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Norman RL, Singh R, Muskett FW, Parrott EL, Rufini A, Langridge JI, Runau F, Dennison A, Shaw JA, Piletska E, Canfarotta F, Ng LL, Piletsky S, Jones DJL. Mass spectrometric detection of KRAS protein mutations using molecular imprinting. NANOSCALE 2021; 13:20401-20411. [PMID: 34854867 PMCID: PMC8675027 DOI: 10.1039/d1nr03180e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/27/2021] [Indexed: 05/07/2023]
Abstract
Cancer is a disease of cellular evolution where single base changes in the genetic code can have significant impact on the translation of proteins and their activity. Thus, in cancer research there is significant interest in methods that can determine mutations and identify the significant binding sites (epitopes) of antibodies to proteins in order to develop novel therapies. Nano molecularly imprinted polymers (nanoMIPs) provide an alternative to antibodies as reagents capable of specifically capturing target molecules depending on their structure. In this study, we used nanoMIPs to capture KRAS, a critical oncogene, to identify mutations which when present are indicative of oncological progress. Herein, coupling nanoMIPs (capture) and liquid chromatography-mass spectrometry (detection), LC-MS has allowed us to investigate mutational assignment and epitope discovery. Specifically, we have shown epitope discovery by generating nanoMIPs to a recombinant KRAS protein and identifying three regions of the protein which have been previously assigned as epitopes using much more time-consuming protocols. The mutation status of the released tryptic peptide was identified by LC-MS following capture of the conserved region of KRAS using nanoMIPS, which were tryptically digested, thus releasing the sequence of a non-conserved (mutated) region. This approach was tested in cell lines where we showed the effective genotyping of a KRAS cell line and in the plasma of cancer patients, thus demonstrating its ability to diagnose precisely the mutational status of a patient. This work provides a clear line-of-sight for the use of nanoMIPs to its translation from research into diagnostic and clinical utility.
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Affiliation(s)
- Rachel L Norman
- Leicester Cancer Research Centre, Leicester Royal Infirmary, University of Leicester, Leicester, LE1 5WW, UK.
| | - Rajinder Singh
- Leicester Cancer Research Centre, Leicester Royal Infirmary, University of Leicester, Leicester, LE1 5WW, UK.
| | - Frederick W Muskett
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, UK
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, UK
| | - Emma L Parrott
- Leicester Cancer Research Centre, Leicester Royal Infirmary, University of Leicester, Leicester, LE1 5WW, UK.
| | - Alessandro Rufini
- Leicester Cancer Research Centre, Leicester Royal Infirmary, University of Leicester, Leicester, LE1 5WW, UK.
| | | | - Franscois Runau
- Leicester Cancer Research Centre, Leicester Royal Infirmary, University of Leicester, Leicester, LE1 5WW, UK.
| | - Ashley Dennison
- Leicester Cancer Research Centre, Leicester Royal Infirmary, University of Leicester, Leicester, LE1 5WW, UK.
| | - Jacqui A Shaw
- Leicester Cancer Research Centre, Leicester Royal Infirmary, University of Leicester, Leicester, LE1 5WW, UK.
| | - Elena Piletska
- MIP Diagnostics, The Exchange Building, Colworth Park, MK44 1LQ, Bedford, UK
- School of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | | | - Leong L Ng
- Department of Cardiovascular Sciences, University of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, LE1 7RH, UK
| | - Sergey Piletsky
- MIP Diagnostics, The Exchange Building, Colworth Park, MK44 1LQ, Bedford, UK
- School of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Donald J L Jones
- Leicester Cancer Research Centre, Leicester Royal Infirmary, University of Leicester, Leicester, LE1 5WW, UK.
- Department of Cardiovascular Sciences, University of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, LE1 7RH, UK
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Bensen JT, Graff M, Young KL, Sethupathy P, Parker J, Pecot CV, Currin K, Haddad SA, Ruiz-Narváez EA, Haiman CA, Hong CC, Sucheston-Campbell LE, Zhu Q, Liu S, Yao S, Bandera EV, Rosenberg L, Lunetta KL, Ambrosone CB, Palmer JR, Troester MA, Olshan AF. A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women. Breast Cancer Res 2018; 20:45. [PMID: 29871690 PMCID: PMC5989404 DOI: 10.1186/s13058-018-0964-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 03/28/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) regulate gene expression and influence cancer. Primary transcripts of miRNAs (pri-miRNAs) are poorly annotated and little is known about the role of germline variation in miRNA genes and breast cancer (BC). We sought to identify germline miRNA variants associated with BC risk and tumor subtype among African-American (AA) women. METHODS Under the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium, genotyping and imputed data from four studies on BC in AA women were combined into a final dataset containing 224,188 miRNA gene single nucleotide polymorphisms (SNPs) for 8350 women: 3663 cases and 4687 controls. The primary miRNA sequence was identified for 566 miRNA genes expressed in Encyclopedia of DNA Elements (ENCODE) Tier 1 cell types and human pancreatic islets. Association analysis was conducted using logistic regression for BC status overall and by tumor subtype. RESULTS A novel BC signal was localized to an 8.6-kb region of 17q25.3 by four SNPs (rs9913477, rs1428882938, rs28585511, and rs7502931) and remained statistically significant after multiple test correction (odds ratio (OR) = 1.44, 95% confidence interval (CI) = 1.26-1.65; p = 3.15 × 10-7; false discovery rate (FDR) = 0.03). These SNPs reside in a genomic location that includes both the predicted primary transcript of the noncoding miRNA gene MIR3065 and the first intron of the gene for brain-specific angiogenesis inhibitor 1-associated protein 2 (BAIAP2). Furthermore, miRNA-associated SNPs on chromosomes 1p32.3, 5q32, and 3p25.1 were the strongest signals for hormone receptor, luminal versus basal-like, and HER2 enrichment status, respectively. A second phase of genotyping (1397 BC cases, 2418 controls) that included two SNPs in the 8.6-kb region was used for validation and meta-analysis. While neither rs4969239 nor rs9913477 was validated, when meta-analyzed with the original dataset their association with BC remained directionally consistent (OR = 1.29, 95% CI = 1.16-1.44 (p = 4.18 × 10-6) and OR = 1.33, 95% CI = 1.17-1.51 (p = 1.6 × 10-5), respectively). CONCLUSION Germline genetic variation indicates that MIR3065 may play an important role in BC development and heterogeneity among AA women. Further investigation to determine the potential functional effects of these SNPs is warranted. This study contributes to our understanding of BC risk in AA women and highlights the complexity in evaluating variation in gene-dense regions of the human genome.
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Affiliation(s)
- Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Joel Parker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chad V Pecot
- Department of Medicine, Division of Oncology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kevin Currin
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Biological and Biomedical Sciences Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephen A Haddad
- Slone Epidemiology Center at Boston University, Boston, MA, 02215, USA
| | - Edward A Ruiz-Narváez
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, USA
| | - Chi-Chen Hong
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA
| | | | - Qianqian Zhu
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA
| | - Song Liu
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA
| | - Song Yao
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA
| | - Elisa V Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08903, USA
| | - Lynn Rosenberg
- Slone Epidemiology Center at Boston University, Boston, MA, 02215, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA
| | - Julie R Palmer
- Slone Epidemiology Center at Boston University, Boston, MA, 02215, USA
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Liang YK, Han ZD, Lu JM, Liu ZZ, Zhuo YJ, Zhu XJ, Chen JX, Ye JH, Liang YX, He HC, Zhong WD. Downregulation of ARID4A and ARID4B promote tumor progression and directly regulated by microRNA-30d in patient with prostate cancer. J Cell Biochem 2018; 119:7245-7255. [PMID: 29797600 DOI: 10.1002/jcb.26913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 04/04/2018] [Indexed: 12/15/2022]
Abstract
AT-rich interaction domain 4A (ARID4A) and AT-rich interaction domain 4B (ARID4B), which are both the AT-rich interaction domain (ARID) family, have been reported to be oncogene or tumor suppressor gene in various human malignances, but there is no involvement about their functions in prostate cancer (PCa). Our previous study has reported that microRNA-30d (miR-30d) expression can predicted poor clinical prognosis in PCa, however, the underlying mechanisms of miR-30d have not been fully described. The aim of our study is to investigate the expression relevance between miR-30d and ARID4A or ARID4B, and examine the clinical significance and biological function of ARID4A and AIRD4B in PCa. In this study, both ARID4A and ARID4B were identified as the target genes of miR-30d. In addition, the mRNA expression of miR-30d in PCa tissues were significantly negative correlated with ARID4A (Pearson correlation coefficient = -0.313, P = 0.001) and ARID4B (Pearson correlation coefficient = -0.349, P < 0.001), while there was a positive correlation between ARID4A and ARID4B (Pearson correlation coefficient = 0.865, P < 0.001). Moreover, both ARID4A and ARID4B were significantly downregulated in PCa tissues with high Gleason scores (P = 0.005, P = 0.033), PSA failure (P = 0.012, P = 0.05) and short biochemical recurrent-free survival (P = 0.033, P = 0.031). Furthermore, the knockout expression of ARID4A and ARID4B promoted PCa cell proliferation, migration and invasion in vitro. In conclusion, our results indicated that ARID4A and ARID4B may serve as tumor suppressor in PCa progression, suggesting that they might be the potential therapeutic targets in prostate cancer.
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Affiliation(s)
- Ying-Ke Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zhao-Dong Han
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China
| | - Jian-Ming Lu
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ze-Zhen Liu
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yang-Jia Zhuo
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xue-Jin Zhu
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jun-Xu Chen
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jian-Heng Ye
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yu-Xiang Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hui-Chan He
- Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Wei-De Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China.,Department of Urology, Huadu District People's Hospital, Southern Medical University, Guangzhou, China
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Goldberger N, Walker RC, Kim CH, Winter S, Hunter KW. Inherited variation in miR-290 expression suppresses breast cancer progression by targeting the metastasis susceptibility gene Arid4b. Cancer Res 2013; 73:2671-81. [PMID: 23447578 PMCID: PMC3630248 DOI: 10.1158/0008-5472.can-12-3513] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The metastatic cascade is a complex and extremely inefficient process with many potential barriers. Understanding this process is of critical importance because the majority of cancer mortality is associated with metastatic disease. Recently, it has become increasingly clear that microRNAs (miRNA) play important roles in tumorigenesis and metastasis, yet few studies have examined how germline variations may dysregulate miRNAs, in turn affecting metastatic potential. To explore this possibility, the highly metastatic MMTV-PyMT mice were crossed with 25 AKXD (AKR/J × DBA/2J) recombinant inbred strains to produce F1 progeny with varying metastatic indices. When mammary tumors from the F1 progeny were analyzed by miRNA microarray, miR-290 (containing miR-290-3p and miR-290-5p) was identified as a top candidate progression-associated miRNA. The microarray results were validated in vivo when miR-290 upregulation in two independent breast cancer cell lines suppressed both primary tumor and metastatic growth. Computational analysis identified breast cancer progression gene Arid4b as a top target of miR-290-3p, which was confirmed by luciferase reporter assay. Surprisingly, pathway analysis identified estrogen receptor (ER) signaling as the top canonical pathway affected by miR-290 upregulation. Further analysis showed that ER levels were elevated in miR-290-expressing tumors and positively correlated with apoptosis. Taken together, our results suggest miR-290 targets Arid4b while simultaneously enhancing ER signaling and increasing apoptosis, thereby suppressing breast cancer progression. This, to the best of our knowledge, is the first example of inherited differences in miRNA expression playing a role in breast cancer progression.
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Affiliation(s)
- Natalie Goldberger
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
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Pan B, Cui D, Sheng Y, Ozkan C, Gao F, He R, Li Q, Xu P, Huang T. Dendrimer-modified magnetic nanoparticles enhance efficiency of gene delivery system. Cancer Res 2007; 67:8156-63. [PMID: 17804728 DOI: 10.1158/0008-5472.can-06-4762] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Magnetic nanoparticles (MNP) with a diameter of 8 nm were modified with different generations of polyamidoamine (PAMAM) dendrimers and mixed with antisense survivin oligodeoxynucleotide (asODN). The MNP then formed asODN-dendrimer-MNP composites, which we incubated with human tumor cell lines such as human breast cancer MCF-7, MDA-MB-435, and liver cancer HepG2 and then analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, quantitative reverse transcription-PCR, Western blotting, laser confocal microscopy, and high-resolution transmission electron microscopy. Results showed that the asODN-dendrimer-MNP composites were successfully synthesized, can enter into tumor cells within 15 min, caused marked down-regulation of the survivin gene and protein, and inhibited cell growth in dose- and time-dependent means. No.5 generation of asODN-dendrimer-MNP composites exhibits the highest efficiency for cellular transfection and inhibition. These results show that PAMAM dendrimer-modified MNPs may be a good gene delivery system and have potential applications in cancer therapy and molecular imaging diagnosis.
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Affiliation(s)
- Bifeng Pan
- Department of Bio-Nano-Science and Engineering, National Key Laboratory of Nano/Micro Fabrication Technology, Shanghai Jiao Tong University, Shanghai, PR China
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Landais S, Landry S, Legault P, Rassart E. Oncogenic potential of the miR-106-363 cluster and its implication in human T-cell leukemia. Cancer Res 2007; 67:5699-707. [PMID: 17575136 DOI: 10.1158/0008-5472.can-06-4478] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We previously reported the identification of the Kis2 common retrovirus integration site, located on mouse chromosome X, in radiation leukemia virus-induced T-cell leukemias. Tumors with a provirus at the Kis2 locus overexpressed a novel noncoding RNA (ncRNA) with a complex splicing pattern and no polyA tail. Database upgrade revealed the presence of a microRNA (miRNA) cluster, miR-106-363, just downstream of the Kis2 ncRNAs. We found that Kis2 ncRNAs are the pri-miRNA of miR-106-363, and we present evidence that Kis2 ncRNA overexpression in mouse tumors results in miR-106a, miR-19b-2, miR-92-2, and miR-20b accumulation. We show the oncogenic potential of those miRNAs in anchorage independence assay and confirm pri-miR-106-363 overexpression in 46% of human T-cell leukemias tested. This overexpression contributes in rising miR-92 and miR-19 levels, as this is the case for miR-17-92 cluster overexpression. Furthermore, we identified myosin regulatory light chain-interacting protein, retinoblastoma-binding protein 1-like, and possibly homeodomain-interacting protein kinase 3 as target genes of this miRNA cluster, which establishes a link between these genes and T-cell leukemia for the first time.
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Affiliation(s)
- Séverine Landais
- Laboratoire de Biologie Moléculaire, Département des Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec, Canada
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