4319 bound with LIN28 and negatively regulated the expression of LIN28. Our data unveiled that LIN28 promoted RFX5 mRNA stability and miR-4319 led to the destabilization of RFX5 by targeting LIN28. In addition, RFX5 motivated the transcription of YAP and enhanced expression of YAP abolished the miR-4319 upregulation-mediated suppressive regulation of NSCLC tumorigenesis. In conclusion, miR-4319 dampened YAP expression to mitigate the tumorigenesis of NSCLC through inhibiting LIN28-mediated RFX5 stability, which offered an insight into the molecular mechanism underlying miR-4319 in NSCLC development.
Collapse
Affiliation(s)
- Yi Yang
- Department of Clinical Skills Center, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - He Li
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325003, China
| | - Yu Liu
- Department of Thoracic Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325003, China
| | - Chuang Chi
- Department of Thoracic Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325003, China
| | - Jiangwei Ni
- Department of Thoracic Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325003, China
| | - Xiaoming Lin
- Department of Thoracic Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325003, China.
| |
Collapse
|