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Saleh AD, Cheng H, Martin SE, Si H, Ormanoglu P, Carlson S, Clavijo PE, Yang X, Das R, Cornelius S, Couper J, Chepeha D, Danilova L, Harris TM, Prystowsky MB, Childs GJ, Smith RV, Robertson AG, Jones SJM, Cherniack AD, Kim SS, Rait A, Pirollo KF, Chang EH, Chen Z, Van Waes C. Integrated Genomic and Functional microRNA Analysis Identifies miR-30-5p as a Tumor Suppressor and Potential Therapeutic Nanomedicine in Head and Neck Cancer. Clin Cancer Res 2019; 25:2860-2873. [PMID: 30723145 DOI: 10.1158/1078-0432.ccr-18-0716] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 11/02/2018] [Accepted: 01/24/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE To identify deregulated and inhibitory miRNAs and generate novel mimics for replacement nanomedicine for head and neck squamous cell carcinomas (HNSCC). EXPERIMENTAL DESIGN We integrated miRNA and mRNA expression, copy number variation, and DNA methylation results from The Cancer Genome Atlas (TCGA), with a functional genome-wide screen. RESULTS We reveal that the miR-30 family is commonly repressed, and all 5 members sharing these seed sequence similarly inhibit HNSCC proliferation in vitro. We uncover a previously unrecognized inverse relationship with overexpression of a network of important predicted target mRNAs deregulated in HNSCC, that includes key molecules involved in proliferation (EGFR, MET, IGF1R, IRS1, E2F7), differentiation (WNT7B, FZD2), adhesion, and invasion (ITGA6, SERPINE1). Reexpression of the most differentially repressed family member, miR-30a-5p, suppressed this mRNA program, selected signaling proteins and pathways, and inhibited cell proliferation, migration, and invasion in vitro. Furthermore, a novel miR-30a-5p mimic formulated into a targeted nanomedicine significantly inhibited HNSCC xenograft tumor growth and target growth receptors EGFR and MET in vivo. Significantly decreased miR-30a/e family expression was related to DNA promoter hypermethylation and/or copy loss in TCGA data, and clinically with decreased disease-specific survival in a validation dataset. Strikingly, decreased miR-30e-5p distinguished oropharyngeal HNSCC with poor prognosis in TCGA (P = 0.002) and validation (P = 0.007) datasets, identifying a novel candidate biomarker and target for this HNSCC subset. CONCLUSIONS We identify the miR-30 family as an important regulator of signal networks and tumor suppressor in a subset of HNSCC patients, which may benefit from miRNA replacement nanomedicine therapy.
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Affiliation(s)
- Anthony D Saleh
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, Maryland.,miRecule, Inc. Rockville, Maryland
| | - Hui Cheng
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Scott E Martin
- RNAi Screening Facility, National Center for Advancing Translational Sciences, NIH, Bethesda, Maryland
| | - Han Si
- Molecular Characterization & Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Pinar Ormanoglu
- RNAi Screening Facility, National Center for Advancing Translational Sciences, NIH, Bethesda, Maryland
| | - Sophie Carlson
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Paul E Clavijo
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Xinping Yang
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Rita Das
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Shaleeka Cornelius
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Jamie Couper
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, Maryland
| | - Douglas Chepeha
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Ludmila Danilova
- Department of Medical Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Vavilov Institute of General Genetics Russian Academy of Science, Moscow, Russia
| | - Thomas M Harris
- Department of Pathology, Einstein School of Medicine, Bronx, New York
| | | | - Geoffrey J Childs
- Department of Pathology, Einstein School of Medicine, Bronx, New York
| | - Richard V Smith
- Department of Otorhinolaryngology-Head and Neck Surgery, Montefiore Medical Center, Bronx, New York
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew D Cherniack
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sang S Kim
- Departments of Oncology and Otolaryngology at the Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown, Washington DC
| | - Antonina Rait
- Departments of Oncology and Otolaryngology at the Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown, Washington DC
| | - Kathleen F Pirollo
- Departments of Oncology and Otolaryngology at the Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown, Washington DC
| | - Esther H Chang
- Departments of Oncology and Otolaryngology at the Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown, Washington DC
| | - Zhong Chen
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, Maryland.
| | - Carter Van Waes
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, Maryland.
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Jimenez L, Sharma VP, Condeelis JS, Harris TM, Ow TJ, Prystowsky MB, Childs GJ, Segall JE. Abstract 185: MicroRNA-375 suppresses extracellular matrix degradation and invadopodial activity in head and neck squamous cell carcinoma. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a highly invasive cancer having an association with locoregional recurrence and lymph node metastasis. We previously reported that patients with lower microRNA-375 (miR-375) tumor:normal expression levels showed significantly decreased disease-specific survival, increased locoregional recurrence and distant metastasis. We also previously described that HNSCC cells with increased miR-375 showed significantly diminished invasion in vitro. The ability of cancer cells to degrade extracellular matrix (ECM) through secreted and membrane-bound proteases allows local invasion into the surrounding stroma, as well as possible metastasis. Invadopodia are specialized actin-rich structures, which mediate ECM degradation. Our objective was to determine whether elevated miR-375 expression in HNSCC cells also affects invadopodia formation and activity.
For the evaluation of the matrix degradation properties of UMSCC1 and OSC19 cell lines, an invadopodial matrix degradation assay was used. Western blot analyses were conducted to measure the total protein levels of selected invadopodia-associated proteins. The tyrosine phosphorylation states of cortactin were evaluated by immunoprecipitation experiments. For the detection of levels of secreted proteases in the conditioned cell growth medium, Human Protease Arrays were used. Quantitative RT-PCR measurements were used to evaluate the mRNA expression levels of the commonly regulated proteases.
We observed that the HNSCC cell lines with elevated miR-375 expression showed significant reductions in ECM degradation. We further identified that HNSCC cells expressing increased miR-375 expression had significantly suppressed amounts of mature invadopodia, although the levels of invadopodium precursors were not significantly altered. We determined that increased miR-375 expression in the HNSCC cell lines did not reduce cellular levels of invadopodia components, such as Tks5, cortactin and fascin. We also did not observe significant alterations to the tyrosine phosphorylation states of cortactin in the HNSCC cell lines. However, we found that the HNSCC cells with higher miR-375 expression had significant reductions in the mRNA expression and secreted levels of specific proteases, including Kallikrein 6, Kallikrein 10, and MMP-9.
In summary, we have extended our understanding of the impact of miR-375 expression levels on HNSCC invasion. We demonstrated that increased miR-375 expression in HNSCC cells reduced ECM degradation and invadopodial activity. Our data suggest that reduced miR-375 expression in HNSCC patients can contribute to the invasive properties of head and neck cancer through increased invadopodial activity.
Citation Format: Lizandra Jimenez, Ved P. Sharma, John S. Condeelis, Thomas M. Harris, Thomas J. Ow, Michael B. Prystowsky, Geoffrey J. Childs, Jeffrey E. Segall. MicroRNA-375 suppresses extracellular matrix degradation and invadopodial activity in head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 185. doi:10.1158/1538-7445.AM2015-185
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Harris TM, Du P, Kawachi N, Belbin TJ, Wang Y, Schlecht NF, Ow TJ, Keller CE, Childs GJ, Smith RV, Angeletti RH, Prystowsky MB, Lim J. Proteomic analysis of oral cavity squamous cell carcinoma specimens identifies patient outcome-associated proteins. Arch Pathol Lab Med 2014; 139:494-507. [PMID: 25295583 DOI: 10.5858/arpa.2014-0131-oa] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
CONTEXT Global proteomic analysis of oral cavity squamous cell carcinoma was performed to identify changes that reflect patient outcomes. OBJECTIVES To identify differentially expressed proteins associated with patient outcomes and to explore the use of imaging mass spectrometry as a clinical tool to identify clinically relevant proteins. DESIGN Two-dimensional separation of digested peptides generated from 43 specimens with high-resolution mass spectrometry identified proteins associated with disease-specific death, distant metastasis, and loco-regional recurrence. RNA expressions had been correlated to protein levels to test transcriptional regulation of clinically relevant proteins. Imaging mass spectrometry explored an alternative platform for assessing clinically relevant proteins that would complement surgical pathologic diagnosis. RESULTS Seventy-two peptide features were found to be associated with 3 patient outcomes: disease-specific death (9), distant metastasis (16), and loco-regional recurrence (39); 8 of them were associated with multiple outcomes. Functional ontology revealed major changes in cell adhesion and calcium binding. Thirteen RNAs showed strong correlation with their encoded proteins, implying transcriptional control. Reduction of DSP, PKP1, and TRIM29 was associated with significantly shorter time to onset of distant metastasis. Reduction of PKP1 and TRIM29 correlated with poorer disease-specific survival. Additionally, S100A8 and S100A9 reductions were verified for their association with poor prognosis using imaging mass spectrometry, a platform more adaptable for use with surgical pathology. CONCLUSIONS Using global proteomic analysis, we have identified proteins associated with clinical outcomes. The list of clinically relevant proteins observed will provide a means to develop clinical assays for prognosis and optimizing treatment selection.
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Affiliation(s)
- Thomas M Harris
- From the Departments of Pathology (Drs Harris, Belbin, Wang, Ow, Childs, Prystowsky, and Lim and Ms Kawachi), Epidemiology & Population Health (Dr Schlecht), Developmental and Molecular Biology (Dr Angeletti), and Biochemistry (Dr Angeletti) and the Laboratory for Macromolecular Analysis & Proteomics (Drs Angeletti and Lim), Albert Einstein College of Medicine, Bronx, New York; High Performance and Research Computing, Department of Information Systems and Technology, UMDNJ, Newark, New Jersey (Dr Du); the Department of Otorhinolaryngology-Head & Neck Surgery, Montefiore Medical Center, Bronx, New York (Drs Ow and Smith); and the Department of Pathology, Henry Ford Hospital and Medical Group, Detroit, Michigan (Dr Keller)
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Abstract
Sea urchin histones are encoded by several multigene families. The temporal expression of one of these families, the late histones, has been studied during the early development of Lytechinus pictus. Using a nuclease S1 assay, we detected about 10,000 transcripts encoding both late H3 and H4 proteins in the unfertilized egg. This suggests that the late genes were active at some point during oogenesis. The number of late gene transcripts begins to increase 6.5 hr after fertilization (64-cell stage), indicating that these genes probably become reactivated 4.5-6.5 hr after fertilization. The maximum rate of accumulation of transcripts (4600 molecules per min per embryo) occurs 9-14 hr after fertilization (from blastula stage to hatching). The number of transcripts peaks 21 hr after fertilization (onset of gastrulation) when the embryo has accumulated 1.8 X 10(6) copies of each late mRNA (a 164-fold increase). A 5.5-fold increase in the relative rate of transcription, between 7 and 15 hr after fertilization, is partly responsible for the accumulation of these gene products. The relative synthesis of early histone message, which is encoded by a different family, decreases 18-fold during this time. Synthesis of the late transcripts continues at the higher rate after accumulation has ceased (24 hr after fertilization). The number of late transcripts begins to decrease 48 hr after fertilization, reaching about 10,000 copies at 72 hr.
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